{"version":2,"lastUpdated":"2026-06-03","source":"ENA MIxS Checklists (https://www.ebi.ac.uk/ena/browser)","checklists":[{"name":"GSC MIxS air","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000012","category":"mixs","accession":"ERC000012","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":true,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"ventilation rate","name":"ventilation_rate","required":false,"visible":true,"helpText":"ventilation rate of the system in the sampled premises","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"L/sec","label":"L/sec"},{"value":"m3/min","label":"m3/min"}],"group":"internal environment"},{"type":"select","label":"ventilation type","name":"ventilation_type","required":false,"visible":true,"helpText":"The intentional movement of air from outside a building to the inside through forced or natural movement of air","options":[{"value":"forced ventilation","label":"forced ventilation"},{"value":"mechanical ventilation","label":"mechanical ventilation"},{"value":"natural ventilation","label":"natural ventilation"}],"group":"internal environment"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"barometric pressure","name":"barometric_pressure","required":false,"visible":true,"helpText":"force per unit area exerted against a surface by the weight of air above that surface","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"in. Hg","label":"in. Hg"},{"value":"millibar(hPa)","label":"millibar(hPa)"},{"value":"Torr","label":"Torr"},{"value":"mm Hg","label":"mm Hg"}],"group":"local environment conditions"},{"type":"text","label":"humidity","name":"humidity","required":false,"visible":true,"helpText":"amount of water vapour in the air, at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/m3","label":"g/m3"},{"value":"%","label":"%"}],"group":"local environment conditions"},{"type":"text","label":"pollutants","name":"pollutants","required":false,"visible":true,"helpText":"pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant","units":[{"value":"mg/L","label":"mg/L"},{"value":"g","label":"g"},{"value":"M/L","label":"M/L"}],"group":"local environment conditions"},{"type":"text","label":"solar irradiance","name":"solar_irradiance","required":false,"visible":true,"helpText":"the amount of solar energy that arrives at a specific area of a surface during a specific time interval","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"W/m2","label":"W/m2"}],"group":"local environment conditions"},{"type":"text","label":"wind direction","name":"wind_direction","required":false,"visible":true,"helpText":"wind direction is the direction from which a wind originates","group":"local environment conditions"},{"type":"text","label":"wind speed","name":"wind_speed","required":false,"visible":true,"helpText":"speed of wind measured at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m/s","label":"m/s"},{"value":"km/h","label":"km/h"}],"group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"carbon dioxide","name":"carbon_dioxide","required":false,"visible":true,"helpText":"carbon dioxide (gas) amount or concentration at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"carbon monoxide","name":"carbon_monoxide","required":false,"visible":true,"helpText":"carbon monoxide (gas) amount or concentration at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µM/L","label":"µM/L"}],"group":"concentration measurement"},{"type":"text","label":"oxygen","name":"oxygen","required":false,"visible":true,"helpText":"oxygen (gas) amount or concentration at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"air particulate matter concentration","name":"air_particulate_matter_concentration","required":false,"visible":true,"helpText":"Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/m3","label":"µg/m3"}],"group":"concentration measurement"},{"type":"text","label":"volatile organic compounds","name":"volatile_organic_compounds","required":false,"visible":true,"helpText":"concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound","units":[{"value":"parts/million","label":"parts/million"},{"value":"µg/m3","label":"µg/m3"}],"group":"concentration measurement"},{"type":"text","label":"methane","name":"methane","required":false,"visible":true,"helpText":"methane (gas) amount or concentration at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µM/L","label":"µM/L"}],"group":"concentration measurement"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/air.png"},{"name":"GSC MIxS host associated","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000013","category":"mixs","accession":"ERC000013","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"observed host symbionts","name":"observed_host_symbionts","required":false,"visible":true,"helpText":"The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample disease stage","name":"sample_disease_stage","required":false,"visible":true,"helpText":"stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen","group":"sample collection: core sample properties"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"text","label":"sample disease status","name":"sample_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the subject has been diagnosed at the time of sample collection; can include multiple diagnoses; the value of the field depends on subject; e.g. Charcoal rot (Macrophomina phaseolina), Late wilt (Cephalosporium maydis)","group":"sample collection: core sample properties"},{"type":"text","label":"sample derived from","name":"sample_derived_from","required":false,"visible":true,"helpText":"Reference to parental sample(s) or original run(s) that the assembly is derived from. The referenced samples or runs should already be registered in INSDC. This should be formatted as one of the following. A single sample/run e.g. ERSxxxxxx OR a comma separated list e.g. ERSxxxxxx,ERSxxxxxx OR a range e.g. ERSxxxxxx-ERSxxxxxx","simpleValidation":{"pattern":"(^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)","patternMessage":"Must match pattern: (^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)"},"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"select","label":"sample capture status","name":"sample_capture_status","required":false,"visible":true,"helpText":"Reason for the sample collection.","options":[{"value":"active surveillance in response to outbreak","label":"active surveillance in response to outbreak"},{"value":"active surveillance not initiated by an outbreak","label":"active surveillance not initiated by an outbreak"},{"value":"farm sample","label":"farm sample"},{"value":"market sample","label":"market sample"},{"value":"other","label":"other"},{"value":"pet sample","label":"pet sample"},{"value":"zoo sample","label":"zoo sample"}],"group":"sample collection"},{"type":"text","label":"biological status","name":"biological_status","required":false,"visible":true,"helpText":"the level of genome modification; controlled vocabulary: wild, natural, semi-natural, inbred line, breeder's line, hybrid, clonal selection, mutant","group":"Organism characteristics"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host common name","name":"host_common_name","required":false,"visible":true,"helpText":"common name of the host, e.g. human","group":"host description"},{"type":"text","label":"host subject id","name":"host_subject_id","required":false,"visible":true,"helpText":"a unique identifier by which each subject can be referred to, de-identified, e.g. #131","group":"host description"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"text","label":"host taxid","name":"host_taxid","required":false,"visible":true,"helpText":"NCBI taxon id of the host, e.g. 9606","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"host description"},{"type":"text","label":"host body habitat","name":"host_body_habitat","required":false,"visible":true,"helpText":"original body habitat where the sample was obtained from","group":"host description"},{"type":"text","label":"host body site","name":"host_body_site","required":false,"visible":true,"helpText":"name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host description"},{"type":"text","label":"host life stage","name":"host_life_stage","required":false,"visible":true,"helpText":"description of life stage of host","group":"host description"},{"type":"text","label":"host height","name":"host_height","required":false,"visible":true,"helpText":"the height of subject","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host length","name":"host_length","required":false,"visible":true,"helpText":"the length of subject","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host growth conditions","name":"host_growth_conditions","required":false,"visible":true,"helpText":"literature reference giving growth conditions of the host","group":"host description"},{"type":"text","label":"host substrate","name":"host_substrate","required":false,"visible":true,"helpText":"the growth substrate of the host","group":"host description"},{"type":"text","label":"host total mass","name":"host_total_mass","required":false,"visible":true,"helpText":"total mass of the host at collection, the unit depends on host","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"host description"},{"type":"text","label":"host phenotype","name":"host_phenotype","required":false,"visible":true,"helpText":"phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO","group":"host description"},{"type":"text","label":"host body temperature","name":"host_body_temperature","required":false,"visible":true,"helpText":"core body temperature of the host when sample was collected","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"host description"},{"type":"text","label":"host color","name":"host_color","required":false,"visible":true,"helpText":"the color of host","group":"host description"},{"type":"text","label":"host shape","name":"host_shape","required":false,"visible":true,"helpText":"morphological shape of host","group":"host description"},{"type":"select","label":"host sex","name":"host_sex","required":false,"visible":true,"helpText":"Gender or sex of the host.","options":[{"value":"female","label":"female"},{"value":"hermaphrodite","label":"hermaphrodite"},{"value":"male","label":"male"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"neuter","label":"neuter"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"other","label":"other"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"host subspecific genetic lineage","name":"host_subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"host description"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"host blood pressure diastolic","name":"host_blood_pressure_diastolic","required":false,"visible":true,"helpText":"resting diastolic blood pressure, measured as mm mercury","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm Hg","label":"mm Hg"}],"group":"host details"},{"type":"text","label":"host blood pressure systolic","name":"host_blood_pressure_systolic","required":false,"visible":true,"helpText":"resting systolic blood pressure, measured as mm mercury","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm Hg","label":"mm Hg"}],"group":"host details"},{"type":"text","label":"host diet","name":"host_diet","required":false,"visible":true,"helpText":"type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, Mediterranean etc.; can include multiple diet types","group":"host details"},{"type":"text","label":"host last meal","name":"host_last_meal","required":false,"visible":true,"helpText":"content of last meal and time since feeding; can include multiple values","group":"host details"},{"type":"text","label":"host family relationship","name":"host_family_relationship","required":false,"visible":true,"helpText":"Familial relationships to other hosts in the same study; can include multiple relationships","group":"host details"},{"type":"text","label":"host genotype","name":"host_genotype","required":false,"visible":true,"helpText":"observed genotype","group":"host details"},{"type":"text","label":"gravidity","name":"gravidity","required":false,"visible":true,"helpText":"Whether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.","group":"host details"},{"type":"text","label":"host dry mass","name":"host_dry_mass","required":false,"visible":true,"helpText":"measurement of dry mass","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"mg","label":"mg"},{"value":"kg","label":"kg"}],"group":"host details"},{"type":"text","label":"host body product","name":"host_body_product","required":false,"visible":true,"helpText":"substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host details"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"genetic modification","name":"genetic_modification","required":false,"visible":true,"helpText":"A genetic modification of the genome of an organism which may occur naturally by spontaneous mutation, or be introduced by some experimental means. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection.","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"ancestral data","name":"ancestral_data","required":false,"visible":true,"helpText":"information about either pedigree or other description of ancestral information (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/host-associated.png"},{"name":"GSC MIxS human associated","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000014","category":"mixs","accession":"ERC000014","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"observed host symbionts","name":"observed_host_symbionts","required":false,"visible":true,"helpText":"The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"urine/collection method","name":"urinecollection_method","required":false,"visible":true,"helpText":"specification of urine collection method","options":[{"value":"catheter","label":"catheter"},{"value":"clean catch","label":"clean catch"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"select","label":"medical history performed","name":"medical_history_performed","required":false,"visible":true,"helpText":"whether full medical history was collected","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"sample collection: core sample properties"},{"type":"select","label":"study completion status","name":"study_completion_status","required":false,"visible":true,"helpText":"specification of study completion status, if no the reason should be specified","options":[{"value":"No - adverse event","label":"No - adverse event"},{"value":"No - lost to follow up","label":"No - lost to follow up"},{"value":"No - non-compliance","label":"No - non-compliance"},{"value":"No - other","label":"No - other"},{"value":"Yes","label":"Yes"}],"group":"non-sample terms: study or project"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"nose/mouth/teeth/throat disorder","name":"nosemouthteeththroat_disorder","required":false,"visible":true,"helpText":"History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974).","group":"host disorder"},{"type":"select","label":"host HIV status","name":"host_hiv_status","required":false,"visible":true,"helpText":"HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO]","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"host disorder"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"lung/pulmonary disorder","name":"lungpulmonary_disorder","required":false,"visible":true,"helpText":"History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850).","group":"host disorder"},{"type":"text","label":"lung/nose-throat disorder","name":"lungnosethroat_disorder","required":false,"visible":true,"helpText":"History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974).","group":"host disorder"},{"type":"text","label":"blood/blood disorder","name":"bloodblood_disorder","required":false,"visible":true,"helpText":"History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74).","group":"host disorder"},{"type":"text","label":"urine/kidney disorder","name":"urinekidney_disorder","required":false,"visible":true,"helpText":"History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557).","group":"host disorder"},{"type":"text","label":"urine/urogenital tract disorder","name":"urineurogenital_tract_disorder","required":false,"visible":true,"helpText":"History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18).","group":"host disorder"},{"type":"text","label":"host subject id","name":"host_subject_id","required":false,"visible":true,"helpText":"a unique identifier by which each subject can be referred to, de-identified, e.g. #131","group":"host description"},{"type":"select","label":"IHMC medication code","name":"ihmc_medication_code","required":false,"visible":true,"helpText":"can include multiple medication codes","options":[{"value":"01=1=Analgesics/NSAIDS","label":"01=1=Analgesics/NSAIDS"},{"value":"02=2=Anesthetics","label":"02=2=Anesthetics"},{"value":"03=3=Antacids/H2 antagonists","label":"03=3=Antacids/H2 antagonists"},{"value":"04=4=Anti-acne","label":"04=4=Anti-acne"},{"value":"05=5=Anti-asthma/bronchodilators","label":"05=5=Anti-asthma/bronchodilators"},{"value":"06=6=Anti-cholesterol/Anti-hyperlipidemic","label":"06=6=Anti-cholesterol/Anti-hyperlipidemic"},{"value":"07=7=Anti-coagulants","label":"07=7=Anti-coagulants"},{"value":"08=8=Antibiotics/(anti)-infectives, parasitics, microbials","label":"08=8=Antibiotics/(anti)-infectives, parasitics, microbials"},{"value":"09=9=Antidepressants/mood-altering drugs","label":"09=9=Antidepressants/mood-altering drugs"},{"value":"10=10=Antihistamines/ Decongestants","label":"10=10=Antihistamines/ Decongestants"},{"value":"11=11=Antihypertensives","label":"11=11=Antihypertensives"},{"value":"12=12=Cardiovascular, other than hyperlipidemic/HTN","label":"12=12=Cardiovascular, other than hyperlipidemic/HTN"},{"value":"13=13=Contraceptives (oral, implant, injectable)","label":"13=13=Contraceptives (oral, implant, injectable)"},{"value":"14=14=Emergency/support medications","label":"14=14=Emergency/support medications"},{"value":"15=15=Endocrine/Metabolic agents","label":"15=15=Endocrine/Metabolic agents"},{"value":"16=16=GI meds (anti-diarrheal, emetic, spasmodics)","label":"16=16=GI meds (anti-diarrheal, emetic, spasmodics)"},{"value":"17=17=Herbal/homeopathic products","label":"17=17=Herbal/homeopathic products"},{"value":"18=18=Hormones/steroids","label":"18=18=Hormones/steroids"},{"value":"19=19=OTC cold & flu","label":"19=19=OTC cold & flu"},{"value":"20=20=Vaccine prophylaxis","label":"20=20=Vaccine prophylaxis"},{"value":"21=21=Vitamins, minerals, food supplements","label":"21=21=Vitamins, minerals, food supplements"},{"value":"99=99=Other","label":"99=99=Other"}],"group":"host description"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"text","label":"host body site","name":"host_body_site","required":false,"visible":true,"helpText":"name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host description"},{"type":"text","label":"drug usage","name":"drug_usage","required":false,"visible":true,"helpText":"any drug used by subject and the frequency of usage; can include multiple drugs used","group":"host description"},{"type":"text","label":"host height","name":"host_height","required":false,"visible":true,"helpText":"the height of subject","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host body-mass index","name":"host_bodymass_index","required":false,"visible":true,"helpText":"body mass index, calculated as weight/(height)squared","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"kg/m2","label":"kg/m2"}],"group":"host description"},{"type":"text","label":"ethnicity","name":"ethnicity","required":false,"visible":true,"helpText":"A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups","group":"host description"},{"type":"select","label":"host occupation","name":"host_occupation","required":false,"visible":true,"helpText":"most frequent job performed by subject","options":[{"value":"01=01 Accounting/Finance","label":"01=01 Accounting/Finance"},{"value":"02=02 Advertising/Public Relations","label":"02=02 Advertising/Public Relations"},{"value":"03=03 Arts/Entertainment/Publishing","label":"03=03 Arts/Entertainment/Publishing"},{"value":"04=04 Automotive","label":"04=04 Automotive"},{"value":"05=05 Banking/ Mortgage","label":"05=05 Banking/ Mortgage"},{"value":"06=06 Biotech","label":"06=06 Biotech"},{"value":"07=07 Broadcast/Journalism","label":"07=07 Broadcast/Journalism"},{"value":"08=08 Business Development","label":"08=08 Business Development"},{"value":"09=09 Clerical/Administrative","label":"09=09 Clerical/Administrative"},{"value":"10=10 Construction/Trades","label":"10=10 Construction/Trades"},{"value":"11=11 Consultant","label":"11=11 Consultant"},{"value":"12=12 Customer Services","label":"12=12 Customer Services"},{"value":"13=13 Design","label":"13=13 Design"},{"value":"14=14 Education","label":"14=14 Education"},{"value":"15=15 Engineering","label":"15=15 Engineering"},{"value":"16=16 Entry Level","label":"16=16 Entry Level"},{"value":"17=17 Executive","label":"17=17 Executive"},{"value":"18=18 Food Service","label":"18=18 Food Service"},{"value":"19=19 Government","label":"19=19 Government"},{"value":"20=20 Grocery","label":"20=20 Grocery"},{"value":"21=21 Healthcare","label":"21=21 Healthcare"},{"value":"22=22 Hospitality","label":"22=22 Hospitality"},{"value":"23=23 Human Resources","label":"23=23 Human Resources"},{"value":"24=24 Information Technology","label":"24=24 Information Technology"},{"value":"25=25 Insurance","label":"25=25 Insurance"},{"value":"26=26 Law/Legal","label":"26=26 Law/Legal"},{"value":"27=27 Management","label":"27=27 Management"},{"value":"28=28 Manufacturing","label":"28=28 Manufacturing"},{"value":"29=29 Marketing","label":"29=29 Marketing"},{"value":"30=30 Pharmaceutical","label":"30=30 Pharmaceutical"},{"value":"31=31 Professional Services","label":"31=31 Professional Services"},{"value":"32=32 Purchasing","label":"32=32 Purchasing"},{"value":"33=33 Quality Assurance (QA)","label":"33=33 Quality Assurance (QA)"},{"value":"34=34 Research","label":"34=34 Research"},{"value":"35=35 Restaurant","label":"35=35 Restaurant"},{"value":"36=36 Retail","label":"36=36 Retail"},{"value":"37=37 Sales","label":"37=37 Sales"},{"value":"38=38 Science","label":"38=38 Science"},{"value":"39=39 Security/Law Enforcement","label":"39=39 Security/Law Enforcement"},{"value":"40=40 Shipping/Distribution","label":"40=40 Shipping/Distribution"},{"value":"41=41 Strategy","label":"41=41 Strategy"},{"value":"42=42 Student","label":"42=42 Student"},{"value":"43=43 Telecommunications","label":"43=43 Telecommunications"},{"value":"44=44 Training","label":"44=44 Training"},{"value":"45=45 Transportation","label":"45=45 Transportation"},{"value":"46=46 Warehouse","label":"46=46 Warehouse"},{"value":"47=47 Other","label":"47=47 Other"},{"value":"99=99 Unknown/Refused","label":"99=99 Unknown/Refused"}],"group":"host description"},{"type":"text","label":"host total mass","name":"host_total_mass","required":false,"visible":true,"helpText":"total mass of the host at collection, the unit depends on host","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"host description"},{"type":"text","label":"host phenotype","name":"host_phenotype","required":false,"visible":true,"helpText":"phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO","group":"host description"},{"type":"text","label":"host body temperature","name":"host_body_temperature","required":false,"visible":true,"helpText":"core body temperature of the host when sample was collected","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"host description"},{"type":"select","label":"host sex","name":"host_sex","required":false,"visible":true,"helpText":"Gender or sex of the host.","options":[{"value":"female","label":"female"},{"value":"hermaphrodite","label":"hermaphrodite"},{"value":"male","label":"male"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"neuter","label":"neuter"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"other","label":"other"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"presence of pets, animals, or insects","name":"presence_of_pets_animals_or_insects","required":false,"visible":true,"helpText":"The type and number of animals or insects present in the sampling space.","group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"select","label":"smoker","name":"smoker","required":false,"visible":true,"helpText":"specification of smoking status","options":[{"value":"ex-smoker","label":"ex-smoker"},{"value":"non-smoker","label":"non-smoker"},{"value":"smoker","label":"smoker"}],"group":"host details"},{"type":"text","label":"major diet change in last six months","name":"major_diet_change_in_last_six_months","required":false,"visible":true,"helpText":"specification of major diet changes in the last six months, if yes the change should be specified","group":"host details"},{"type":"text","label":"weight loss in last three months","name":"weight_loss_in_last_three_months","required":false,"visible":true,"helpText":"specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss","units":[{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"host details"},{"type":"text","label":"travel outside the country in last six months","name":"travel_outside_the_country_in_last_six_months","required":false,"visible":true,"helpText":"specification of the countries travelled in the last six months; can include multiple travels","group":"host details"},{"type":"text","label":"host diet","name":"host_diet","required":false,"visible":true,"helpText":"type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, Mediterranean etc.; can include multiple diet types","group":"host details"},{"type":"text","label":"twin sibling presence","name":"twin_sibling_presence","required":false,"visible":true,"helpText":"specification of twin sibling presence","group":"host details"},{"type":"text","label":"host last meal","name":"host_last_meal","required":false,"visible":true,"helpText":"content of last meal and time since feeding; can include multiple values","group":"host details"},{"type":"text","label":"amniotic fluid/gestation state","name":"amniotic_fluidgestation_state","required":false,"visible":true,"helpText":"specification of the gestation state","group":"host details"},{"type":"text","label":"host family relationship","name":"host_family_relationship","required":false,"visible":true,"helpText":"Familial relationships to other hosts in the same study; can include multiple relationships","group":"host details"},{"type":"text","label":"amniotic fluid/maternal health status","name":"amniotic_fluidmaternal_health_status","required":false,"visible":true,"helpText":"specification of the maternal health status","group":"host details"},{"type":"text","label":"host genotype","name":"host_genotype","required":false,"visible":true,"helpText":"observed genotype","group":"host details"},{"type":"text","label":"amniotic fluid/foetal health status","name":"amniotic_fluidfoetal_health_status","required":false,"visible":true,"helpText":"specification of foetal health status, should also include abortion","group":"host details"},{"type":"text","label":"host pulse","name":"host_pulse","required":false,"visible":true,"helpText":"resting pulse, measured as beats per minute","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"units":[{"value":"bpm","label":"bpm"}],"group":"host details"},{"type":"text","label":"amniotic fluid/color","name":"amniotic_fluidcolor","required":false,"visible":true,"helpText":"specification of the color of the amniotic fluid sample","group":"host details"},{"type":"text","label":"host body product","name":"host_body_product","required":false,"visible":true,"helpText":"substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host details"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/human-associated.png"},{"name":"GSC MIxS human gut","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000015","category":"mixs","accession":"ERC000015","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"observed host symbionts","name":"observed_host_symbionts","required":false,"visible":true,"helpText":"The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"select","label":"medical history performed","name":"medical_history_performed","required":false,"visible":true,"helpText":"whether full medical history was collected","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"gastrointestinal tract disorder","name":"gastrointestinal_tract_disorder","required":false,"visible":true,"helpText":"History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77).","group":"host disorder"},{"type":"text","label":"liver disorder","name":"liver_disorder","required":false,"visible":true,"helpText":"History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409).","group":"host disorder"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host subject id","name":"host_subject_id","required":false,"visible":true,"helpText":"a unique identifier by which each subject can be referred to, de-identified, e.g. #131","group":"host description"},{"type":"select","label":"IHMC medication code","name":"ihmc_medication_code","required":false,"visible":true,"helpText":"can include multiple medication codes","options":[{"value":"01=1=Analgesics/NSAIDS","label":"01=1=Analgesics/NSAIDS"},{"value":"02=2=Anesthetics","label":"02=2=Anesthetics"},{"value":"03=3=Antacids/H2 antagonists","label":"03=3=Antacids/H2 antagonists"},{"value":"04=4=Anti-acne","label":"04=4=Anti-acne"},{"value":"05=5=Anti-asthma/bronchodilators","label":"05=5=Anti-asthma/bronchodilators"},{"value":"06=6=Anti-cholesterol/Anti-hyperlipidemic","label":"06=6=Anti-cholesterol/Anti-hyperlipidemic"},{"value":"07=7=Anti-coagulants","label":"07=7=Anti-coagulants"},{"value":"08=8=Antibiotics/(anti)-infectives, parasitics, microbials","label":"08=8=Antibiotics/(anti)-infectives, parasitics, microbials"},{"value":"09=9=Antidepressants/mood-altering drugs","label":"09=9=Antidepressants/mood-altering drugs"},{"value":"10=10=Antihistamines/ Decongestants","label":"10=10=Antihistamines/ Decongestants"},{"value":"11=11=Antihypertensives","label":"11=11=Antihypertensives"},{"value":"12=12=Cardiovascular, other than hyperlipidemic/HTN","label":"12=12=Cardiovascular, other than hyperlipidemic/HTN"},{"value":"13=13=Contraceptives (oral, implant, injectable)","label":"13=13=Contraceptives (oral, implant, injectable)"},{"value":"14=14=Emergency/support medications","label":"14=14=Emergency/support medications"},{"value":"15=15=Endocrine/Metabolic agents","label":"15=15=Endocrine/Metabolic agents"},{"value":"16=16=GI meds (anti-diarrheal, emetic, spasmodics)","label":"16=16=GI meds (anti-diarrheal, emetic, spasmodics)"},{"value":"17=17=Herbal/homeopathic products","label":"17=17=Herbal/homeopathic products"},{"value":"18=18=Hormones/steroids","label":"18=18=Hormones/steroids"},{"value":"19=19=OTC cold & flu","label":"19=19=OTC cold & flu"},{"value":"20=20=Vaccine prophylaxis","label":"20=20=Vaccine prophylaxis"},{"value":"21=21=Vitamins, minerals, food supplements","label":"21=21=Vitamins, minerals, food supplements"},{"value":"99=99=Other","label":"99=99=Other"}],"group":"host description"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"text","label":"host body site","name":"host_body_site","required":false,"visible":true,"helpText":"name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host description"},{"type":"text","label":"host height","name":"host_height","required":false,"visible":true,"helpText":"the height of subject","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host body-mass index","name":"host_bodymass_index","required":false,"visible":true,"helpText":"body mass index, calculated as weight/(height)squared","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"kg/m2","label":"kg/m2"}],"group":"host description"},{"type":"text","label":"ethnicity","name":"ethnicity","required":false,"visible":true,"helpText":"A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups","group":"host description"},{"type":"select","label":"host occupation","name":"host_occupation","required":false,"visible":true,"helpText":"most frequent job performed by subject","options":[{"value":"01=01 Accounting/Finance","label":"01=01 Accounting/Finance"},{"value":"02=02 Advertising/Public Relations","label":"02=02 Advertising/Public Relations"},{"value":"03=03 Arts/Entertainment/Publishing","label":"03=03 Arts/Entertainment/Publishing"},{"value":"04=04 Automotive","label":"04=04 Automotive"},{"value":"05=05 Banking/ Mortgage","label":"05=05 Banking/ Mortgage"},{"value":"06=06 Biotech","label":"06=06 Biotech"},{"value":"07=07 Broadcast/Journalism","label":"07=07 Broadcast/Journalism"},{"value":"08=08 Business Development","label":"08=08 Business Development"},{"value":"09=09 Clerical/Administrative","label":"09=09 Clerical/Administrative"},{"value":"10=10 Construction/Trades","label":"10=10 Construction/Trades"},{"value":"11=11 Consultant","label":"11=11 Consultant"},{"value":"12=12 Customer Services","label":"12=12 Customer Services"},{"value":"13=13 Design","label":"13=13 Design"},{"value":"14=14 Education","label":"14=14 Education"},{"value":"15=15 Engineering","label":"15=15 Engineering"},{"value":"16=16 Entry Level","label":"16=16 Entry Level"},{"value":"17=17 Executive","label":"17=17 Executive"},{"value":"18=18 Food Service","label":"18=18 Food Service"},{"value":"19=19 Government","label":"19=19 Government"},{"value":"20=20 Grocery","label":"20=20 Grocery"},{"value":"21=21 Healthcare","label":"21=21 Healthcare"},{"value":"22=22 Hospitality","label":"22=22 Hospitality"},{"value":"23=23 Human Resources","label":"23=23 Human Resources"},{"value":"24=24 Information Technology","label":"24=24 Information Technology"},{"value":"25=25 Insurance","label":"25=25 Insurance"},{"value":"26=26 Law/Legal","label":"26=26 Law/Legal"},{"value":"27=27 Management","label":"27=27 Management"},{"value":"28=28 Manufacturing","label":"28=28 Manufacturing"},{"value":"29=29 Marketing","label":"29=29 Marketing"},{"value":"30=30 Pharmaceutical","label":"30=30 Pharmaceutical"},{"value":"31=31 Professional Services","label":"31=31 Professional Services"},{"value":"32=32 Purchasing","label":"32=32 Purchasing"},{"value":"33=33 Quality Assurance (QA)","label":"33=33 Quality Assurance (QA)"},{"value":"34=34 Research","label":"34=34 Research"},{"value":"35=35 Restaurant","label":"35=35 Restaurant"},{"value":"36=36 Retail","label":"36=36 Retail"},{"value":"37=37 Sales","label":"37=37 Sales"},{"value":"38=38 Science","label":"38=38 Science"},{"value":"39=39 Security/Law Enforcement","label":"39=39 Security/Law Enforcement"},{"value":"40=40 Shipping/Distribution","label":"40=40 Shipping/Distribution"},{"value":"41=41 Strategy","label":"41=41 Strategy"},{"value":"42=42 Student","label":"42=42 Student"},{"value":"43=43 Telecommunications","label":"43=43 Telecommunications"},{"value":"44=44 Training","label":"44=44 Training"},{"value":"45=45 Transportation","label":"45=45 Transportation"},{"value":"46=46 Warehouse","label":"46=46 Warehouse"},{"value":"47=47 Other","label":"47=47 Other"},{"value":"99=99 Unknown/Refused","label":"99=99 Unknown/Refused"}],"group":"host description"},{"type":"text","label":"host total mass","name":"host_total_mass","required":false,"visible":true,"helpText":"total mass of the host at collection, the unit depends on host","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"host description"},{"type":"text","label":"host phenotype","name":"host_phenotype","required":false,"visible":true,"helpText":"phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO","group":"host description"},{"type":"text","label":"host body temperature","name":"host_body_temperature","required":false,"visible":true,"helpText":"core body temperature of the host when sample was collected","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"host description"},{"type":"select","label":"host sex","name":"host_sex","required":false,"visible":true,"helpText":"Gender or sex of the host.","options":[{"value":"female","label":"female"},{"value":"hermaphrodite","label":"hermaphrodite"},{"value":"male","label":"male"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"neuter","label":"neuter"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"other","label":"other"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"special diet","name":"special_diet","required":false,"visible":true,"helpText":"specification of special diet; can include multiple special diets","group":"host details"},{"type":"text","label":"host diet","name":"host_diet","required":false,"visible":true,"helpText":"type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, Mediterranean etc.; can include multiple diet types","group":"host details"},{"type":"text","label":"host last meal","name":"host_last_meal","required":false,"visible":true,"helpText":"content of last meal and time since feeding; can include multiple values","group":"host details"},{"type":"text","label":"host family relationship","name":"host_family_relationship","required":false,"visible":true,"helpText":"Familial relationships to other hosts in the same study; can include multiple relationships","group":"host details"},{"type":"text","label":"host genotype","name":"host_genotype","required":false,"visible":true,"helpText":"observed genotype","group":"host details"},{"type":"text","label":"host pulse","name":"host_pulse","required":false,"visible":true,"helpText":"resting pulse, measured as beats per minute","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"units":[{"value":"bpm","label":"bpm"}],"group":"host details"},{"type":"text","label":"host body product","name":"host_body_product","required":false,"visible":true,"helpText":"substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host details"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/human-gut.png"},{"name":"GSC MIxS human oral","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000016","category":"mixs","accession":"ERC000016","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"observed host symbionts","name":"observed_host_symbionts","required":false,"visible":true,"helpText":"The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"select","label":"medical history performed","name":"medical_history_performed","required":false,"visible":true,"helpText":"whether full medical history was collected","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"lat_lon","name":"lat_lon","required":false,"visible":true,"helpText":"geographical coordinates of the location where the specimen was collected","group":"Collection event information"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"nose/mouth/teeth/throat disorder","name":"nosemouthteeththroat_disorder","required":false,"visible":true,"helpText":"History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974).","group":"host disorder"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host subject id","name":"host_subject_id","required":false,"visible":true,"helpText":"a unique identifier by which each subject can be referred to, de-identified, e.g. #131","group":"host description"},{"type":"select","label":"IHMC medication code","name":"ihmc_medication_code","required":false,"visible":true,"helpText":"can include multiple medication codes","options":[{"value":"01=1=Analgesics/NSAIDS","label":"01=1=Analgesics/NSAIDS"},{"value":"02=2=Anesthetics","label":"02=2=Anesthetics"},{"value":"03=3=Antacids/H2 antagonists","label":"03=3=Antacids/H2 antagonists"},{"value":"04=4=Anti-acne","label":"04=4=Anti-acne"},{"value":"05=5=Anti-asthma/bronchodilators","label":"05=5=Anti-asthma/bronchodilators"},{"value":"06=6=Anti-cholesterol/Anti-hyperlipidemic","label":"06=6=Anti-cholesterol/Anti-hyperlipidemic"},{"value":"07=7=Anti-coagulants","label":"07=7=Anti-coagulants"},{"value":"08=8=Antibiotics/(anti)-infectives, parasitics, microbials","label":"08=8=Antibiotics/(anti)-infectives, parasitics, microbials"},{"value":"09=9=Antidepressants/mood-altering drugs","label":"09=9=Antidepressants/mood-altering drugs"},{"value":"10=10=Antihistamines/ Decongestants","label":"10=10=Antihistamines/ Decongestants"},{"value":"11=11=Antihypertensives","label":"11=11=Antihypertensives"},{"value":"12=12=Cardiovascular, other than hyperlipidemic/HTN","label":"12=12=Cardiovascular, other than hyperlipidemic/HTN"},{"value":"13=13=Contraceptives (oral, implant, injectable)","label":"13=13=Contraceptives (oral, implant, injectable)"},{"value":"14=14=Emergency/support medications","label":"14=14=Emergency/support medications"},{"value":"15=15=Endocrine/Metabolic agents","label":"15=15=Endocrine/Metabolic agents"},{"value":"16=16=GI meds (anti-diarrheal, emetic, spasmodics)","label":"16=16=GI meds (anti-diarrheal, emetic, spasmodics)"},{"value":"17=17=Herbal/homeopathic products","label":"17=17=Herbal/homeopathic products"},{"value":"18=18=Hormones/steroids","label":"18=18=Hormones/steroids"},{"value":"19=19=OTC cold & flu","label":"19=19=OTC cold & flu"},{"value":"20=20=Vaccine prophylaxis","label":"20=20=Vaccine prophylaxis"},{"value":"21=21=Vitamins, minerals, food supplements","label":"21=21=Vitamins, minerals, food supplements"},{"value":"99=99=Other","label":"99=99=Other"}],"group":"host description"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"text","label":"host body site","name":"host_body_site","required":false,"visible":true,"helpText":"name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host description"},{"type":"text","label":"host height","name":"host_height","required":false,"visible":true,"helpText":"the height of subject","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host body-mass index","name":"host_bodymass_index","required":false,"visible":true,"helpText":"body mass index, calculated as weight/(height)squared","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"kg/m2","label":"kg/m2"}],"group":"host description"},{"type":"text","label":"ethnicity","name":"ethnicity","required":false,"visible":true,"helpText":"A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups","group":"host description"},{"type":"select","label":"host occupation","name":"host_occupation","required":false,"visible":true,"helpText":"most frequent job performed by subject","options":[{"value":"01=01 Accounting/Finance","label":"01=01 Accounting/Finance"},{"value":"02=02 Advertising/Public Relations","label":"02=02 Advertising/Public Relations"},{"value":"03=03 Arts/Entertainment/Publishing","label":"03=03 Arts/Entertainment/Publishing"},{"value":"04=04 Automotive","label":"04=04 Automotive"},{"value":"05=05 Banking/ Mortgage","label":"05=05 Banking/ Mortgage"},{"value":"06=06 Biotech","label":"06=06 Biotech"},{"value":"07=07 Broadcast/Journalism","label":"07=07 Broadcast/Journalism"},{"value":"08=08 Business Development","label":"08=08 Business Development"},{"value":"09=09 Clerical/Administrative","label":"09=09 Clerical/Administrative"},{"value":"10=10 Construction/Trades","label":"10=10 Construction/Trades"},{"value":"11=11 Consultant","label":"11=11 Consultant"},{"value":"12=12 Customer Services","label":"12=12 Customer Services"},{"value":"13=13 Design","label":"13=13 Design"},{"value":"14=14 Education","label":"14=14 Education"},{"value":"15=15 Engineering","label":"15=15 Engineering"},{"value":"16=16 Entry Level","label":"16=16 Entry Level"},{"value":"17=17 Executive","label":"17=17 Executive"},{"value":"18=18 Food Service","label":"18=18 Food Service"},{"value":"19=19 Government","label":"19=19 Government"},{"value":"20=20 Grocery","label":"20=20 Grocery"},{"value":"21=21 Healthcare","label":"21=21 Healthcare"},{"value":"22=22 Hospitality","label":"22=22 Hospitality"},{"value":"23=23 Human Resources","label":"23=23 Human Resources"},{"value":"24=24 Information Technology","label":"24=24 Information Technology"},{"value":"25=25 Insurance","label":"25=25 Insurance"},{"value":"26=26 Law/Legal","label":"26=26 Law/Legal"},{"value":"27=27 Management","label":"27=27 Management"},{"value":"28=28 Manufacturing","label":"28=28 Manufacturing"},{"value":"29=29 Marketing","label":"29=29 Marketing"},{"value":"30=30 Pharmaceutical","label":"30=30 Pharmaceutical"},{"value":"31=31 Professional Services","label":"31=31 Professional Services"},{"value":"32=32 Purchasing","label":"32=32 Purchasing"},{"value":"33=33 Quality Assurance (QA)","label":"33=33 Quality Assurance (QA)"},{"value":"34=34 Research","label":"34=34 Research"},{"value":"35=35 Restaurant","label":"35=35 Restaurant"},{"value":"36=36 Retail","label":"36=36 Retail"},{"value":"37=37 Sales","label":"37=37 Sales"},{"value":"38=38 Science","label":"38=38 Science"},{"value":"39=39 Security/Law Enforcement","label":"39=39 Security/Law Enforcement"},{"value":"40=40 Shipping/Distribution","label":"40=40 Shipping/Distribution"},{"value":"41=41 Strategy","label":"41=41 Strategy"},{"value":"42=42 Student","label":"42=42 Student"},{"value":"43=43 Telecommunications","label":"43=43 Telecommunications"},{"value":"44=44 Training","label":"44=44 Training"},{"value":"45=45 Transportation","label":"45=45 Transportation"},{"value":"46=46 Warehouse","label":"46=46 Warehouse"},{"value":"47=47 Other","label":"47=47 Other"},{"value":"99=99 Unknown/Refused","label":"99=99 Unknown/Refused"}],"group":"host description"},{"type":"text","label":"host total mass","name":"host_total_mass","required":false,"visible":true,"helpText":"total mass of the host at collection, the unit depends on host","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"host description"},{"type":"text","label":"host phenotype","name":"host_phenotype","required":false,"visible":true,"helpText":"phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO","group":"host description"},{"type":"text","label":"host body temperature","name":"host_body_temperature","required":false,"visible":true,"helpText":"core body temperature of the host when sample was collected","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"host description"},{"type":"select","label":"host sex","name":"host_sex","required":false,"visible":true,"helpText":"Gender or sex of the host.","options":[{"value":"female","label":"female"},{"value":"hermaphrodite","label":"hermaphrodite"},{"value":"male","label":"male"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"neuter","label":"neuter"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"other","label":"other"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"time since last toothbrushing","name":"time_since_last_toothbrushing","required":false,"visible":true,"helpText":"specification of the time since last toothbrushing","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"hours","label":"hours"},{"value":"minutes","label":"minutes"}],"group":"host details"},{"type":"text","label":"host diet","name":"host_diet","required":false,"visible":true,"helpText":"type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, Mediterranean etc.; can include multiple diet types","group":"host details"},{"type":"text","label":"host last meal","name":"host_last_meal","required":false,"visible":true,"helpText":"content of last meal and time since feeding; can include multiple values","group":"host details"},{"type":"text","label":"host family relationship","name":"host_family_relationship","required":false,"visible":true,"helpText":"Familial relationships to other hosts in the same study; can include multiple relationships","group":"host details"},{"type":"text","label":"host genotype","name":"host_genotype","required":false,"visible":true,"helpText":"observed genotype","group":"host details"},{"type":"text","label":"host pulse","name":"host_pulse","required":false,"visible":true,"helpText":"resting pulse, measured as beats per minute","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"units":[{"value":"bpm","label":"bpm"}],"group":"host details"},{"type":"text","label":"host body product","name":"host_body_product","required":false,"visible":true,"helpText":"substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host details"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/human-oral.png"},{"name":"GSC MIxS human skin","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000017","category":"mixs","accession":"ERC000017","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"observed host symbionts","name":"observed_host_symbionts","required":false,"visible":true,"helpText":"The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"select","label":"medical history performed","name":"medical_history_performed","required":false,"visible":true,"helpText":"whether full medical history was collected","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"dermatology disorder","name":"dermatology_disorder","required":false,"visible":true,"helpText":"History of dermatology disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, skin disease (https://disease-ontology.org/?id=DOID:37).","group":"host disorder"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host subject id","name":"host_subject_id","required":false,"visible":true,"helpText":"a unique identifier by which each subject can be referred to, de-identified, e.g. #131","group":"host description"},{"type":"select","label":"IHMC medication code","name":"ihmc_medication_code","required":false,"visible":true,"helpText":"can include multiple medication codes","options":[{"value":"01=1=Analgesics/NSAIDS","label":"01=1=Analgesics/NSAIDS"},{"value":"02=2=Anesthetics","label":"02=2=Anesthetics"},{"value":"03=3=Antacids/H2 antagonists","label":"03=3=Antacids/H2 antagonists"},{"value":"04=4=Anti-acne","label":"04=4=Anti-acne"},{"value":"05=5=Anti-asthma/bronchodilators","label":"05=5=Anti-asthma/bronchodilators"},{"value":"06=6=Anti-cholesterol/Anti-hyperlipidemic","label":"06=6=Anti-cholesterol/Anti-hyperlipidemic"},{"value":"07=7=Anti-coagulants","label":"07=7=Anti-coagulants"},{"value":"08=8=Antibiotics/(anti)-infectives, parasitics, microbials","label":"08=8=Antibiotics/(anti)-infectives, parasitics, microbials"},{"value":"09=9=Antidepressants/mood-altering drugs","label":"09=9=Antidepressants/mood-altering drugs"},{"value":"10=10=Antihistamines/ Decongestants","label":"10=10=Antihistamines/ Decongestants"},{"value":"11=11=Antihypertensives","label":"11=11=Antihypertensives"},{"value":"12=12=Cardiovascular, other than hyperlipidemic/HTN","label":"12=12=Cardiovascular, other than hyperlipidemic/HTN"},{"value":"13=13=Contraceptives (oral, implant, injectable)","label":"13=13=Contraceptives (oral, implant, injectable)"},{"value":"14=14=Emergency/support medications","label":"14=14=Emergency/support medications"},{"value":"15=15=Endocrine/Metabolic agents","label":"15=15=Endocrine/Metabolic agents"},{"value":"16=16=GI meds (anti-diarrheal, emetic, spasmodics)","label":"16=16=GI meds (anti-diarrheal, emetic, spasmodics)"},{"value":"17=17=Herbal/homeopathic products","label":"17=17=Herbal/homeopathic products"},{"value":"18=18=Hormones/steroids","label":"18=18=Hormones/steroids"},{"value":"19=19=OTC cold & flu","label":"19=19=OTC cold & flu"},{"value":"20=20=Vaccine prophylaxis","label":"20=20=Vaccine prophylaxis"},{"value":"21=21=Vitamins, minerals, food supplements","label":"21=21=Vitamins, minerals, food supplements"},{"value":"99=99=Other","label":"99=99=Other"}],"group":"host description"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"text","label":"host body site","name":"host_body_site","required":false,"visible":true,"helpText":"name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host description"},{"type":"text","label":"host height","name":"host_height","required":false,"visible":true,"helpText":"the height of subject","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host body-mass index","name":"host_bodymass_index","required":false,"visible":true,"helpText":"body mass index, calculated as weight/(height)squared","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"kg/m2","label":"kg/m2"}],"group":"host description"},{"type":"text","label":"ethnicity","name":"ethnicity","required":false,"visible":true,"helpText":"A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups","group":"host description"},{"type":"select","label":"host occupation","name":"host_occupation","required":false,"visible":true,"helpText":"most frequent job performed by subject","options":[{"value":"01=01 Accounting/Finance","label":"01=01 Accounting/Finance"},{"value":"02=02 Advertising/Public Relations","label":"02=02 Advertising/Public Relations"},{"value":"03=03 Arts/Entertainment/Publishing","label":"03=03 Arts/Entertainment/Publishing"},{"value":"04=04 Automotive","label":"04=04 Automotive"},{"value":"05=05 Banking/ Mortgage","label":"05=05 Banking/ Mortgage"},{"value":"06=06 Biotech","label":"06=06 Biotech"},{"value":"07=07 Broadcast/Journalism","label":"07=07 Broadcast/Journalism"},{"value":"08=08 Business Development","label":"08=08 Business Development"},{"value":"09=09 Clerical/Administrative","label":"09=09 Clerical/Administrative"},{"value":"10=10 Construction/Trades","label":"10=10 Construction/Trades"},{"value":"11=11 Consultant","label":"11=11 Consultant"},{"value":"12=12 Customer Services","label":"12=12 Customer Services"},{"value":"13=13 Design","label":"13=13 Design"},{"value":"14=14 Education","label":"14=14 Education"},{"value":"15=15 Engineering","label":"15=15 Engineering"},{"value":"16=16 Entry Level","label":"16=16 Entry Level"},{"value":"17=17 Executive","label":"17=17 Executive"},{"value":"18=18 Food Service","label":"18=18 Food Service"},{"value":"19=19 Government","label":"19=19 Government"},{"value":"20=20 Grocery","label":"20=20 Grocery"},{"value":"21=21 Healthcare","label":"21=21 Healthcare"},{"value":"22=22 Hospitality","label":"22=22 Hospitality"},{"value":"23=23 Human Resources","label":"23=23 Human Resources"},{"value":"24=24 Information Technology","label":"24=24 Information Technology"},{"value":"25=25 Insurance","label":"25=25 Insurance"},{"value":"26=26 Law/Legal","label":"26=26 Law/Legal"},{"value":"27=27 Management","label":"27=27 Management"},{"value":"28=28 Manufacturing","label":"28=28 Manufacturing"},{"value":"29=29 Marketing","label":"29=29 Marketing"},{"value":"30=30 Pharmaceutical","label":"30=30 Pharmaceutical"},{"value":"31=31 Professional Services","label":"31=31 Professional Services"},{"value":"32=32 Purchasing","label":"32=32 Purchasing"},{"value":"33=33 Quality Assurance (QA)","label":"33=33 Quality Assurance (QA)"},{"value":"34=34 Research","label":"34=34 Research"},{"value":"35=35 Restaurant","label":"35=35 Restaurant"},{"value":"36=36 Retail","label":"36=36 Retail"},{"value":"37=37 Sales","label":"37=37 Sales"},{"value":"38=38 Science","label":"38=38 Science"},{"value":"39=39 Security/Law Enforcement","label":"39=39 Security/Law Enforcement"},{"value":"40=40 Shipping/Distribution","label":"40=40 Shipping/Distribution"},{"value":"41=41 Strategy","label":"41=41 Strategy"},{"value":"42=42 Student","label":"42=42 Student"},{"value":"43=43 Telecommunications","label":"43=43 Telecommunications"},{"value":"44=44 Training","label":"44=44 Training"},{"value":"45=45 Transportation","label":"45=45 Transportation"},{"value":"46=46 Warehouse","label":"46=46 Warehouse"},{"value":"47=47 Other","label":"47=47 Other"},{"value":"99=99 Unknown/Refused","label":"99=99 Unknown/Refused"}],"group":"host description"},{"type":"text","label":"host total mass","name":"host_total_mass","required":false,"visible":true,"helpText":"total mass of the host at collection, the unit depends on host","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"host description"},{"type":"text","label":"host phenotype","name":"host_phenotype","required":false,"visible":true,"helpText":"phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO","group":"host description"},{"type":"text","label":"host body temperature","name":"host_body_temperature","required":false,"visible":true,"helpText":"core body temperature of the host when sample was collected","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"host description"},{"type":"select","label":"host sex","name":"host_sex","required":false,"visible":true,"helpText":"Gender or sex of the host.","options":[{"value":"female","label":"female"},{"value":"hermaphrodite","label":"hermaphrodite"},{"value":"male","label":"male"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"neuter","label":"neuter"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"other","label":"other"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"time since last wash","name":"time_since_last_wash","required":false,"visible":true,"helpText":"specification of the time since last wash","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"hours","label":"hours"},{"value":"minutes","label":"minutes"}],"group":"host details"},{"type":"select","label":"dominant hand","name":"dominant_hand","required":false,"visible":true,"helpText":"dominant hand of the subject","options":[{"value":"ambidextrous","label":"ambidextrous"},{"value":"left","label":"left"},{"value":"right","label":"right"}],"group":"host details"},{"type":"text","label":"host diet","name":"host_diet","required":false,"visible":true,"helpText":"type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, Mediterranean etc.; can include multiple diet types","group":"host details"},{"type":"text","label":"host last meal","name":"host_last_meal","required":false,"visible":true,"helpText":"content of last meal and time since feeding; can include multiple values","group":"host details"},{"type":"text","label":"host family relationship","name":"host_family_relationship","required":false,"visible":true,"helpText":"Familial relationships to other hosts in the same study; can include multiple relationships","group":"host details"},{"type":"text","label":"host genotype","name":"host_genotype","required":false,"visible":true,"helpText":"observed genotype","group":"host details"},{"type":"text","label":"host pulse","name":"host_pulse","required":false,"visible":true,"helpText":"resting pulse, measured as beats per minute","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"units":[{"value":"bpm","label":"bpm"}],"group":"host details"},{"type":"text","label":"host body product","name":"host_body_product","required":false,"visible":true,"helpText":"substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host details"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/human-skin.png"},{"name":"GSC MIxS human vaginal","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000018","category":"mixs","accession":"ERC000018","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"observed host symbionts","name":"observed_host_symbionts","required":false,"visible":true,"helpText":"The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"select","label":"medical history performed","name":"medical_history_performed","required":false,"visible":true,"helpText":"whether full medical history was collected","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"gynecological disorder","name":"gynecological_disorder","required":false,"visible":true,"helpText":"History of gynecological disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, female reproductive system disease (https://disease-ontology.org/?id=DOID:229).","group":"host disorder"},{"type":"text","label":"urogenital disorder","name":"urogenital_disorder","required":false,"visible":true,"helpText":"History of urogenital disorders, can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, reproductive system disease (https://disease-ontology.org/?id=DOID:15) or urinary system disease (https://disease-ontology.org/?id=DOID:18).","group":"host disorder"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host subject id","name":"host_subject_id","required":false,"visible":true,"helpText":"a unique identifier by which each subject can be referred to, de-identified, e.g. #131","group":"host description"},{"type":"select","label":"IHMC medication code","name":"ihmc_medication_code","required":false,"visible":true,"helpText":"can include multiple medication codes","options":[{"value":"01=1=Analgesics/NSAIDS","label":"01=1=Analgesics/NSAIDS"},{"value":"02=2=Anesthetics","label":"02=2=Anesthetics"},{"value":"03=3=Antacids/H2 antagonists","label":"03=3=Antacids/H2 antagonists"},{"value":"04=4=Anti-acne","label":"04=4=Anti-acne"},{"value":"05=5=Anti-asthma/bronchodilators","label":"05=5=Anti-asthma/bronchodilators"},{"value":"06=6=Anti-cholesterol/Anti-hyperlipidemic","label":"06=6=Anti-cholesterol/Anti-hyperlipidemic"},{"value":"07=7=Anti-coagulants","label":"07=7=Anti-coagulants"},{"value":"08=8=Antibiotics/(anti)-infectives, parasitics, microbials","label":"08=8=Antibiotics/(anti)-infectives, parasitics, microbials"},{"value":"09=9=Antidepressants/mood-altering drugs","label":"09=9=Antidepressants/mood-altering drugs"},{"value":"10=10=Antihistamines/ Decongestants","label":"10=10=Antihistamines/ Decongestants"},{"value":"11=11=Antihypertensives","label":"11=11=Antihypertensives"},{"value":"12=12=Cardiovascular, other than hyperlipidemic/HTN","label":"12=12=Cardiovascular, other than hyperlipidemic/HTN"},{"value":"13=13=Contraceptives (oral, implant, injectable)","label":"13=13=Contraceptives (oral, implant, injectable)"},{"value":"14=14=Emergency/support medications","label":"14=14=Emergency/support medications"},{"value":"15=15=Endocrine/Metabolic agents","label":"15=15=Endocrine/Metabolic agents"},{"value":"16=16=GI meds (anti-diarrheal, emetic, spasmodics)","label":"16=16=GI meds (anti-diarrheal, emetic, spasmodics)"},{"value":"17=17=Herbal/homeopathic products","label":"17=17=Herbal/homeopathic products"},{"value":"18=18=Hormones/steroids","label":"18=18=Hormones/steroids"},{"value":"19=19=OTC cold & flu","label":"19=19=OTC cold & flu"},{"value":"20=20=Vaccine prophylaxis","label":"20=20=Vaccine prophylaxis"},{"value":"21=21=Vitamins, minerals, food supplements","label":"21=21=Vitamins, minerals, food supplements"},{"value":"99=99=Other","label":"99=99=Other"}],"group":"host description"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"text","label":"host body site","name":"host_body_site","required":false,"visible":true,"helpText":"name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host description"},{"type":"text","label":"host height","name":"host_height","required":false,"visible":true,"helpText":"the height of subject","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host body-mass index","name":"host_bodymass_index","required":false,"visible":true,"helpText":"body mass index, calculated as weight/(height)squared","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"kg/m2","label":"kg/m2"}],"group":"host description"},{"type":"text","label":"ethnicity","name":"ethnicity","required":false,"visible":true,"helpText":"A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups","group":"host description"},{"type":"select","label":"host occupation","name":"host_occupation","required":false,"visible":true,"helpText":"most frequent job performed by subject","options":[{"value":"01=01 Accounting/Finance","label":"01=01 Accounting/Finance"},{"value":"02=02 Advertising/Public Relations","label":"02=02 Advertising/Public Relations"},{"value":"03=03 Arts/Entertainment/Publishing","label":"03=03 Arts/Entertainment/Publishing"},{"value":"04=04 Automotive","label":"04=04 Automotive"},{"value":"05=05 Banking/ Mortgage","label":"05=05 Banking/ Mortgage"},{"value":"06=06 Biotech","label":"06=06 Biotech"},{"value":"07=07 Broadcast/Journalism","label":"07=07 Broadcast/Journalism"},{"value":"08=08 Business Development","label":"08=08 Business Development"},{"value":"09=09 Clerical/Administrative","label":"09=09 Clerical/Administrative"},{"value":"10=10 Construction/Trades","label":"10=10 Construction/Trades"},{"value":"11=11 Consultant","label":"11=11 Consultant"},{"value":"12=12 Customer Services","label":"12=12 Customer Services"},{"value":"13=13 Design","label":"13=13 Design"},{"value":"14=14 Education","label":"14=14 Education"},{"value":"15=15 Engineering","label":"15=15 Engineering"},{"value":"16=16 Entry Level","label":"16=16 Entry Level"},{"value":"17=17 Executive","label":"17=17 Executive"},{"value":"18=18 Food Service","label":"18=18 Food Service"},{"value":"19=19 Government","label":"19=19 Government"},{"value":"20=20 Grocery","label":"20=20 Grocery"},{"value":"21=21 Healthcare","label":"21=21 Healthcare"},{"value":"22=22 Hospitality","label":"22=22 Hospitality"},{"value":"23=23 Human Resources","label":"23=23 Human Resources"},{"value":"24=24 Information Technology","label":"24=24 Information Technology"},{"value":"25=25 Insurance","label":"25=25 Insurance"},{"value":"26=26 Law/Legal","label":"26=26 Law/Legal"},{"value":"27=27 Management","label":"27=27 Management"},{"value":"28=28 Manufacturing","label":"28=28 Manufacturing"},{"value":"29=29 Marketing","label":"29=29 Marketing"},{"value":"30=30 Pharmaceutical","label":"30=30 Pharmaceutical"},{"value":"31=31 Professional Services","label":"31=31 Professional Services"},{"value":"32=32 Purchasing","label":"32=32 Purchasing"},{"value":"33=33 Quality Assurance (QA)","label":"33=33 Quality Assurance (QA)"},{"value":"34=34 Research","label":"34=34 Research"},{"value":"35=35 Restaurant","label":"35=35 Restaurant"},{"value":"36=36 Retail","label":"36=36 Retail"},{"value":"37=37 Sales","label":"37=37 Sales"},{"value":"38=38 Science","label":"38=38 Science"},{"value":"39=39 Security/Law Enforcement","label":"39=39 Security/Law Enforcement"},{"value":"40=40 Shipping/Distribution","label":"40=40 Shipping/Distribution"},{"value":"41=41 Strategy","label":"41=41 Strategy"},{"value":"42=42 Student","label":"42=42 Student"},{"value":"43=43 Telecommunications","label":"43=43 Telecommunications"},{"value":"44=44 Training","label":"44=44 Training"},{"value":"45=45 Transportation","label":"45=45 Transportation"},{"value":"46=46 Warehouse","label":"46=46 Warehouse"},{"value":"47=47 Other","label":"47=47 Other"},{"value":"99=99 Unknown/Refused","label":"99=99 Unknown/Refused"}],"group":"host description"},{"type":"text","label":"host total mass","name":"host_total_mass","required":false,"visible":true,"helpText":"total mass of the host at collection, the unit depends on host","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"host description"},{"type":"text","label":"host phenotype","name":"host_phenotype","required":false,"visible":true,"helpText":"phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO","group":"host description"},{"type":"text","label":"host body temperature","name":"host_body_temperature","required":false,"visible":true,"helpText":"core body temperature of the host when sample was collected","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"host description"},{"type":"select","label":"host sex","name":"host_sex","required":false,"visible":true,"helpText":"Gender or sex of the host.","options":[{"value":"female","label":"female"},{"value":"hermaphrodite","label":"hermaphrodite"},{"value":"male","label":"male"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"neuter","label":"neuter"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"other","label":"other"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"sample salinity","name":"sample_salinity","required":false,"visible":true,"helpText":"Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"menarche","name":"menarche","required":false,"visible":true,"helpText":"date of most recent menstruation","group":"host details"},{"type":"text","label":"sexual activity","name":"sexual_activity","required":false,"visible":true,"helpText":"current sexual partner and frequency of sex","group":"host details"},{"type":"text","label":"pregnancy","name":"pregnancy","required":false,"visible":true,"helpText":"date due of pregnancy","group":"host details"},{"type":"text","label":"douche","name":"douche","required":false,"visible":true,"helpText":"date of most recent douche","group":"host details"},{"type":"text","label":"birth control","name":"birth_control","required":false,"visible":true,"helpText":"specification of birth control medication used","group":"host details"},{"type":"text","label":"menopause","name":"menopause","required":false,"visible":true,"helpText":"date of onset of menopause","group":"host details"},{"type":"text","label":"HRT","name":"hrt","required":false,"visible":true,"helpText":"whether subject had hormone replacement theraphy, and if yes start date","group":"host details"},{"type":"select","label":"hysterectomy","name":"hysterectomy","required":false,"visible":true,"helpText":"specification of whether hysterectomy was performed","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"host details"},{"type":"text","label":"host diet","name":"host_diet","required":false,"visible":true,"helpText":"type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, Mediterranean etc.; can include multiple diet types","group":"host details"},{"type":"text","label":"host last meal","name":"host_last_meal","required":false,"visible":true,"helpText":"content of last meal and time since feeding; can include multiple values","group":"host details"},{"type":"text","label":"host family relationship","name":"host_family_relationship","required":false,"visible":true,"helpText":"Familial relationships to other hosts in the same study; can include multiple relationships","group":"host details"},{"type":"text","label":"host genotype","name":"host_genotype","required":false,"visible":true,"helpText":"observed genotype","group":"host details"},{"type":"text","label":"host pulse","name":"host_pulse","required":false,"visible":true,"helpText":"resting pulse, measured as beats per minute","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"units":[{"value":"bpm","label":"bpm"}],"group":"host details"},{"type":"text","label":"host body product","name":"host_body_product","required":false,"visible":true,"helpText":"substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host details"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/human-vaginal.png"},{"name":"GSC MIxS microbial mat biolfilm","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000019","category":"mixs","accession":"ERC000019","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":true,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"biomass","name":"biomass","required":false,"visible":true,"helpText":"amount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements","units":[{"value":"t","label":"t"},{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"mean friction velocity","name":"mean_friction_velocity","required":false,"visible":true,"helpText":"measurement of mean friction velocity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m/s","label":"m/s"}],"group":"local environment conditions"},{"type":"text","label":"mean peak friction velocity","name":"mean_peak_friction_velocity","required":false,"visible":true,"helpText":"measurement of mean peak friction velocity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m/s","label":"m/s"}],"group":"local environment conditions"},{"type":"text","label":"pressure","name":"pressure","required":false,"visible":true,"helpText":"pressure to which the sample is subject, in atmospheres","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"bar","label":"bar"},{"value":"atm","label":"atm"}],"group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"turbidity","name":"turbidity","required":false,"visible":true,"helpText":"turbidity measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"FTU","label":"FTU"},{"value":"NTU","label":"NTU"}],"group":"local environment conditions"},{"type":"text","label":"pH","name":"ph","required":false,"visible":true,"helpText":"pH measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"local environment conditions"},{"type":"text","label":"water content","name":"water_content","required":false,"visible":true,"helpText":"Water content measurement e.g. soil water content of 13.6%","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"%","label":"%"},{"value":"cm3/cm3","label":"cm3/cm3"},{"value":"g/g","label":"g/g"}],"group":"local environment conditions"},{"type":"text","label":"alkyl diethers","name":"alkyl_diethers","required":false,"visible":true,"helpText":"concentration of alkyl diethers","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"M/L","label":"M/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"aminopeptidase activity","name":"aminopeptidase_activity","required":false,"visible":true,"helpText":"measurement of aminopeptidase activity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mol/L/h","label":"mol/L/h"}],"group":"concentration measurement"},{"type":"text","label":"ammonium","name":"ammonium","required":false,"visible":true,"helpText":"concentration of ammonium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"bacterial carbon production","name":"bacterial_carbon_production","required":false,"visible":true,"helpText":"measurement of bacterial carbon production","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ng/h","label":"ng/h"}],"group":"concentration measurement"},{"type":"text","label":"bishomohopanol","name":"bishomohopanol","required":false,"visible":true,"helpText":"concentration of bishomohopanol","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/g","label":"µg/g"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"bromide","name":"bromide","required":false,"visible":true,"helpText":"concentration of bromide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"calcium","name":"calcium","required":false,"visible":true,"helpText":"concentration of calcium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"carbon/nitrogen ratio","name":"carbonnitrogen_ratio","required":false,"visible":true,"helpText":"ratio of amount or concentrations of carbon to nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"concentration measurement"},{"type":"text","label":"chloride","name":"chloride","required":false,"visible":true,"helpText":"concentration of chloride","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"chlorophyll","name":"chlorophyll","required":false,"visible":true,"helpText":"concentration of chlorophyll","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/m3","label":"mg/m3"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"diether lipids","name":"diether_lipids","required":false,"visible":true,"helpText":"concentration of diether lipids; can include multiple types of diether lipids","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ng/L","label":"ng/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved carbon dioxide","name":"dissolved_carbon_dioxide","required":false,"visible":true,"helpText":"concentration of dissolved carbon dioxide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved hydrogen","name":"dissolved_hydrogen","required":false,"visible":true,"helpText":"concentration of dissolved hydrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved inorganic carbon","name":"dissolved_inorganic_carbon","required":false,"visible":true,"helpText":"dissolved inorganic carbon concentration","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved organic carbon","name":"dissolved_organic_carbon","required":false,"visible":true,"helpText":"concentration of dissolved organic carbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved organic nitrogen","name":"dissolved_organic_nitrogen","required":false,"visible":true,"helpText":"dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"methane","name":"methane","required":false,"visible":true,"helpText":"methane (gas) amount or concentration at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µM/L","label":"µM/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved oxygen","name":"dissolved_oxygen","required":false,"visible":true,"helpText":"concentration of dissolved oxygen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/kg","label":"µmol/kg"}],"group":"concentration measurement"},{"type":"text","label":"glucosidase activity","name":"glucosidase_activity","required":false,"visible":true,"helpText":"measurement of glucosidase activity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mol/L/h","label":"mol/L/h"}],"group":"concentration measurement"},{"type":"text","label":"magnesium","name":"magnesium","required":false,"visible":true,"helpText":"concentration of magnesium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"mol/L","label":"mol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"n-alkanes","name":"nalkanes","required":false,"visible":true,"helpText":"concentration of n-alkanes; can include multiple n-alkanes","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"nitrate","name":"nitrate","required":false,"visible":true,"helpText":"concentration of nitrate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"nitrite","name":"nitrite","required":false,"visible":true,"helpText":"concentration of nitrite","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen concentration","name":"total_nitrogen_concentration","required":false,"visible":true,"helpText":"Concentration of nitrogen (total). Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"organic carbon","name":"organic_carbon","required":false,"visible":true,"helpText":"concentration of organic carbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"organic matter","name":"organic_matter","required":false,"visible":true,"helpText":"concentration of organic matter","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"organic nitrogen","name":"organic_nitrogen","required":false,"visible":true,"helpText":"concentration of organic nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"particulate organic carbon","name":"particulate_organic_carbon","required":false,"visible":true,"helpText":"concentration of particulate organic carbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"petroleum hydrocarbon","name":"petroleum_hydrocarbon","required":false,"visible":true,"helpText":"concentration of petroleum hydrocarbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"phaeopigments","name":"phaeopigments","required":false,"visible":true,"helpText":"concentration of phaeopigments; can include multiple phaeopigments","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/m3","label":"mg/m3"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"phosphate","name":"phosphate","required":false,"visible":true,"helpText":"concentration of phosphate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"phospholipid fatty acid","name":"phospholipid_fatty_acid","required":false,"visible":true,"helpText":"concentration of phospholipid fatty acids; can include multiple values","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mol/L","label":"mol/L"},{"value":"mol/g","label":"mol/g"}],"group":"concentration measurement"},{"type":"text","label":"potassium","name":"potassium","required":false,"visible":true,"helpText":"concentration of potassium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"redox potential","name":"redox_potential","required":false,"visible":true,"helpText":"redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mV","label":"mV"}],"group":"concentration measurement"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"total carbon","name":"total_carbon","required":false,"visible":true,"helpText":"total carbon content","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"silicate","name":"silicate","required":false,"visible":true,"helpText":"concentration of silicate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"sodium","name":"sodium","required":false,"visible":true,"helpText":"sodium concentration","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"total organic carbon","name":"total_organic_carbon","required":false,"visible":true,"helpText":"Definition for soil: total organic C content of the soil units of g C/kg soil. Definition otherwise: total organic carbon content","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/kg","label":"g/kg"}],"group":"concentration measurement"},{"type":"text","label":"sulfate","name":"sulfate","required":false,"visible":true,"helpText":"concentration of sulfate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"sulfide","name":"sulfide","required":false,"visible":true,"helpText":"concentration of sulfide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen content","name":"total_nitrogen_content","required":false,"visible":true,"helpText":"Total nitrogen content of the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"alkalinity","name":"alkalinity","required":false,"visible":true,"helpText":"alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mEq/L","label":"mEq/L"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"depth","name":"depth","required":true,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/microbial-mat-biofilm.png"},{"name":"GSC MIxS plant associated","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000020","category":"mixs","accession":"ERC000020","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"observed host symbionts","name":"observed_host_symbionts","required":false,"visible":true,"helpText":"The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"growth facility","name":"growth_facility","required":false,"visible":true,"helpText":"type of facility where the sampled plant was grown","options":[{"value":"experimental garden","label":"experimental garden"},{"value":"field","label":"field"},{"value":"glasshouse","label":"glasshouse"},{"value":"growth chamber","label":"growth chamber"},{"value":"open top chamber","label":"open top chamber"},{"value":"other","label":"other"}],"group":"sample collection: site related"},{"type":"text","label":"sample disease stage","name":"sample_disease_stage","required":false,"visible":true,"helpText":"stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen","group":"sample collection: core sample properties"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"text","label":"sample disease status","name":"sample_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the subject has been diagnosed at the time of sample collection; can include multiple diagnoses; the value of the field depends on subject; e.g. Charcoal rot (Macrophomina phaseolina), Late wilt (Cephalosporium maydis)","group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"select","label":"sample capture status","name":"sample_capture_status","required":false,"visible":true,"helpText":"Reason for the sample collection.","options":[{"value":"active surveillance in response to outbreak","label":"active surveillance in response to outbreak"},{"value":"active surveillance not initiated by an outbreak","label":"active surveillance not initiated by an outbreak"},{"value":"farm sample","label":"farm sample"},{"value":"market sample","label":"market sample"},{"value":"other","label":"other"},{"value":"pet sample","label":"pet sample"},{"value":"zoo sample","label":"zoo sample"}],"group":"sample collection"},{"type":"select","label":"growth habit","name":"growth_habit","required":false,"visible":true,"helpText":"characteristic shape, appearance or growth form of a plant species","options":[{"value":"erect","label":"erect"},{"value":"prostrate","label":"prostrate"},{"value":"semi-erect","label":"semi-erect"},{"value":"spreading","label":"spreading"}],"group":"Organism characteristics"},{"type":"text","label":"plant sex","name":"plant_sex","required":false,"visible":true,"helpText":"sex of the reproductive parts on the whole plant, e.g. pistilate, staminate, monoecieous, hermaphrodite","group":"Organism characteristics"},{"type":"text","label":"plant structure","name":"plant_structure","required":false,"visible":true,"helpText":"name of plant structure that the sample was obtained from; for Plant Ontology (PO) terms see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051); if an individual flower is sampled the sex of it can be recorded here","group":"Organism characteristics"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host common name","name":"host_common_name","required":false,"visible":true,"helpText":"common name of the host, e.g. human","group":"host description"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"text","label":"host taxid","name":"host_taxid","required":false,"visible":true,"helpText":"NCBI taxon id of the host, e.g. 9606","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"host description"},{"type":"text","label":"host life stage","name":"host_life_stage","required":false,"visible":true,"helpText":"description of life stage of host","group":"host description"},{"type":"text","label":"host height","name":"host_height","required":false,"visible":true,"helpText":"the height of subject","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host length","name":"host_length","required":false,"visible":true,"helpText":"the length of subject","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"plant body site","name":"plant_body_site","required":false,"visible":true,"helpText":"name of body site that the sample was obtained from. For Plant Ontology (PO) (v 20) terms, see http://purl.bioontology.org/ontology/PO","group":"host description"},{"type":"text","label":"host total mass","name":"host_total_mass","required":false,"visible":true,"helpText":"total mass of the host at collection, the unit depends on host","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"host description"},{"type":"text","label":"host phenotype","name":"host_phenotype","required":false,"visible":true,"helpText":"phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO","group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"host subspecific genetic lineage","name":"host_subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"host description"},{"type":"text","label":"climate environment","name":"climate_environment","required":false,"visible":true,"helpText":"treatment involving an exposure to a particular climate; can include multiple climates","group":"local environment conditions"},{"type":"text","label":"gaseous environment","name":"gaseous_environment","required":false,"visible":true,"helpText":"use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens","group":"local environment conditions"},{"type":"text","label":"seasonal environment","name":"seasonal_environment","required":false,"visible":true,"helpText":"treatment involving an exposure to a particular season (e.g. winter, summer, rabi, rainy etc.)","group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"host genotype","name":"host_genotype","required":false,"visible":true,"helpText":"observed genotype","group":"host details"},{"type":"text","label":"host dry mass","name":"host_dry_mass","required":false,"visible":true,"helpText":"measurement of dry mass","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"mg","label":"mg"},{"value":"kg","label":"kg"}],"group":"host details"},{"type":"text","label":"host wet mass","name":"host_wet_mass","required":false,"visible":true,"helpText":"measurement of wet mass","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"mg","label":"mg"},{"value":"kg","label":"kg"}],"group":"host details"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"genetic modification","name":"genetic_modification","required":false,"visible":true,"helpText":"A genetic modification of the genome of an organism which may occur naturally by spontaneous mutation, or be introduced by some experimental means. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection.","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"ancestral data","name":"ancestral_data","required":false,"visible":true,"helpText":"information about either pedigree or other description of ancestral information (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"plant growth medium","name":"plant_growth_medium","required":false,"visible":true,"helpText":"Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147).","group":"growth medium"},{"type":"text","label":"rooting conditions","name":"rooting_conditions","required":false,"visible":true,"helpText":"relevant rooting conditions, such as field plot size, sowing density, container dimensions, number of plants per container","group":"growth medium"},{"type":"text","label":"culture rooting medium","name":"culture_rooting_medium","required":false,"visible":true,"helpText":"name or reference for the hydroponic or in vitro culture rooting medium, can be a name of a commonly used medium or reference to a specific medium; e.g. Murashige and Skoog medium, if the medium has not been formally published, use the rooting medium descriptors","group":"growth medium"},{"type":"text","label":"rooting medium macronutrients","name":"rooting_medium_macronutrients","required":false,"visible":true,"helpText":"measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L)","group":"growth medium"},{"type":"text","label":"rooting medium micronutrients","name":"rooting_medium_micronutrients","required":false,"visible":true,"helpText":"measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L)","group":"growth medium"},{"type":"text","label":"rooting medium organic supplements","name":"rooting_medium_organic_supplements","required":false,"visible":true,"helpText":"organic supplements of the culture rooting medium, such as vitaimins, amino acids, organic acids, antibiotics activated charcoal; e.g. Nicotinic acid (0.5mg/L)","group":"growth medium"},{"type":"text","label":"rooting medium carbon","name":"rooting_medium_carbon","required":false,"visible":true,"helpText":"source of organic carbon in the culture rooting medium; e.g. sucrose","group":"growth medium"},{"type":"text","label":"rooting medium regulators","name":"rooting_medium_regulators","required":false,"visible":true,"helpText":"growth regulators in the culture rooting medium, such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5mg/L NAA","group":"growth medium"},{"type":"text","label":"rooting medium solidifier","name":"rooting_medium_solidifier","required":false,"visible":true,"helpText":"specification of the solidifying agent in the culture rooting medium; e.g. agar","group":"growth medium"},{"type":"text","label":"rooting medium pH","name":"rooting_medium_ph","required":false,"visible":true,"helpText":"pH measurement of the culture rooting medium; e.g. 5.5","group":"growth medium"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"plant product","name":"plant_product","required":false,"visible":true,"helpText":"substance produced by the plant, where the sample was obtained from","group":"food and agriculture"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"air temperature regimen","name":"air_temperature_regimen","required":false,"visible":true,"helpText":"information about treatment involving an exposure to varying temperatures; should include the temperature, treatment duration, interval and total experimental duration; can include different temperature regimens","group":"local environment conditions imposed"},{"type":"text","label":"antibiotic regimen","name":"antibiotic_regimen","required":false,"visible":true,"helpText":"information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment duration, interval and total experimental duration; can include multiple antibiotic regimens","group":"local environment conditions imposed"},{"type":"text","label":"chemical mutagen","name":"chemical_mutagen","required":false,"visible":true,"helpText":"treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment duration, interval and total experimental duration; can include multiple mutagen regimens","group":"local environment conditions imposed"},{"type":"text","label":"fertilizer administration","name":"fertilizer_administration","required":false,"visible":true,"helpText":"Type of fertilizer or amendment added to the soil or water for the purpose of improving substrate health and quality for plant growth. This field accepts terms listed under agronomic fertilizer (http://purl.obolibrary.org/obo/AGRO_00002062). Multiple terms may apply and can be separated by pipes, listing in reverse chronological order. N.B. Old ENA definition as \"fertilizer regimen\": information about treatment involving the use of fertilizers; should include the name fertilizer, amount administered, treatment duration, interval and total experimental duration; can include multiple fertilizer regimens","group":"local environment conditions imposed"},{"type":"text","label":"fungicide regimen","name":"fungicide_regimen","required":false,"visible":true,"helpText":"information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment duration, interval and total experimental duration; can include multiple fungicide regimens","group":"local environment conditions imposed"},{"type":"text","label":"gravity","name":"gravity","required":false,"visible":true,"helpText":"information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; can include multiple treatments","group":"local environment conditions imposed"},{"type":"text","label":"growth hormone regimen","name":"growth_hormone_regimen","required":false,"visible":true,"helpText":"information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment duration, interval and total experimental duration; can include multiple growth hormone regimens","group":"local environment conditions imposed"},{"type":"text","label":"growth media","name":"growth_media","required":false,"visible":true,"helpText":"information about growth media for growing the plants or tissue cultured samples","group":"local environment conditions imposed"},{"type":"text","label":"herbicide regimen","name":"herbicide_regimen","required":false,"visible":true,"helpText":"information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment duration, interval and total experimental duration; can include multiple regimens","group":"local environment conditions imposed"},{"type":"text","label":"humidity regimen","name":"humidity_regimen","required":false,"visible":true,"helpText":"information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment duration, interval and total experimental duration; can include multiple regimens","group":"local environment conditions imposed"},{"type":"text","label":"mineral nutrient regimen","name":"mineral_nutrient_regimen","required":false,"visible":true,"helpText":"information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment duration, interval and total experimental duration; can include multiple mineral nutrient regimens","group":"local environment conditions imposed"},{"type":"text","label":"non-mineral nutrient regimen","name":"nonmineral_nutrient_regimen","required":false,"visible":true,"helpText":"information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment duration, interval and total experimental duration; can include multiple non-mineral nutrient regimens","group":"local environment conditions imposed"},{"type":"text","label":"pesticide regimen","name":"pesticide_regimen","required":false,"visible":true,"helpText":"information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment duration, interval and total experimental duration; can include multiple pesticide regimens","group":"local environment conditions imposed"},{"type":"text","label":"pH regimen","name":"ph_regimen","required":false,"visible":true,"helpText":"information about treatment involving exposure of plants to varying levels of pH of the growth media; can include multiple regimen","group":"local environment conditions imposed"},{"type":"text","label":"radiation regimen","name":"radiation_regimen","required":false,"visible":true,"helpText":"information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment duration, interval and total experimental duration; can include multiple radiation regimens","group":"local environment conditions imposed"},{"type":"text","label":"rainfall regimen","name":"rainfall_regimen","required":false,"visible":true,"helpText":"information about treatment involving an exposure to a given amount of rainfall; can include multiple regimens","group":"local environment conditions imposed"},{"type":"text","label":"salt regimen","name":"salt_regimen","required":false,"visible":true,"helpText":"information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment duration, interval and total experimental duration; can include multiple salt regimens","group":"local environment conditions imposed"},{"type":"text","label":"standing water regimen","name":"standing_water_regimen","required":false,"visible":true,"helpText":"treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water; can include multiple regimens","group":"local environment conditions imposed"},{"type":"text","label":"tissue culture growth media","name":"tissue_culture_growth_media","required":false,"visible":true,"helpText":"description of plant tissue culture growth media used","group":"local environment conditions imposed"},{"type":"text","label":"watering regimen","name":"watering_regimen","required":false,"visible":true,"helpText":"information about treatment involving an exposure to watering frequencies; can include multiple regimens","group":"local environment conditions imposed"},{"type":"text","label":"water temperature regimen","name":"water_temperature_regimen","required":false,"visible":true,"helpText":"information about treatment involving an exposure to water with varying degree of temperature; can include multiple regimens","group":"local environment conditions imposed"},{"type":"text","label":"light regimen","name":"light_regimen","required":false,"visible":true,"helpText":"information about treatment involving an exposure to light, this includes both light intensity and quality","group":"local environment conditions imposed"},{"type":"text","label":"biotic regimen","name":"biotic_regimen","required":false,"visible":true,"helpText":"information about treatment involving use of biotic factors, such as bacteria, viruses or fungi","group":"local environment conditions imposed"},{"type":"text","label":"mechanical damage","name":"mechanical_damage","required":false,"visible":true,"helpText":"information about any mechanical damage exerted on the plant; can include multiple damages and sites","group":"local environment conditions imposed"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/plant-associated.png"},{"name":"GSC MIxS sediment","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000021","category":"mixs","accession":"ERC000021","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"particle classification","name":"particle_classification","required":false,"visible":true,"helpText":"Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values","group":"local environment conditions: soil"},{"type":"text","label":"sediment type","name":"sediment_type","required":false,"visible":true,"helpText":"Information about the sediment type based on major constituents","group":"local environment conditions: soil"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"text","label":"density","name":"density","required":false,"visible":true,"helpText":"density of sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/m3","label":"g/m3"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":true,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"biomass","name":"biomass","required":false,"visible":true,"helpText":"amount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements","units":[{"value":"t","label":"t"},{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"mean friction velocity","name":"mean_friction_velocity","required":false,"visible":true,"helpText":"measurement of mean friction velocity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m/s","label":"m/s"}],"group":"local environment conditions"},{"type":"text","label":"mean peak friction velocity","name":"mean_peak_friction_velocity","required":false,"visible":true,"helpText":"measurement of mean peak friction velocity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m/s","label":"m/s"}],"group":"local environment conditions"},{"type":"text","label":"pressure","name":"pressure","required":false,"visible":true,"helpText":"pressure to which the sample is subject, in atmospheres","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"bar","label":"bar"},{"value":"atm","label":"atm"}],"group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"select","label":"tidal stage","name":"tidal_stage","required":false,"visible":true,"helpText":"stage of tide","options":[{"value":"high","label":"high"},{"value":"low","label":"low"}],"group":"local environment conditions"},{"type":"text","label":"turbidity","name":"turbidity","required":false,"visible":true,"helpText":"turbidity measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"FTU","label":"FTU"},{"value":"NTU","label":"NTU"}],"group":"local environment conditions"},{"type":"text","label":"pH","name":"ph","required":false,"visible":true,"helpText":"pH measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"local environment conditions"},{"type":"text","label":"total depth of water column","name":"total_depth_of_water_column","required":false,"visible":true,"helpText":"measurement of total depth of water column","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m","label":"m"}],"group":"local environment conditions"},{"type":"text","label":"water content","name":"water_content","required":false,"visible":true,"helpText":"Water content measurement e.g. soil water content of 13.6%","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"%","label":"%"},{"value":"cm3/cm3","label":"cm3/cm3"},{"value":"g/g","label":"g/g"}],"group":"local environment conditions"},{"type":"text","label":"alkyl diethers","name":"alkyl_diethers","required":false,"visible":true,"helpText":"concentration of alkyl diethers","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"M/L","label":"M/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"aminopeptidase activity","name":"aminopeptidase_activity","required":false,"visible":true,"helpText":"measurement of aminopeptidase activity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mol/L/h","label":"mol/L/h"}],"group":"concentration measurement"},{"type":"text","label":"ammonium","name":"ammonium","required":false,"visible":true,"helpText":"concentration of ammonium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"bacterial carbon production","name":"bacterial_carbon_production","required":false,"visible":true,"helpText":"measurement of bacterial carbon production","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ng/h","label":"ng/h"}],"group":"concentration measurement"},{"type":"text","label":"bishomohopanol","name":"bishomohopanol","required":false,"visible":true,"helpText":"concentration of bishomohopanol","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/g","label":"µg/g"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"bromide","name":"bromide","required":false,"visible":true,"helpText":"concentration of bromide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"calcium","name":"calcium","required":false,"visible":true,"helpText":"concentration of calcium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"carbon/nitrogen ratio","name":"carbonnitrogen_ratio","required":false,"visible":true,"helpText":"ratio of amount or concentrations of carbon to nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"concentration measurement"},{"type":"text","label":"chloride","name":"chloride","required":false,"visible":true,"helpText":"concentration of chloride","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"chlorophyll","name":"chlorophyll","required":false,"visible":true,"helpText":"concentration of chlorophyll","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/m3","label":"mg/m3"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"diether lipids","name":"diether_lipids","required":false,"visible":true,"helpText":"concentration of diether lipids; can include multiple types of diether lipids","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ng/L","label":"ng/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved carbon dioxide","name":"dissolved_carbon_dioxide","required":false,"visible":true,"helpText":"concentration of dissolved carbon dioxide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved hydrogen","name":"dissolved_hydrogen","required":false,"visible":true,"helpText":"concentration of dissolved hydrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved inorganic carbon","name":"dissolved_inorganic_carbon","required":false,"visible":true,"helpText":"dissolved inorganic carbon concentration","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved organic carbon","name":"dissolved_organic_carbon","required":false,"visible":true,"helpText":"concentration of dissolved organic carbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved organic nitrogen","name":"dissolved_organic_nitrogen","required":false,"visible":true,"helpText":"dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"methane","name":"methane","required":false,"visible":true,"helpText":"methane (gas) amount or concentration at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µM/L","label":"µM/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved oxygen","name":"dissolved_oxygen","required":false,"visible":true,"helpText":"concentration of dissolved oxygen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/kg","label":"µmol/kg"}],"group":"concentration measurement"},{"type":"text","label":"glucosidase activity","name":"glucosidase_activity","required":false,"visible":true,"helpText":"measurement of glucosidase activity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mol/L/h","label":"mol/L/h"}],"group":"concentration measurement"},{"type":"text","label":"magnesium","name":"magnesium","required":false,"visible":true,"helpText":"concentration of magnesium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"mol/L","label":"mol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"n-alkanes","name":"nalkanes","required":false,"visible":true,"helpText":"concentration of n-alkanes; can include multiple n-alkanes","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"nitrate","name":"nitrate","required":false,"visible":true,"helpText":"concentration of nitrate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"nitrite","name":"nitrite","required":false,"visible":true,"helpText":"concentration of nitrite","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen concentration","name":"total_nitrogen_concentration","required":false,"visible":true,"helpText":"Concentration of nitrogen (total). Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"organic carbon","name":"organic_carbon","required":false,"visible":true,"helpText":"concentration of organic carbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"organic matter","name":"organic_matter","required":false,"visible":true,"helpText":"concentration of organic matter","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"organic nitrogen","name":"organic_nitrogen","required":false,"visible":true,"helpText":"concentration of organic nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"particulate organic carbon","name":"particulate_organic_carbon","required":false,"visible":true,"helpText":"concentration of particulate organic carbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"petroleum hydrocarbon","name":"petroleum_hydrocarbon","required":false,"visible":true,"helpText":"concentration of petroleum hydrocarbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"phaeopigments","name":"phaeopigments","required":false,"visible":true,"helpText":"concentration of phaeopigments; can include multiple phaeopigments","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/m3","label":"mg/m3"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"phosphate","name":"phosphate","required":false,"visible":true,"helpText":"concentration of phosphate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"phospholipid fatty acid","name":"phospholipid_fatty_acid","required":false,"visible":true,"helpText":"concentration of phospholipid fatty acids; can include multiple values","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mol/L","label":"mol/L"},{"value":"mol/g","label":"mol/g"}],"group":"concentration measurement"},{"type":"text","label":"potassium","name":"potassium","required":false,"visible":true,"helpText":"concentration of potassium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"redox potential","name":"redox_potential","required":false,"visible":true,"helpText":"redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mV","label":"mV"}],"group":"concentration measurement"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"total carbon","name":"total_carbon","required":false,"visible":true,"helpText":"total carbon content","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"silicate","name":"silicate","required":false,"visible":true,"helpText":"concentration of silicate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"sodium","name":"sodium","required":false,"visible":true,"helpText":"sodium concentration","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"total organic carbon","name":"total_organic_carbon","required":false,"visible":true,"helpText":"Definition for soil: total organic C content of the soil units of g C/kg soil. Definition otherwise: total organic carbon content","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/kg","label":"g/kg"}],"group":"concentration measurement"},{"type":"text","label":"sulfate","name":"sulfate","required":false,"visible":true,"helpText":"concentration of sulfate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"sulfide","name":"sulfide","required":false,"visible":true,"helpText":"concentration of sulfide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen content","name":"total_nitrogen_content","required":false,"visible":true,"helpText":"Total nitrogen content of the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"alkalinity","name":"alkalinity","required":false,"visible":true,"helpText":"alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mEq/L","label":"mEq/L"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"porosity","name":"porosity","required":false,"visible":true,"helpText":"Porosity of deposited sediment is volume of voids divided by the total volume of sample","simpleValidation":{"pattern":"[0-9]+","patternMessage":"Must match pattern: [0-9]+"},"group":"Environmental information"},{"type":"text","label":"depth","name":"depth","required":true,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/sediment.png"},{"name":"GSC MIxS soil","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000022","category":"mixs","accession":"ERC000022","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage conditions","name":"sample_storage_conditions","required":false,"visible":true,"helpText":"Conditions at which sample was stored, usually storage temperature, duration and location. In soil context: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"soil_taxonomic/FAO classification","name":"soil_taxonomicfao_classification","required":false,"visible":true,"helpText":"soil classification from the FAO World Reference Database for Soil Resources","group":"local environment conditions: soil"},{"type":"text","label":"soil_taxonomic/local classification","name":"soil_taxonomiclocal_classification","required":false,"visible":true,"helpText":"soil classification based on local soil classification system","group":"local environment conditions: soil"},{"type":"text","label":"soil_taxonomic/local classification method","name":"soil_taxonomiclocal_classification_method","required":false,"visible":true,"helpText":"reference or method used in determining the local soil classification","group":"local environment conditions: soil"},{"type":"select","label":"soil type","name":"soil_type","required":false,"visible":true,"helpText":"Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.","options":[{"value":"Acrisol","label":"Acrisol"},{"value":"Albeluvisol","label":"Albeluvisol"},{"value":"Alisol","label":"Alisol"},{"value":"Andosol","label":"Andosol"},{"value":"Anthrosol","label":"Anthrosol"},{"value":"Arenosol","label":"Arenosol"},{"value":"Calcisol","label":"Calcisol"},{"value":"Cambisol","label":"Cambisol"},{"value":"Chernozem","label":"Chernozem"},{"value":"Cryosol","label":"Cryosol"},{"value":"Durisol","label":"Durisol"},{"value":"Ferralsol","label":"Ferralsol"},{"value":"Fluvisol","label":"Fluvisol"},{"value":"Gleysol","label":"Gleysol"},{"value":"Gypsisol","label":"Gypsisol"},{"value":"Histosol","label":"Histosol"},{"value":"Kastanozem","label":"Kastanozem"},{"value":"Leptosol","label":"Leptosol"},{"value":"Lixisol","label":"Lixisol"},{"value":"Luvisol","label":"Luvisol"},{"value":"Nitisol","label":"Nitisol"},{"value":"Phaeozem","label":"Phaeozem"},{"value":"Planosol","label":"Planosol"},{"value":"Plinthosol","label":"Plinthosol"},{"value":"Podzol","label":"Podzol"},{"value":"Regosol","label":"Regosol"},{"value":"Solonchak","label":"Solonchak"},{"value":"Solonetz","label":"Solonetz"},{"value":"Stagnosol","label":"Stagnosol"},{"value":"Technosol","label":"Technosol"},{"value":"Umbrisol","label":"Umbrisol"},{"value":"Vertisol","label":"Vertisol"}],"group":"local environment conditions: soil"},{"type":"text","label":"soil type method","name":"soil_type_method","required":false,"visible":true,"helpText":"reference or method used in determining soil series name or other lower-level classification","group":"local environment conditions: soil"},{"type":"text","label":"soil texture measurement","name":"soil_texture_measurement","required":false,"visible":true,"helpText":"the relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.","units":[{"value":"% sand/silt/clay","label":"% sand/silt/clay"}],"group":"local environment conditions: soil"},{"type":"text","label":"soil texture method","name":"soil_texture_method","required":false,"visible":true,"helpText":"reference or method used in determining soil texture","group":"local environment conditions: soil"},{"type":"text","label":"microbial biomass","name":"microbial_biomass","required":false,"visible":true,"helpText":"the part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 µm. IF you keep this, you would need to have correction factors used for conversion to the final units, which should be mg C (or N)/kg soil).","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/kg","label":"g/kg"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":true,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"sieving","name":"sieving","required":false,"visible":true,"helpText":"Collection design of pooled samples and/or sieve size and amount of sample sieved","group":"sample collection"},{"type":"text","label":"microbial biomass method","name":"microbial_biomass_method","required":false,"visible":true,"helpText":"Reference or method used in determining microbial biomass","group":"sample collection"},{"type":"text","label":"horizon method","name":"horizon_method","required":false,"visible":true,"helpText":"Reference or method used in determining the horizon","group":"sample collection"},{"type":"text","label":"extreme_unusual_properties/heavy metals","name":"extreme_unusual_propertiesheavy_metals","required":false,"visible":true,"helpText":"heavy metals present and concentrations of any drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations","group":"unusual properties"},{"type":"text","label":"extreme_unusual_properties/heavy metals method","name":"extreme_unusual_propertiesheavy_metals_method","required":false,"visible":true,"helpText":"reference or method used in determining heavy metals","group":"unusual properties"},{"type":"text","label":"extreme_unusual_properties/Al saturation","name":"extreme_unusual_propertiesal_saturation","required":false,"visible":true,"helpText":"aluminum saturation (esp. for tropical soils)","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"%","label":"%"}],"group":"unusual properties"},{"type":"text","label":"extreme_unusual_properties/Al saturation method","name":"extreme_unusual_propertiesal_saturation_method","required":false,"visible":true,"helpText":"reference or method used in determining Al saturation","group":"unusual properties"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"link to climate information","name":"link_to_climate_information","required":false,"visible":true,"helpText":"link to climate resource","group":"link"},{"type":"text","label":"link to classification information","name":"link_to_classification_information","required":false,"visible":true,"helpText":"link to digitized soil maps or other soil classification information","group":"link"},{"type":"text","label":"links to additional analysis","name":"links_to_additional_analysis","required":false,"visible":true,"helpText":"link to additional analysis results performed on the sample","group":"link"},{"type":"text","label":"current land use","name":"current_land_use","required":false,"visible":true,"helpText":"present state of sample site","group":"local environment conditions"},{"type":"text","label":"current vegetation","name":"current_vegetation","required":false,"visible":true,"helpText":"vegetation classification from one or more standard classification systems, or agricultural crop","group":"local environment conditions"},{"type":"text","label":"current vegetation method","name":"current_vegetation_method","required":false,"visible":true,"helpText":"reference or method used in vegetation classification","group":"local environment conditions"},{"type":"select","label":"soil horizon","name":"soil_horizon","required":false,"visible":true,"helpText":"specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath","options":[{"value":"A horizon","label":"A horizon"},{"value":"B horizon","label":"B horizon"},{"value":"E horizon","label":"E horizon"},{"value":"O horizon","label":"O horizon"},{"value":"Permafrost","label":"Permafrost"},{"value":"R layer","label":"R layer"}],"group":"local environment conditions"},{"type":"select","label":"drainage classification","name":"drainage_classification","required":false,"visible":true,"helpText":"drainage classification from a standard system such as the USDA system","options":[{"value":"excessively drained","label":"excessively drained"},{"value":"moderately well","label":"moderately well"},{"value":"poorly","label":"poorly"},{"value":"somewhat poorly","label":"somewhat poorly"},{"value":"very poorly","label":"very poorly"},{"value":"well","label":"well"}],"group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"pH","name":"ph","required":false,"visible":true,"helpText":"pH measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"local environment conditions"},{"type":"text","label":"pH method","name":"ph_method","required":false,"visible":true,"helpText":"reference or method used in determining pH","group":"local environment conditions"},{"type":"text","label":"water content","name":"water_content","required":false,"visible":true,"helpText":"Water content measurement e.g. soil water content of 13.6%","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"%","label":"%"},{"value":"cm3/cm3","label":"cm3/cm3"},{"value":"g/g","label":"g/g"}],"group":"local environment conditions"},{"type":"text","label":"slope gradient","name":"slope_gradient","required":false,"visible":true,"helpText":"commonly called slope. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"%","label":"%"}],"group":"local environment conditions"},{"type":"text","label":"slope aspect","name":"slope_aspect","required":false,"visible":true,"helpText":"the direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., NW or 315°. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.","group":"local environment conditions"},{"type":"select","label":"profile position","name":"profile_position","required":false,"visible":true,"helpText":"cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas","options":[{"value":"backslope","label":"backslope"},{"value":"footslope","label":"footslope"},{"value":"shoulder","label":"shoulder"},{"value":"summit","label":"summit"},{"value":"toeslope","label":"toeslope"}],"group":"local environment conditions"},{"type":"text","label":"water content method","name":"water_content_method","required":false,"visible":true,"helpText":"reference or method used in determining the water content of soil","group":"concentration measurement"},{"type":"text","label":"total organic carbon method","name":"total_organic_carbon_method","required":false,"visible":true,"helpText":"Reference or method used in determining total organic carbon","group":"concentration measurement"},{"type":"text","label":"total nitrogen content method","name":"total_nitrogen_content_method","required":false,"visible":true,"helpText":"Reference or method used in determining the total nitrogen","group":"concentration measurement"},{"type":"text","label":"organic matter","name":"organic_matter","required":false,"visible":true,"helpText":"concentration of organic matter","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"organic nitrogen","name":"organic_nitrogen","required":false,"visible":true,"helpText":"concentration of organic nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"total organic carbon","name":"total_organic_carbon","required":false,"visible":true,"helpText":"Definition for soil: total organic C content of the soil units of g C/kg soil. Definition otherwise: total organic carbon content","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/kg","label":"g/kg"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen content","name":"total_nitrogen_content","required":false,"visible":true,"helpText":"Total nitrogen content of the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"salinity method","name":"salinity_method","required":false,"visible":true,"helpText":"reference or method used in determining salinity","group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"history/previous land use","name":"historyprevious_land_use","required":false,"visible":true,"helpText":"previous land use and dates","group":"local environment history"},{"type":"text","label":"previous land use method","name":"previous_land_use_method","required":false,"visible":true,"helpText":"Reference or method used in determining previous land use and dates","group":"local environment history"},{"type":"text","label":"history/crop rotation","name":"historycrop_rotation","required":false,"visible":true,"helpText":"whether or not crop is rotated, and if yes, rotation schedule","group":"local environment history"},{"type":"text","label":"history/agrochemical additions","name":"historyagrochemical_additions","required":false,"visible":true,"helpText":"addition of fertilizers, pesticides, etc. - amount and time of applications","group":"local environment history"},{"type":"select","label":"history/tillage","name":"historytillage","required":false,"visible":true,"helpText":"note method(s) used for tilling","options":[{"value":"chisel","label":"chisel"},{"value":"cutting disc","label":"cutting disc"},{"value":"disc plough","label":"disc plough"},{"value":"drill","label":"drill"},{"value":"mouldboard","label":"mouldboard"},{"value":"ridge till","label":"ridge till"},{"value":"strip tillage","label":"strip tillage"},{"value":"tined","label":"tined"},{"value":"zonal tillage","label":"zonal tillage"}],"group":"local environment history"},{"type":"text","label":"history/fire","name":"historyfire","required":false,"visible":true,"helpText":"historical and/or physical evidence of fire","group":"local environment history"},{"type":"text","label":"history/flooding","name":"historyflooding","required":false,"visible":true,"helpText":"historical and/or physical evidence of flooding","group":"local environment history"},{"type":"text","label":"history/extreme events","name":"historyextreme_events","required":false,"visible":true,"helpText":"unusual physical events that may have affected microbial populations","group":"local environment history"},{"type":"text","label":"mean seasonal temperature","name":"mean_seasonal_temperature","required":false,"visible":true,"helpText":"Mean seasonal temperature","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"local environment history"},{"type":"text","label":"mean seasonal precipitation","name":"mean_seasonal_precipitation","required":false,"visible":true,"helpText":"The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"}],"group":"local environment history"},{"type":"text","label":"mean annual precipitation","name":"mean_annual_precipitation","required":false,"visible":true,"helpText":"The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"}],"group":"local environment history"},{"type":"text","label":"mean annual temperature","name":"mean_annual_temperature","required":false,"visible":true,"helpText":"Mean annual temperature","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment history"},{"type":"text","label":"host specificity or range","name":"host_specificity_or_range","required":false,"visible":true,"helpText":"The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier.","group":"host details"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample pooling","name":"sample_pooling","required":false,"visible":true,"helpText":"Physical combination of several instances of like material, e.g. RNA extracted from samples or dishes of cell cultures into one big aliquot of cells. Please provide a short description of the samples that were pooled.","group":"sample processing"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"depth","name":"depth","required":true,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"}],"image":"/images/environments/soil.png"},{"name":"GSC MIxS wastewater sludge","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000023","category":"mixs","accession":"ERC000023","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"biochemical oxygen demand","name":"biochemical_oxygen_demand","required":false,"visible":true,"helpText":"a measure of the relative oxygen-depletion effect of a waste contaminant","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L (over 5 days at 20C)","label":"mg/L (over 5 days at 20C)"}],"group":"bioreactor"},{"type":"text","label":"chemical oxygen demand","name":"chemical_oxygen_demand","required":false,"visible":true,"helpText":"a measure of the relative oxygen-depletion effect of a waste contaminant","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L (over 5 days at 20C)","label":"mg/L (over 5 days at 20C)"}],"group":"bioreactor"},{"type":"text","label":"pre-treatment","name":"pretreatment","required":false,"visible":true,"helpText":"the process of pre-treatment removes materials that can be easily collected from the raw wastewater","group":"bioreactor"},{"type":"text","label":"primary treatment","name":"primary_treatment","required":false,"visible":true,"helpText":"the process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed","group":"bioreactor"},{"type":"text","label":"reactor type","name":"reactor_type","required":false,"visible":true,"helpText":"anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage","group":"bioreactor"},{"type":"text","label":"secondary treatment","name":"secondary_treatment","required":false,"visible":true,"helpText":"the process for substantially degrading the biological content of the sewage","group":"bioreactor"},{"type":"text","label":"sludge retention time","name":"sludge_retention_time","required":false,"visible":true,"helpText":"the time activated sludge remains in reactor","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"hours","label":"hours"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"}],"group":"bioreactor"},{"type":"text","label":"tertiary treatment","name":"tertiary_treatment","required":false,"visible":true,"helpText":"the process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment","group":"bioreactor"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"industrial effluent percent","name":"industrial_effluent_percent","required":false,"visible":true,"helpText":"percentage of industrial effluents received by wastewater treatment plant","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"%","label":"%"}],"group":"local environment conditions"},{"type":"text","label":"sewage type","name":"sewage_type","required":false,"visible":true,"helpText":"Type of sewage based on origin: wastewater treatment plant (municipal or industrial), open sewer line, river, stream, stagnant pool, or other.","group":"local environment conditions"},{"type":"text","label":"wastewater type","name":"wastewater_type","required":false,"visible":true,"helpText":"the origin of wastewater such as human waste, rainfall, storm drains, etc.","group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"pH","name":"ph","required":false,"visible":true,"helpText":"pH measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"local environment conditions"},{"type":"text","label":"efficiency percent","name":"efficiency_percent","required":false,"visible":true,"helpText":"percentage of volatile solids removed from the anaerobic digestor","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"%","label":"%"}],"group":"concentration measurement"},{"type":"text","label":"emulsions","name":"emulsions","required":false,"visible":true,"helpText":"amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/L","label":"g/L"},{"value":"ng/L","label":"ng/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"gaseous substances","name":"gaseous_substances","required":false,"visible":true,"helpText":"amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"inorganic particles","name":"inorganic_particles","required":false,"visible":true,"helpText":"concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mol/L","label":"mol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"organic particles","name":"organic_particles","required":false,"visible":true,"helpText":"concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/L","label":"g/L"}],"group":"concentration measurement"},{"type":"text","label":"soluble inorganic material","name":"soluble_inorganic_material","required":false,"visible":true,"helpText":"concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"mol/L","label":"mol/L"},{"value":"g/L","label":"g/L"}],"group":"concentration measurement"},{"type":"text","label":"soluble organic material","name":"soluble_organic_material","required":false,"visible":true,"helpText":"concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"mol/L","label":"mol/L"},{"value":"g/L","label":"g/L"}],"group":"concentration measurement"},{"type":"text","label":"suspended solids","name":"suspended_solids","required":false,"visible":true,"helpText":"concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter, etc,; can include multiple substances","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"mol/L","label":"mol/L"},{"value":"g/L","label":"g/L"}],"group":"concentration measurement"},{"type":"text","label":"total phosphate","name":"total_phosphate","required":false,"visible":true,"helpText":"total amount or concentration of phosphate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"nitrate","name":"nitrate","required":false,"visible":true,"helpText":"concentration of nitrate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen concentration","name":"total_nitrogen_concentration","required":false,"visible":true,"helpText":"Concentration of nitrogen (total). Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"phosphate","name":"phosphate","required":false,"visible":true,"helpText":"concentration of phosphate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"sodium","name":"sodium","required":false,"visible":true,"helpText":"sodium concentration","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen content","name":"total_nitrogen_content","required":false,"visible":true,"helpText":"Total nitrogen content of the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"alkalinity","name":"alkalinity","required":false,"visible":true,"helpText":"alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mEq/L","label":"mEq/L"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/wastewater-sludge.png"},{"name":"GSC MIxS water","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000024","category":"mixs","accession":"ERC000024","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"size-fraction lower threshold","name":"sizefraction_lower_threshold","required":false,"visible":true,"helpText":"Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"mm","label":"mm"},{"value":"µm","label":"µm"},{"value":"nm","label":"nm"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"size-fraction upper threshold","name":"sizefraction_upper_threshold","required":false,"visible":true,"helpText":"Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"},{"value":"µm","label":"µm"},{"value":"nm","label":"nm"}],"group":"sample collection: methods, storage and transport"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"text","label":"density","name":"density","required":false,"visible":true,"helpText":"density of sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/m3","label":"g/m3"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"biomass","name":"biomass","required":false,"visible":true,"helpText":"amount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements","units":[{"value":"t","label":"t"},{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"atmospheric data","name":"atmospheric_data","required":false,"visible":true,"helpText":"measurement of atmospheric data; can include multiple data","group":"local environment conditions"},{"type":"text","label":"conductivity","name":"conductivity","required":false,"visible":true,"helpText":"electrical conductivity of water","simpleValidation":{"pattern":"[1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?"},"units":[{"value":"mS/cm","label":"mS/cm"}],"group":"local environment conditions"},{"type":"text","label":"water current","name":"water_current","required":false,"visible":true,"helpText":"measurement of magnitude and direction of flow within a fluid","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m3/s","label":"m3/s"},{"value":"knot","label":"knot"}],"group":"local environment conditions"},{"type":"text","label":"fluorescence","name":"fluorescence","required":false,"visible":true,"helpText":"raw (volts) or converted (mg Chla/m^3) fluorescence of the water","simpleValidation":{"pattern":"[1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?"},"units":[{"value":"V","label":"V"},{"value":"mg Chla/m3","label":"mg Chla/m3"}],"group":"local environment conditions"},{"type":"text","label":"light intensity","name":"light_intensity","required":false,"visible":true,"helpText":"measurement of light intensity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"lux","label":"lux"}],"group":"local environment conditions"},{"type":"text","label":"mean friction velocity","name":"mean_friction_velocity","required":false,"visible":true,"helpText":"measurement of mean friction velocity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m/s","label":"m/s"}],"group":"local environment conditions"},{"type":"text","label":"mean peak friction velocity","name":"mean_peak_friction_velocity","required":false,"visible":true,"helpText":"measurement of mean peak friction velocity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m/s","label":"m/s"}],"group":"local environment conditions"},{"type":"text","label":"downward PAR","name":"downward_par","required":false,"visible":true,"helpText":"visible waveband radiance and irradiance measurements in the water column","simpleValidation":{"pattern":"[1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?"},"units":[{"value":"µE/m2/s","label":"µE/m2/s"}],"group":"local environment conditions"},{"type":"text","label":"photon flux","name":"photon_flux","required":false,"visible":true,"helpText":"measurement of photon flux","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/m2/s","label":"µmol/m2/s"}],"group":"local environment conditions"},{"type":"text","label":"pressure","name":"pressure","required":false,"visible":true,"helpText":"pressure to which the sample is subject, in atmospheres","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"bar","label":"bar"},{"value":"atm","label":"atm"}],"group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"select","label":"tidal stage","name":"tidal_stage","required":false,"visible":true,"helpText":"stage of tide","options":[{"value":"high","label":"high"},{"value":"low","label":"low"}],"group":"local environment conditions"},{"type":"text","label":"turbidity","name":"turbidity","required":false,"visible":true,"helpText":"turbidity measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"FTU","label":"FTU"},{"value":"NTU","label":"NTU"}],"group":"local environment conditions"},{"type":"text","label":"pH","name":"ph","required":false,"visible":true,"helpText":"pH measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"local environment conditions"},{"type":"text","label":"total depth of water column","name":"total_depth_of_water_column","required":false,"visible":true,"helpText":"measurement of total depth of water column","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m","label":"m"}],"group":"local environment conditions"},{"type":"text","label":"alkyl diethers","name":"alkyl_diethers","required":false,"visible":true,"helpText":"concentration of alkyl diethers","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"M/L","label":"M/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"aminopeptidase activity","name":"aminopeptidase_activity","required":false,"visible":true,"helpText":"measurement of aminopeptidase activity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mol/L/h","label":"mol/L/h"}],"group":"concentration measurement"},{"type":"text","label":"ammonium","name":"ammonium","required":false,"visible":true,"helpText":"concentration of ammonium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"bacterial carbon production","name":"bacterial_carbon_production","required":false,"visible":true,"helpText":"measurement of bacterial carbon production","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ng/h","label":"ng/h"}],"group":"concentration measurement"},{"type":"text","label":"bacterial production","name":"bacterial_production","required":false,"visible":true,"helpText":"bacterial production in the water column measured by isotope uptake","simpleValidation":{"pattern":"[1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/m3/d","label":"mg/m3/d"}],"group":"concentration measurement"},{"type":"text","label":"bacterial respiration","name":"bacterial_respiration","required":false,"visible":true,"helpText":"measurement of bacterial respiration in the water column","simpleValidation":{"pattern":"[1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/m3/d","label":"mg/m3/d"}],"group":"concentration measurement"},{"type":"text","label":"bishomohopanol","name":"bishomohopanol","required":false,"visible":true,"helpText":"concentration of bishomohopanol","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/g","label":"µg/g"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"bromide","name":"bromide","required":false,"visible":true,"helpText":"concentration of bromide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"calcium","name":"calcium","required":false,"visible":true,"helpText":"concentration of calcium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"carbon/nitrogen ratio","name":"carbonnitrogen_ratio","required":false,"visible":true,"helpText":"ratio of amount or concentrations of carbon to nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"concentration measurement"},{"type":"text","label":"chloride","name":"chloride","required":false,"visible":true,"helpText":"concentration of chloride","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"chlorophyll","name":"chlorophyll","required":false,"visible":true,"helpText":"concentration of chlorophyll","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/m3","label":"mg/m3"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"diether lipids","name":"diether_lipids","required":false,"visible":true,"helpText":"concentration of diether lipids; can include multiple types of diether lipids","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ng/L","label":"ng/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved carbon dioxide","name":"dissolved_carbon_dioxide","required":false,"visible":true,"helpText":"concentration of dissolved carbon dioxide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved hydrogen","name":"dissolved_hydrogen","required":false,"visible":true,"helpText":"concentration of dissolved hydrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved inorganic carbon","name":"dissolved_inorganic_carbon","required":false,"visible":true,"helpText":"dissolved inorganic carbon concentration","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved inorganic nitrogen","name":"dissolved_inorganic_nitrogen","required":false,"visible":true,"helpText":"concentration of dissolved inorganic nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved inorganic phosphorus","name":"dissolved_inorganic_phosphorus","required":false,"visible":true,"helpText":"concentration of dissolved inorganic phosphorus","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved organic carbon","name":"dissolved_organic_carbon","required":false,"visible":true,"helpText":"concentration of dissolved organic carbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved organic nitrogen","name":"dissolved_organic_nitrogen","required":false,"visible":true,"helpText":"dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved oxygen","name":"dissolved_oxygen","required":false,"visible":true,"helpText":"concentration of dissolved oxygen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/kg","label":"µmol/kg"}],"group":"concentration measurement"},{"type":"text","label":"glucosidase activity","name":"glucosidase_activity","required":false,"visible":true,"helpText":"measurement of glucosidase activity","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mol/L/h","label":"mol/L/h"}],"group":"concentration measurement"},{"type":"text","label":"magnesium","name":"magnesium","required":false,"visible":true,"helpText":"concentration of magnesium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"mol/L","label":"mol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"n-alkanes","name":"nalkanes","required":false,"visible":true,"helpText":"concentration of n-alkanes; can include multiple n-alkanes","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"nitrate","name":"nitrate","required":false,"visible":true,"helpText":"concentration of nitrate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"nitrite","name":"nitrite","required":false,"visible":true,"helpText":"concentration of nitrite","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen concentration","name":"total_nitrogen_concentration","required":false,"visible":true,"helpText":"Concentration of nitrogen (total). Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"organic carbon","name":"organic_carbon","required":false,"visible":true,"helpText":"concentration of organic carbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"organic matter","name":"organic_matter","required":false,"visible":true,"helpText":"concentration of organic matter","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"organic nitrogen","name":"organic_nitrogen","required":false,"visible":true,"helpText":"concentration of organic nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"particulate organic carbon","name":"particulate_organic_carbon","required":false,"visible":true,"helpText":"concentration of particulate organic carbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"particulate organic nitrogen","name":"particulate_organic_nitrogen","required":false,"visible":true,"helpText":"concentration of particulate organic nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"petroleum hydrocarbon","name":"petroleum_hydrocarbon","required":false,"visible":true,"helpText":"concentration of petroleum hydrocarbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"phaeopigments","name":"phaeopigments","required":false,"visible":true,"helpText":"concentration of phaeopigments; can include multiple phaeopigments","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/m3","label":"mg/m3"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"phosphate","name":"phosphate","required":false,"visible":true,"helpText":"concentration of phosphate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"phospholipid fatty acid","name":"phospholipid_fatty_acid","required":false,"visible":true,"helpText":"concentration of phospholipid fatty acids; can include multiple values","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mol/L","label":"mol/L"},{"value":"mol/g","label":"mol/g"}],"group":"concentration measurement"},{"type":"text","label":"potassium","name":"potassium","required":false,"visible":true,"helpText":"concentration of potassium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"primary production","name":"primary_production","required":false,"visible":true,"helpText":"measurement of primary production","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/m3/day","label":"mg/m3/day"},{"value":"g/m2/day","label":"g/m2/day"}],"group":"concentration measurement"},{"type":"text","label":"redox potential","name":"redox_potential","required":false,"visible":true,"helpText":"redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mV","label":"mV"}],"group":"concentration measurement"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"silicate","name":"silicate","required":false,"visible":true,"helpText":"concentration of silicate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"sodium","name":"sodium","required":false,"visible":true,"helpText":"sodium concentration","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"soluble reactive phosphorus","name":"soluble_reactive_phosphorus","required":false,"visible":true,"helpText":"concentration of soluble reactive phosphorus","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"sulfate","name":"sulfate","required":false,"visible":true,"helpText":"concentration of sulfate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"sulfide","name":"sulfide","required":false,"visible":true,"helpText":"concentration of sulfide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"suspended particulate matter","name":"suspended_particulate_matter","required":false,"visible":true,"helpText":"concentration of suspended particulate matter","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"total dissolved nitrogen","name":"total_dissolved_nitrogen","required":false,"visible":true,"helpText":"total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"total inorganic nitrogen","name":"total_inorganic_nitrogen","required":false,"visible":true,"helpText":"total inorganic nitrogen content","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen content","name":"total_nitrogen_content","required":false,"visible":true,"helpText":"Total nitrogen content of the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"total particulate carbon","name":"total_particulate_carbon","required":false,"visible":true,"helpText":"total particulate carbon content","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"total phosphorus","name":"total_phosphorus","required":false,"visible":true,"helpText":"total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"alkalinity method","name":"alkalinity_method","required":false,"visible":true,"helpText":"Method used for alkalinity measurement","units":[{"value":"m2","label":"m2"}],"group":"concentration measurement"},{"type":"text","label":"alkalinity","name":"alkalinity","required":false,"visible":true,"helpText":"alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mEq/L","label":"mEq/L"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"depth","name":"depth","required":true,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/water.png"},{"name":"GSC MIxS miscellaneous natural or artificial environment","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000025","category":"mixs","accession":"ERC000025","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"text","label":"density","name":"density","required":false,"visible":true,"helpText":"density of sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/m3","label":"g/m3"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"biomass","name":"biomass","required":false,"visible":true,"helpText":"amount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements","units":[{"value":"t","label":"t"},{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"water current","name":"water_current","required":false,"visible":true,"helpText":"measurement of magnitude and direction of flow within a fluid","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m3/s","label":"m3/s"},{"value":"knot","label":"knot"}],"group":"local environment conditions"},{"type":"text","label":"pressure","name":"pressure","required":false,"visible":true,"helpText":"pressure to which the sample is subject, in atmospheres","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"bar","label":"bar"},{"value":"atm","label":"atm"}],"group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"pH","name":"ph","required":false,"visible":true,"helpText":"pH measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"local environment conditions"},{"type":"text","label":"ammonium","name":"ammonium","required":false,"visible":true,"helpText":"concentration of ammonium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"bromide","name":"bromide","required":false,"visible":true,"helpText":"concentration of bromide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"calcium","name":"calcium","required":false,"visible":true,"helpText":"concentration of calcium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"chloride","name":"chloride","required":false,"visible":true,"helpText":"concentration of chloride","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"chlorophyll","name":"chlorophyll","required":false,"visible":true,"helpText":"concentration of chlorophyll","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/m3","label":"mg/m3"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"diether lipids","name":"diether_lipids","required":false,"visible":true,"helpText":"concentration of diether lipids; can include multiple types of diether lipids","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ng/L","label":"ng/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved carbon dioxide","name":"dissolved_carbon_dioxide","required":false,"visible":true,"helpText":"concentration of dissolved carbon dioxide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved hydrogen","name":"dissolved_hydrogen","required":false,"visible":true,"helpText":"concentration of dissolved hydrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved inorganic carbon","name":"dissolved_inorganic_carbon","required":false,"visible":true,"helpText":"dissolved inorganic carbon concentration","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved organic nitrogen","name":"dissolved_organic_nitrogen","required":false,"visible":true,"helpText":"dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved oxygen","name":"dissolved_oxygen","required":false,"visible":true,"helpText":"concentration of dissolved oxygen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/kg","label":"µmol/kg"}],"group":"concentration measurement"},{"type":"text","label":"nitrate","name":"nitrate","required":false,"visible":true,"helpText":"concentration of nitrate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"nitrite","name":"nitrite","required":false,"visible":true,"helpText":"concentration of nitrite","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen concentration","name":"total_nitrogen_concentration","required":false,"visible":true,"helpText":"Concentration of nitrogen (total). Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"organic carbon","name":"organic_carbon","required":false,"visible":true,"helpText":"concentration of organic carbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"organic matter","name":"organic_matter","required":false,"visible":true,"helpText":"concentration of organic matter","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"organic nitrogen","name":"organic_nitrogen","required":false,"visible":true,"helpText":"concentration of organic nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"phosphate","name":"phosphate","required":false,"visible":true,"helpText":"concentration of phosphate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"phospholipid fatty acid","name":"phospholipid_fatty_acid","required":false,"visible":true,"helpText":"concentration of phospholipid fatty acids; can include multiple values","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mol/L","label":"mol/L"},{"value":"mol/g","label":"mol/g"}],"group":"concentration measurement"},{"type":"text","label":"potassium","name":"potassium","required":false,"visible":true,"helpText":"concentration of potassium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"silicate","name":"silicate","required":false,"visible":true,"helpText":"concentration of silicate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"sodium","name":"sodium","required":false,"visible":true,"helpText":"sodium concentration","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"sulfate","name":"sulfate","required":false,"visible":true,"helpText":"concentration of sulfate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"sulfide","name":"sulfide","required":false,"visible":true,"helpText":"concentration of sulfide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"alkalinity","name":"alkalinity","required":false,"visible":true,"helpText":"alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mEq/L","label":"mEq/L"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}],"image":"/images/environments/miscellaneous.png"},{"name":"GSC MIxS built environment","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000031","category":"mixs","accession":"ERC000031","fields":[{"type":"text","label":"number of inoculated individuals","name":"number_of_inoculated_individuals","required":false,"visible":true,"helpText":"Number of host individuals inoculated for the experiment.","group":"Host inoculation"},{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"frequency of cooking","name":"frequency_of_cooking","required":false,"visible":true,"helpText":"The number of times a meal is cooked per week","group":"Human surveillance data"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"sampling time outside","name":"sampling_time_outside","required":false,"visible":true,"helpText":"The recent and long term history of outside sampling","group":"Collection event information"},{"type":"text","label":"temperature outside house","name":"temperature_outside_house","required":false,"visible":true,"helpText":"The recorded temperature value at sampling time outside","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"°C","label":"°C"}],"group":"Collection event information"},{"type":"text","label":"train station collection location","name":"train_station_collection_location","required":false,"visible":true,"helpText":"The train station collection location","group":"Collection event information"},{"type":"text","label":"train stop collection location","name":"train_stop_collection_location","required":false,"visible":true,"helpText":"The train stop collection location","group":"Collection event information"},{"type":"select","label":"surface material","name":"surface_material","required":false,"visible":true,"helpText":"surface materials at the point of sampling","options":[{"value":"adobe","label":"adobe"},{"value":"carpet","label":"carpet"},{"value":"concrete","label":"concrete"},{"value":"cinder blocks","label":"cinder blocks"},{"value":"epoxy resin","label":"epoxy resin"},{"value":"glass","label":"glass"},{"value":"hay bales","label":"hay bales"},{"value":"metal","label":"metal"},{"value":"paint","label":"paint"},{"value":"plastic","label":"plastic"},{"value":"stainless steel","label":"stainless steel"},{"value":"stone","label":"stone"},{"value":"stucco","label":"stucco"},{"value":"tile","label":"tile"},{"value":"vinyl","label":"vinyl"},{"value":"wood","label":"wood"}],"group":"internal environment"},{"type":"select","label":"surface-air contaminant","name":"surfaceair_contaminant","required":false,"visible":true,"helpText":"contaminant identified on surface","options":[{"value":"biocides","label":"biocides"},{"value":"biological contaminants","label":"biological contaminants"},{"value":"dust","label":"dust"},{"value":"nutrients","label":"nutrients"},{"value":"organic matter","label":"organic matter"},{"value":"particulate matter","label":"particulate matter"},{"value":"radon","label":"radon"},{"value":"volatile organic compounds","label":"volatile organic compounds"}],"group":"internal environment"},{"type":"select","label":"indoor surface","name":"indoor_surface","required":false,"visible":true,"helpText":"type of indoor surface","options":[{"value":"cabinet","label":"cabinet"},{"value":"ceiling","label":"ceiling"},{"value":"counter top","label":"counter top"},{"value":"door","label":"door"},{"value":"floor","label":"floor"},{"value":"shelving","label":"shelving"},{"value":"vent cover","label":"vent cover"},{"value":"wall","label":"wall"},{"value":"window","label":"window"}],"group":"internal environment"},{"type":"select","label":"indoor space","name":"indoor_space","required":true,"visible":true,"helpText":"a distinguishable space within a structure, the purpose for which discrete areas of a building is used","options":[{"value":"bathroom","label":"bathroom"},{"value":"bedroom","label":"bedroom"},{"value":"cleanroom","label":"cleanroom"},{"value":"elevator","label":"elevator"},{"value":"foyer","label":"foyer"},{"value":"hallway","label":"hallway"},{"value":"kitchen","label":"kitchen"},{"value":"locker room","label":"locker room"},{"value":"office","label":"office"},{"value":"space analog","label":"space analog"},{"value":"space habitat","label":"space habitat"},{"value":"space station","label":"space station"}],"group":"internal environment"},{"type":"select","label":"filter type","name":"filter_type","required":true,"visible":true,"helpText":"a device which removes solid particulates or airborne molecular contaminants","options":[{"value":"HEPA filter","label":"HEPA filter"},{"value":"chemical air filter","label":"chemical air filter"},{"value":"electrostatic air treatment","label":"electrostatic air treatment"},{"value":"gas-phase air treatment","label":"gas-phase air treatment"},{"value":"low-MERV pleated media","label":"low-MERV pleated media"},{"value":"particulate air filter","label":"particulate air filter"},{"value":"ultraviolet air treatment","label":"ultraviolet air treatment"}],"group":"internal environment"},{"type":"select","label":"heating and cooling system type","name":"heating_and_cooling_system_type","required":true,"visible":true,"helpText":"methods of conditioning or heating a room or building","options":[{"value":"forced air system","label":"forced air system"},{"value":"heat pump","label":"heat pump"},{"value":"radiant system","label":"radiant system"},{"value":"steam forced heat","label":"steam forced heat"},{"value":"wood stove","label":"wood stove"}],"group":"internal environment"},{"type":"select","label":"substructure type","name":"substructure_type","required":false,"visible":true,"helpText":"the substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level","options":[{"value":"basement","label":"basement"},{"value":"crawlspace","label":"crawlspace"},{"value":"slab on grade","label":"slab on grade"}],"group":"internal environment"},{"type":"select","label":"light type","name":"light_type","required":true,"visible":true,"helpText":"application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light","options":[{"value":"electric light","label":"electric light"},{"value":"natural light","label":"natural light"},{"value":"no light","label":"no light"}],"group":"internal environment"},{"type":"select","label":"building setting","name":"building_setting","required":true,"visible":true,"helpText":"a location (geography) where a building is set","options":[{"value":"exurban","label":"exurban"},{"value":"rural","label":"rural"},{"value":"suburban","label":"suburban"},{"value":"urban","label":"urban"}],"group":"internal environment"},{"type":"select","label":"building occupancy type","name":"building_occupancy_type","required":true,"visible":true,"helpText":"the primary function for which a building or discrete part of a building is intended to be used","options":[{"value":"agricultural","label":"agricultural"},{"value":"airport","label":"airport"},{"value":"commercial","label":"commercial"},{"value":"educational","label":"educational"},{"value":"goverment","label":"goverment"},{"value":"health care","label":"health care"},{"value":"high rise","label":"high rise"},{"value":"industrial","label":"industrial"},{"value":"low rise","label":"low rise"},{"value":"market","label":"market"},{"value":"military","label":"military"},{"value":"office","label":"office"},{"value":"parking","label":"parking"},{"value":"religious","label":"religious"},{"value":"residential","label":"residential"},{"value":"restaurant","label":"restaurant"},{"value":"school","label":"school"},{"value":"sports complex","label":"sports complex"},{"value":"storage","label":"storage"},{"value":"transport","label":"transport"},{"value":"wood framed","label":"wood framed"}],"group":"internal environment"},{"type":"select","label":"space typical state","name":"space_typical_state","required":true,"visible":true,"helpText":"customary or normal state of the space","options":[{"value":"typically occupied","label":"typically occupied"},{"value":"typically unoccupied","label":"typically unoccupied"}],"group":"internal environment"},{"type":"text","label":"typical occupant density","name":"typical_occupant_density","required":true,"visible":true,"helpText":"customary or normal density of occupants","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"internal environment"},{"type":"text","label":"occupancy at sampling","name":"occupancy_at_sampling","required":true,"visible":true,"helpText":"number of occupants present at time of sample within the given space","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"internal environment"},{"type":"text","label":"occupant density at sampling","name":"occupant_density_at_sampling","required":true,"visible":true,"helpText":"average number of occupants at time of sampling per square footage","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"internal environment"},{"type":"select","label":"ventilation type","name":"ventilation_type","required":true,"visible":true,"helpText":"The intentional movement of air from outside a building to the inside through forced or natural movement of air","options":[{"value":"forced ventilation","label":"forced ventilation"},{"value":"mechanical ventilation","label":"mechanical ventilation"},{"value":"natural ventilation","label":"natural ventilation"}],"group":"internal environment"},{"type":"text","label":"rooms that are on the same hallway","name":"rooms_that_are_on_the_same_hallway","required":false,"visible":true,"helpText":"List of room(s) (room number, room name) located in the same hallway as sampling room","group":"internal environment"},{"type":"text","label":"wall surface treatment","name":"wall_surface_treatment","required":false,"visible":true,"helpText":"The surface treatment of interior wall","simpleValidation":{"pattern":"[0-9]+(\\.[0-9]*)?","patternMessage":"Must match pattern: [0-9]+(\\.[0-9]*)?"},"group":"internal environment"},{"type":"text","label":"wall area","name":"wall_area","required":false,"visible":true,"helpText":"The total area of the sampled room's walls","group":"internal environment"},{"type":"text","label":"elevator count","name":"elevator_count","required":false,"visible":true,"helpText":"The number of elevators within the built structure","simpleValidation":{"pattern":"[0-9]+","patternMessage":"Must match pattern: [0-9]+"},"group":"internal environment"},{"type":"text","label":"floor area","name":"floor_area","required":false,"visible":true,"helpText":"The area of the floor space within the room","simpleValidation":{"pattern":"[0-9]*(\\.[0-9]*)?","patternMessage":"Must match pattern: [0-9]*(\\.[0-9]*)?"},"group":"internal environment"},{"type":"text","label":"furniture","name":"furniture","required":false,"visible":true,"helpText":"The types of furniture present in the sampled room","group":"internal environment"},{"type":"text","label":"water feature type","name":"water_feature_type","required":false,"visible":true,"helpText":"The type of water feature present within the building being sampled","group":"internal environment"},{"type":"text","label":"room door distance","name":"room_door_distance","required":false,"visible":true,"helpText":"Distance between doors (meters) in the hallway between the sampling room and adjacent rooms","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"internal environment"},{"type":"select","label":"room type","name":"room_type","required":false,"visible":true,"helpText":"The main purpose or activity of the sampling room. A room is any distinguishable space within a structure","options":[{"value":"attic","label":"attic"},{"value":"auditorium","label":"auditorium"},{"value":"bathoom","label":"bathoom"},{"value":"cafe","label":"cafe"},{"value":"cleanroom ISO 1","label":"cleanroom ISO 1"},{"value":"cleanroom ISO 5","label":"cleanroom ISO 5"},{"value":"cleanroom ISO 7","label":"cleanroom ISO 7"},{"value":"cleanroom ISO 8","label":"cleanroom ISO 8"},{"value":"closet","label":"closet"},{"value":"conference room","label":"conference room"},{"value":"data center","label":"data center"},{"value":"elevator","label":"elevator"},{"value":"gymnasium","label":"gymnasium"},{"value":"hallway","label":"hallway"},{"value":"kitchen","label":"kitchen"},{"value":"laboratory_dry","label":"laboratory_dry"},{"value":"laboratory_wet","label":"laboratory_wet"},{"value":"lobby","label":"lobby"},{"value":"lockers","label":"lockers"},{"value":"mail room","label":"mail room"},{"value":"mechanical or electrical room","label":"mechanical or electrical room"},{"value":"natatorium","label":"natatorium"},{"value":"open office","label":"open office"},{"value":"private office","label":"private office"},{"value":"restroom","label":"restroom"},{"value":"stairwell","label":"stairwell"},{"value":"warehouse","label":"warehouse"}],"group":"internal environment"},{"type":"text","label":"window location","name":"window_location","required":false,"visible":true,"helpText":"The relative location of the window within the room","group":"internal environment"},{"type":"text","label":"ceiling type","name":"ceiling_type","required":false,"visible":true,"helpText":"The type of ceiling according to the ceiling's appearance or construction","group":"internal environment"},{"type":"text","label":"door direction of opening","name":"door_direction_of_opening","required":false,"visible":true,"helpText":"The direction the door opens","group":"internal environment"},{"type":"text","label":"exposed pipes","name":"exposed_pipes","required":false,"visible":true,"helpText":"The number of exposed pipes in the room","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*)))","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*)))"},"group":"internal environment"},{"type":"text","label":"wall height","name":"wall_height","required":false,"visible":true,"helpText":"The average height of the walls in the sampled room","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*)))","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*)))"},"group":"internal environment"},{"type":"text","label":"door type, metal","name":"door_type_metal","required":false,"visible":true,"helpText":"The type of metal door","group":"internal environment"},{"type":"text","label":"inside lux light","name":"inside_lux_light","required":false,"visible":true,"helpText":"The recorded value at sampling time (power density)","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"W/m2","label":"W/m2"},{"value":"kg s−3","label":"kg s−3"}],"group":"internal environment"},{"type":"text","label":"exposed ductwork","name":"exposed_ductwork","required":false,"visible":true,"helpText":"The amount of exposed ductwork in the room","units":[{"value":"W/m2","label":"W/m2"},{"value":"kg s−3","label":"kg s−3"}],"group":"internal environment"},{"type":"text","label":"door material","name":"door_material","required":false,"visible":true,"helpText":"The material the door is composed of","group":"internal environment"},{"type":"text","label":"adjacent rooms","name":"adjacent_rooms","required":false,"visible":true,"helpText":"List of rooms (room number, room name) immediately adjacent to the sampling room","group":"internal environment"},{"type":"text","label":"wall thermal mass","name":"wall_thermal_mass","required":false,"visible":true,"helpText":"The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"Cth","label":"Cth"},{"value":"J/K","label":"J/K"},{"value":"J/°C","label":"J/°C"}],"group":"internal environment"},{"type":"text","label":"ceiling signs of water/mold","name":"ceiling_signs_of_watermold","required":false,"visible":true,"helpText":"Signs of the presence of mold or mildew on the ceiling","group":"internal environment"},{"type":"text","label":"window status","name":"window_status","required":false,"visible":true,"helpText":"Defines whether the windows were open or closed during environmental testing","units":[{"value":"%","label":"%"}],"group":"internal environment"},{"type":"text","label":"door location","name":"door_location","required":false,"visible":true,"helpText":"The relative location of the door in the room","group":"internal environment"},{"type":"text","label":"window signs of water/mold","name":"window_signs_of_watermold","required":false,"visible":true,"helpText":"Signs of the presence of mold or mildew on the window.","group":"internal environment"},{"type":"text","label":"window type","name":"window_type","required":false,"visible":true,"helpText":"The type of windows","group":"internal environment"},{"type":"text","label":"window material","name":"window_material","required":false,"visible":true,"helpText":"The type of material used to finish a window","group":"internal environment"},{"type":"text","label":"window horizontal position","name":"window_horizontal_position","required":false,"visible":true,"helpText":"The horizontal position of the window on the wall","group":"internal environment"},{"type":"text","label":"room condition","name":"room_condition","required":false,"visible":true,"helpText":"The condition of the room at the time of sampling","group":"internal environment"},{"type":"text","label":"window area/size","name":"window_areasize","required":false,"visible":true,"helpText":"The window's length and width","units":[{"value":"mm","label":"mm"},{"value":"km","label":"km"},{"value":"m","label":"m"}],"group":"internal environment"},{"type":"text","label":"sampling floor","name":"sampling_floor","required":false,"visible":true,"helpText":"The floor of the building, where the sampling room is located","group":"internal environment"},{"type":"text","label":"room count","name":"room_count","required":false,"visible":true,"helpText":"The total count of rooms in the built structure including all room types","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"internal environment"},{"type":"text","label":"average daily occupancy","name":"average_daily_occupancy","required":false,"visible":true,"helpText":"Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"internal environment"},{"type":"text","label":"floor condition","name":"floor_condition","required":false,"visible":true,"helpText":"The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas","group":"internal environment"},{"type":"text","label":"door type, wood","name":"door_type_wood","required":false,"visible":true,"helpText":"The type of wood door","group":"internal environment"},{"type":"text","label":"door condition","name":"door_condition","required":false,"visible":true,"helpText":"The physical condition of the door","group":"internal environment"},{"type":"text","label":"door movement","name":"door_movement","required":false,"visible":true,"helpText":"The type of movement of the door","group":"internal environment"},{"type":"text","label":"interior wall condition","name":"interior_wall_condition","required":false,"visible":true,"helpText":"The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas","group":"internal environment"},{"type":"text","label":"floor signs of water/mold","name":"floor_signs_of_watermold","required":false,"visible":true,"helpText":"Signs of the presence of mold or mildew in a room","group":"internal environment"},{"type":"text","label":"ceiling structure","name":"ceiling_structure","required":false,"visible":true,"helpText":"The construction format of the ceiling","group":"internal environment"},{"type":"text","label":"wall texture","name":"wall_texture","required":false,"visible":true,"helpText":"The feel, appearance, or consistency of a wall surface","group":"internal environment"},{"type":"text","label":"floor thermal mass","name":"floor_thermal_mass","required":false,"visible":true,"helpText":"The ability of the floor to provide inertia against temperature fluctuations","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"J/°C","label":"J/°C"}],"group":"internal environment"},{"type":"text","label":"room air exchange rate","name":"room_air_exchange_rate","required":false,"visible":true,"helpText":"The rate at which outside air replaces indoor air in a given space","group":"internal environment"},{"type":"text","label":"bathroom count","name":"bathroom_count","required":false,"visible":true,"helpText":"The number of bathrooms in the building","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"internal environment"},{"type":"text","label":"shading device signs of water/mold","name":"shading_device_signs_of_watermold","required":false,"visible":true,"helpText":"Signs of the presence of mold or mildew on the shading device","group":"internal environment"},{"type":"text","label":"window covering","name":"window_covering","required":false,"visible":true,"helpText":"The type of window covering","group":"internal environment"},{"type":"text","label":"ceiling texture","name":"ceiling_texture","required":false,"visible":true,"helpText":"The feel, appearance, or consistency of a ceiling surface","group":"internal environment"},{"type":"text","label":"maximum occupancy","name":"maximum_occupancy","required":false,"visible":true,"helpText":"The maximum amount of people allowed in the indoor environment","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"internal environment"},{"type":"text","label":"gender of restroom","name":"gender_of_restroom","required":false,"visible":true,"helpText":"The gender type of the restroom","group":"internal environment"},{"type":"text","label":"ceiling condition","name":"ceiling_condition","required":false,"visible":true,"helpText":"The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas","group":"internal environment"},{"type":"text","label":"floor structure","name":"floor_structure","required":false,"visible":true,"helpText":"Refers to the structural elements and subfloor upon which the finish flooring is installed","group":"internal environment"},{"type":"text","label":"rooms that share a wall with sampling room","name":"rooms_that_share_a_wall_with_sampling_room","required":false,"visible":true,"helpText":"List of room(s) (room number, room name) sharing a wall with the sampling room","group":"internal environment"},{"type":"text","label":"wall finish material","name":"wall_finish_material","required":false,"visible":true,"helpText":"The material utilized to finish the outer most layer of the wall","group":"internal environment"},{"type":"text","label":"room occupancy","name":"room_occupancy","required":false,"visible":true,"helpText":"Count of room occupancy at time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"},{"value":"minute","label":"minute"}],"group":"internal environment"},{"type":"text","label":"room location in building","name":"room_location_in_building","required":false,"visible":true,"helpText":"The position of the room within the building","group":"internal environment"},{"type":"text","label":"floor finish material","name":"floor_finish_material","required":false,"visible":true,"helpText":"The floor covering type; the finished surface that is walked on","group":"internal environment"},{"type":"text","label":"room window count","name":"room_window_count","required":false,"visible":true,"helpText":"Number of windows in the room","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"internal environment"},{"type":"text","label":"sampling room id or name","name":"sampling_room_id_or_name","required":false,"visible":true,"helpText":"Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).","group":"internal environment"},{"type":"text","label":"height carpet fiber mat","name":"height_carpet_fiber_mat","required":false,"visible":true,"helpText":"The average carpet fiber height in the indoor environment","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"}],"group":"internal environment"},{"type":"text","label":"ceiling area","name":"ceiling_area","required":false,"visible":true,"helpText":"The area of the ceiling space within the room","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"m2","label":"m2"}],"group":"internal environment"},{"type":"text","label":"heating system delivery method","name":"heating_system_delivery_method","required":false,"visible":true,"helpText":"The method by which the heat is delivered through the system","group":"internal environment"},{"type":"text","label":"room sampling position","name":"room_sampling_position","required":false,"visible":true,"helpText":"The horizontal sampling position in the room relative to architectural elements","group":"internal environment"},{"type":"text","label":"room moisture damage or mold history","name":"room_moisture_damage_or_mold_history","required":false,"visible":true,"helpText":"The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed","group":"internal environment"},{"type":"text","label":"door signs of water/mold","name":"door_signs_of_watermold","required":false,"visible":true,"helpText":"Signs of the presence of mold or mildew on a door","group":"internal environment"},{"type":"text","label":"room net area","name":"room_net_area","required":false,"visible":true,"helpText":"The net floor area of sampling room. Net area excludes wall thicknesses","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"m2","label":"m2"}],"group":"internal environment"},{"type":"text","label":"ceiling thermal mass","name":"ceiling_thermal_mass","required":false,"visible":true,"helpText":"The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"Cth","label":"Cth"},{"value":"J/K","label":"J/K"},{"value":"J/°C","label":"J/°C"}],"group":"internal environment"},{"type":"text","label":"rooms that share a door with sampling room","name":"rooms_that_share_a_door_with_sampling_room","required":false,"visible":true,"helpText":"List of room(s) (room number, room name) sharing a door with the sampling room","group":"internal environment"},{"type":"text","label":"orientations of exterior window","name":"orientations_of_exterior_window","required":false,"visible":true,"helpText":"The compass direction the exterior window of the room is facing","group":"internal environment"},{"type":"text","label":"wall location","name":"wall_location","required":false,"visible":true,"helpText":"The relative location of the wall within the room","group":"internal environment"},{"type":"text","label":"room volume","name":"room_volume","required":false,"visible":true,"helpText":"Volume of sampling room","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"m2","label":"m2"}],"group":"internal environment"},{"type":"text","label":"door type, composite","name":"door_type_composite","required":false,"visible":true,"helpText":"The composite type of the door","group":"internal environment"},{"type":"text","label":"bedroom count","name":"bedroom_count","required":false,"visible":true,"helpText":"The number of bedrooms in the building","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"internal environment"},{"type":"text","label":"wall construction type","name":"wall_construction_type","required":false,"visible":true,"helpText":"The building class of the wall defined by the composition of the building elements and fire-resistance rating.","group":"internal environment"},{"type":"text","label":"wall signs of water/mold","name":"wall_signs_of_watermold","required":false,"visible":true,"helpText":"Signs of the presence of mold or mildew on a wall","group":"internal environment"},{"type":"text","label":"window condition","name":"window_condition","required":false,"visible":true,"helpText":"The physical condition of the window at the time of sampling","group":"internal environment"},{"type":"text","label":"escalator count","name":"escalator_count","required":false,"visible":true,"helpText":"The number of escalators within the built structure","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"internal environment"},{"type":"text","label":"cooling system identifier","name":"cooling_system_identifier","required":false,"visible":true,"helpText":"The cooling system identifier","group":"internal environment"},{"type":"text","label":"quadrant position","name":"quadrant_position","required":false,"visible":true,"helpText":"The quadrant position of the sampling room within the building","group":"internal environment"},{"type":"text","label":"number of pets","name":"number_of_pets","required":false,"visible":true,"helpText":"The number of pets residing in the sampled space","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"internal environment"},{"type":"text","label":"window vertical position","name":"window_vertical_position","required":false,"visible":true,"helpText":"The vertical position of the window on the wall","group":"internal environment"},{"type":"text","label":"fireplace type","name":"fireplace_type","required":false,"visible":true,"helpText":"A firebox with chimney","group":"internal environment"},{"type":"text","label":"heating delivery locations","name":"heating_delivery_locations","required":false,"visible":true,"helpText":"The location of heat delivery within the room","group":"internal environment"},{"type":"text","label":"ceiling finish material","name":"ceiling_finish_material","required":false,"visible":true,"helpText":"The type of material used to finish a ceiling","group":"internal environment"},{"type":"text","label":"door type","name":"door_type","required":false,"visible":true,"helpText":"The type of door material","group":"internal environment"},{"type":"text","label":"number of houseplants","name":"number_of_houseplants","required":false,"visible":true,"helpText":"The number of plant(s) in the sampling space","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"internal environment"},{"type":"text","label":"floor age","name":"floor_age","required":false,"visible":true,"helpText":"The time period since instalment of the carpet or flooring","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"century","label":"century"},{"value":"week","label":"week"},{"value":"month","label":"month"},{"value":"year","label":"year"}],"group":"internal environment"},{"type":"text","label":"rooms connected by a doorway","name":"rooms_connected_by_a_doorway","required":false,"visible":true,"helpText":"List of rooms connected to the sampling room by a doorway","group":"internal environment"},{"type":"text","label":"specifications","name":"specifications","required":false,"visible":true,"helpText":"The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents","group":"internal environment"},{"type":"text","label":"specific humidity","name":"specific_humidity","required":false,"visible":true,"helpText":"The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"g/m3","label":"g/m3"}],"group":"internal environment"},{"type":"text","label":"window open frequency","name":"window_open_frequency","required":false,"visible":true,"helpText":"The number of times windows are opened per week","group":"internal environment"},{"type":"text","label":"room dimensions","name":"room_dimensions","required":false,"visible":true,"helpText":"The length, width and height of sampling room","group":"internal environment"},{"type":"text","label":"water feature size","name":"water_feature_size","required":false,"visible":true,"helpText":"The size of the water feature","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"km2","label":"km2"},{"value":"m2","label":"m2"},{"value":"cm2","label":"cm2"},{"value":"ha","label":"ha"}],"group":"internal environment"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"sample size sorting method","name":"sample_size_sorting_method","required":false,"visible":true,"helpText":"method by which samples are sorted","group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"mechanical structure","name":"mechanical_structure","required":false,"visible":true,"helpText":"mechanical structure: a moving structure","group":"unusual properties"},{"type":"text","label":"handidness","name":"handidness","required":false,"visible":true,"helpText":"The handidness of the individual sampled","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"relative air humidity","name":"relative_air_humidity","required":true,"visible":true,"helpText":"partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"%","label":"%"}],"group":"local environment conditions"},{"type":"text","label":"absolute air humidity","name":"absolute_air_humidity","required":true,"visible":true,"helpText":"actual mass of water vapor - mh20 - present in the air water vapor mixture","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"kg","label":"kg"}],"group":"local environment conditions"},{"type":"text","label":"surface humidity","name":"surface_humidity","required":false,"visible":true,"helpText":"surface water activity as a function of air and material moisture","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"%","label":"%"}],"group":"local environment conditions"},{"type":"text","label":"air temperature","name":"air_temperature","required":false,"visible":true,"helpText":"temperature of the air at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"surface temperature","name":"surface_temperature","required":false,"visible":true,"helpText":"temperature of the surface at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"surface moisture","name":"surface_moisture","required":false,"visible":true,"helpText":"water held on the surface","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/m3","label":"g/m3"},{"value":"g/m2","label":"g/m2"},{"value":"parts/million","label":"parts/million"}],"group":"local environment conditions"},{"type":"text","label":"surface moisture pH","name":"surface_moisture_ph","required":false,"visible":true,"helpText":"pH measurement of surface","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"local environment conditions"},{"type":"text","label":"dew point","name":"dew_point","required":false,"visible":true,"helpText":"The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"last time swept/mopped/vacuumed","name":"last_time_sweptmoppedvacuumed","required":false,"visible":true,"helpText":"The last time the floor was cleaned (swept, mopped, vacuumed)","group":"local environment conditions"},{"type":"text","label":"number of residents","name":"number_of_residents","required":false,"visible":true,"helpText":"The number of individuals currently occupying in the sampling location","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"local environment conditions"},{"type":"text","label":"average dew point","name":"average_dew_point","required":false,"visible":true,"helpText":"The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"°C","label":"°C"}],"group":"local environment conditions"},{"type":"select","label":"frequency of cleaning","name":"frequency_of_cleaning","required":false,"visible":true,"helpText":"The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.","options":[{"value":"Annually","label":"Annually"},{"value":"Daily","label":"Daily"},{"value":"Monthly","label":"Monthly"},{"value":"Quarterly","label":"Quarterly"},{"value":"Weekly","label":"Weekly"}],"units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"},{"value":"minute","label":"minute"}],"group":"local environment conditions"},{"type":"text","label":"carbon dioxide","name":"carbon_dioxide","required":false,"visible":true,"helpText":"carbon dioxide (gas) amount or concentration at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"seasonal use","name":"seasonal_use","required":false,"visible":true,"helpText":"The seasons the space is occupied","group":"local environment history"},{"type":"text","label":"season","name":"season","required":false,"visible":true,"helpText":"The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).","group":"local environment history"},{"type":"text","label":"average temperature","name":"average_temperature","required":false,"visible":true,"helpText":"The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"local environment history"},{"type":"text","label":"host specificity or range","name":"host_specificity_or_range","required":false,"visible":true,"helpText":"The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier.","group":"host details"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"date last rain","name":"date_last_rain","required":false,"visible":true,"helpText":"The date of the last time it rained","group":"Environmental information"},{"type":"text","label":"sampling day weather","name":"sampling_day_weather","required":false,"visible":true,"helpText":"The weather on the sampling day","group":"Environmental information"},{"type":"text","label":"amount of light","name":"amount_of_light","required":false,"visible":true,"helpText":"The unit of illuminance and luminous emittance, measuring luminous flux per unit area","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"W/m2","label":"W/m2"}],"group":"Environmental information"},{"type":"text","label":"train line","name":"train_line","required":false,"visible":true,"helpText":"The subway line name","group":"Environmental information"},{"type":"text","label":"outside relative humidity","name":"outside_relative_humidity","required":false,"visible":true,"helpText":"The recorded outside relative humidity value at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"g/m3","label":"g/m3"},{"value":"%","label":"%"}],"group":"Environmental information"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"door area or size","name":"door_area_or_size","required":false,"visible":true,"helpText":"The size of the door","group":"building related"},{"type":"text","label":"visual media","name":"visual_media","required":false,"visible":true,"helpText":"The building visual media","group":"building related"},{"type":"text","label":"built structure setting","name":"built_structure_setting","required":false,"visible":true,"helpText":"The characterization of the location of the built structure as high or low human density","group":"building related"},{"type":"text","label":"built structure type","name":"built_structure_type","required":false,"visible":true,"helpText":"A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads","group":"building related"},{"type":"text","label":"exterior door count","name":"exterior_door_count","required":false,"visible":true,"helpText":"The number of exterior doors in the built structure","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"building related"},{"type":"text","label":"design, construction, and operation documents","name":"design_construction_and_operation_documents","required":false,"visible":true,"helpText":"The building design, construction and operation documents","group":"building related"},{"type":"text","label":"shading device condition","name":"shading_device_condition","required":false,"visible":true,"helpText":"The physical condition of the shading device at the time of sampling","group":"building related"},{"type":"text","label":"occupancy documentation","name":"occupancy_documentation","required":false,"visible":true,"helpText":"The type of documentation of occupancy","group":"building related"},{"type":"text","label":"floor count","name":"floor_count","required":false,"visible":true,"helpText":"The number of floors in the building, including basements and mechanical penthouse","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"building related"},{"type":"text","label":"shading device material","name":"shading_device_material","required":false,"visible":true,"helpText":"The material the shading device is composed of","group":"building related"},{"type":"text","label":"built structure age","name":"built_structure_age","required":false,"visible":true,"helpText":"The age of the built structure since construction","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"}],"group":"building related"},{"type":"text","label":"hallway/corridor count","name":"hallwaycorridor_count","required":false,"visible":true,"helpText":"The total count of hallways and corridors in the built structure","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"building related"},{"type":"text","label":"architectural structure","name":"architectural_structure","required":false,"visible":true,"helpText":"An architectural structure is a human-made, free-standing, immobile outdoor construction","group":"building related"},{"type":"text","label":"shading device type","name":"shading_device_type","required":false,"visible":true,"helpText":"The type of shading device","units":[{"value":"m2","label":"m2"}],"group":"building related"},{"type":"text","label":"shading device location","name":"shading_device_location","required":false,"visible":true,"helpText":"The location of the shading device in relation to the built structure","group":"building related"},{"type":"text","label":"drawings","name":"drawings","required":false,"visible":true,"helpText":"The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents","group":"building related"},{"type":"text","label":"address","name":"address","required":false,"visible":true,"helpText":"The street name and building number where the sampling occurred.","group":"building related"},{"type":"text","label":"room architectural elements","name":"room_architectural_elements","required":false,"visible":true,"helpText":"The unique details and component parts that, together, form the architecture of a distinguishable space within a built structure","group":"building related"},{"type":"text","label":"aerospace structure","name":"aerospace_structure","required":false,"visible":true,"helpText":"Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together","group":"building related"}]},{"name":"GSC MIxS agriculture","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000055","category":"mixs","accession":"ERC000055","fields":[{"type":"text","label":"biotic relationship [deprecated]","name":"biotic_relationship_deprecated","required":false,"visible":true,"helpText":"free text description of relationship(s) between the subject organism and other organism(s) it is associate with, e.g., parasite on species X; mutualist with species Y, the target organism is the subject of the relationship, and the other organism(s) is the object","group":"Organism characteristics: ecosystem"},{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"observed host symbionts","name":"observed_host_symbionts","required":false,"visible":true,"helpText":"The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"size-fraction lower threshold","name":"sizefraction_lower_threshold","required":false,"visible":true,"helpText":"Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"mm","label":"mm"},{"value":"µm","label":"µm"},{"value":"nm","label":"nm"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"size-fraction upper threshold","name":"sizefraction_upper_threshold","required":false,"visible":true,"helpText":"Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"},{"value":"µm","label":"µm"},{"value":"nm","label":"nm"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"soil_taxonomic/FAO classification","name":"soil_taxonomicfao_classification","required":false,"visible":true,"helpText":"soil classification from the FAO World Reference Database for Soil Resources","group":"local environment conditions: soil"},{"type":"text","label":"soil_taxonomic/local classification","name":"soil_taxonomiclocal_classification","required":false,"visible":true,"helpText":"soil classification based on local soil classification system","group":"local environment conditions: soil"},{"type":"text","label":"soil_taxonomic/local classification method","name":"soil_taxonomiclocal_classification_method","required":false,"visible":true,"helpText":"reference or method used in determining the local soil classification","group":"local environment conditions: soil"},{"type":"select","label":"soil type","name":"soil_type","required":false,"visible":true,"helpText":"Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.","options":[{"value":"Acrisol","label":"Acrisol"},{"value":"Albeluvisol","label":"Albeluvisol"},{"value":"Alisol","label":"Alisol"},{"value":"Andosol","label":"Andosol"},{"value":"Anthrosol","label":"Anthrosol"},{"value":"Arenosol","label":"Arenosol"},{"value":"Calcisol","label":"Calcisol"},{"value":"Cambisol","label":"Cambisol"},{"value":"Chernozem","label":"Chernozem"},{"value":"Cryosol","label":"Cryosol"},{"value":"Durisol","label":"Durisol"},{"value":"Ferralsol","label":"Ferralsol"},{"value":"Fluvisol","label":"Fluvisol"},{"value":"Gleysol","label":"Gleysol"},{"value":"Gypsisol","label":"Gypsisol"},{"value":"Histosol","label":"Histosol"},{"value":"Kastanozem","label":"Kastanozem"},{"value":"Leptosol","label":"Leptosol"},{"value":"Lixisol","label":"Lixisol"},{"value":"Luvisol","label":"Luvisol"},{"value":"Nitisol","label":"Nitisol"},{"value":"Phaeozem","label":"Phaeozem"},{"value":"Planosol","label":"Planosol"},{"value":"Plinthosol","label":"Plinthosol"},{"value":"Podzol","label":"Podzol"},{"value":"Regosol","label":"Regosol"},{"value":"Solonchak","label":"Solonchak"},{"value":"Solonetz","label":"Solonetz"},{"value":"Stagnosol","label":"Stagnosol"},{"value":"Technosol","label":"Technosol"},{"value":"Umbrisol","label":"Umbrisol"},{"value":"Vertisol","label":"Vertisol"}],"group":"local environment conditions: soil"},{"type":"text","label":"soil type method","name":"soil_type_method","required":false,"visible":true,"helpText":"reference or method used in determining soil series name or other lower-level classification","group":"local environment conditions: soil"},{"type":"text","label":"soil texture measurement","name":"soil_texture_measurement","required":false,"visible":true,"helpText":"the relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.","units":[{"value":"% sand/silt/clay","label":"% sand/silt/clay"}],"group":"local environment conditions: soil"},{"type":"text","label":"soil texture method","name":"soil_texture_method","required":false,"visible":true,"helpText":"reference or method used in determining soil texture","group":"local environment conditions: soil"},{"type":"text","label":"soil pH","name":"soil_ph","required":false,"visible":true,"helpText":"pH measurement of the soil; e.g. 6.2","group":"local environment conditions: soil"},{"type":"text","label":"soil cover","name":"soil_cover","required":false,"visible":true,"helpText":"Description of the material covering the sampled soil. This field accepts terms under ENVO:00010483, environmental material.","group":"local environment conditions: soil"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"text","label":"microbial biomass","name":"microbial_biomass","required":false,"visible":true,"helpText":"the part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 µm. IF you keep this, you would need to have correction factors used for conversion to the final units, which should be mg C (or N)/kg soil).","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/kg","label":"g/kg"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":false,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"farm equipment sanitization","name":"farm_equipment_sanitization","required":false,"visible":true,"helpText":"Method used to sanitize growing and harvesting equipment. This can including type and concentration of sanitizing solution. Multiple terms can be separated by one or more pipes.","group":"food and agriculture: farm"},{"type":"text","label":"equipment shared with other farms","name":"equipment_shared_with_other_farms","required":false,"visible":true,"helpText":"List of planting, growing or harvesting equipment shared with other farms. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes.","group":"food and agriculture: farm"},{"type":"text","label":"farm equipment used","name":"farm_equipment_used","required":false,"visible":true,"helpText":"List of equipment used for planting, fertilization, harvesting, irrigation, land levelling, residue management, weeding or transplanting during the growing season. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes.","group":"food and agriculture: farm"},{"type":"text","label":"farm watering water source","name":"farm_watering_water_source","required":false,"visible":true,"helpText":"Source of water used on the farm for irrigation of crops or watering of livestock.","group":"food and agriculture: farm"},{"type":"text","label":"food production system characteristics","name":"food_production_system_characteristics","required":false,"visible":true,"helpText":"Descriptors of the food production system or of the agricultural environment and growing conditions related to the farm production system, such as wild caught, organic, free-range, industrial, dairy, beef, domestic or cultivated food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206). Multiple terms may apply and can be separated by pipes.","group":"food and agriculture: farm"},{"type":"text","label":"animal water delivery method","name":"animal_water_delivery_method","required":false,"visible":true,"helpText":"Description of the equipment or method used to distribute water to livestock. This field accepts termed listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653). Multiple terms can be separated by pipes.","group":"food and agriculture: farm"},{"type":"text","label":"plant water delivery method","name":"plant_water_delivery_method","required":false,"visible":true,"helpText":"Description of the equipment or method used to distribute water to crops. This field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006). Multiple terms can be separated by pipes.","group":"food and agriculture: farm"},{"type":"text","label":"food harvesting process","name":"food_harvesting_process","required":false,"visible":true,"helpText":"A harvesting process is a process which takes in some food material from an individual or community of plant or animal organisms in a given context and time, and outputs a precursor or consumable food product. This may include a part of an organism or the whole, and may involve killing the organism.","group":"food and agriculture: farm"},{"type":"text","label":"food production characteristics","name":"food_production_characteristics","required":false,"visible":true,"helpText":"Descriptors of the food production system such as wild caught, free-range, organic, free-range, industrial, dairy, beef.","group":"food and agriculture: farm"},{"type":"text","label":"fertilizer administration date","name":"fertilizer_administration_date","required":false,"visible":true,"helpText":"Date of administration of soil amendment or fertilizer. Multiple terms may apply and can be separated by pipes, listing in reverse chronological order.","group":"food and agriculture: farm"},{"type":"text","label":"crop yield","name":"crop_yield","required":false,"visible":true,"helpText":"Amount of crop produced per unit or area of land.","group":"food and agriculture: farm"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"select","label":"16s recovered","name":"16s_recovered","required":false,"visible":true,"helpText":"Can a 16S gene be recovered from the submitted bin, SAG or MAG?","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"non-sample terms"},{"type":"text","label":"16S recovery software","name":"16s_recovery_software","required":false,"visible":true,"helpText":"Tools used for 16S rRNA gene extraction. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":false,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":false,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":false,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"culture isolation date","name":"culture_isolation_date","required":false,"visible":true,"helpText":"A culture isolation date is a date-time entity marking the end of a process in which a sample yields a positive result for the target microbial analyte(s) in the form of an isolated colony or colonies.","group":"Collection event information"},{"type":"text","label":"sieving","name":"sieving","required":false,"visible":true,"helpText":"Collection design of pooled samples and/or sieve size and amount of sample sieved","group":"sample collection"},{"type":"text","label":"microbial biomass method","name":"microbial_biomass_method","required":false,"visible":true,"helpText":"Reference or method used in determining microbial biomass","group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"horizon method","name":"horizon_method","required":false,"visible":true,"helpText":"Reference or method used in determining the horizon","group":"sample collection"},{"type":"text","label":"extreme_unusual_properties/heavy metals","name":"extreme_unusual_propertiesheavy_metals","required":false,"visible":true,"helpText":"heavy metals present and concentrations of any drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations","group":"unusual properties"},{"type":"text","label":"extreme_unusual_properties/heavy metals method","name":"extreme_unusual_propertiesheavy_metals_method","required":false,"visible":true,"helpText":"reference or method used in determining heavy metals","group":"unusual properties"},{"type":"text","label":"plant structure","name":"plant_structure","required":false,"visible":true,"helpText":"name of plant structure that the sample was obtained from; for Plant Ontology (PO) terms see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051); if an individual flower is sampled the sex of it can be recorded here","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host common name","name":"host_common_name","required":false,"visible":true,"helpText":"common name of the host, e.g. human","group":"host description"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"text","label":"host taxid","name":"host_taxid","required":false,"visible":true,"helpText":"NCBI taxon id of the host, e.g. 9606","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"host description"},{"type":"text","label":"host life stage","name":"host_life_stage","required":false,"visible":true,"helpText":"description of life stage of host","group":"host description"},{"type":"text","label":"host height","name":"host_height","required":false,"visible":true,"helpText":"the height of subject","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host length","name":"host_length","required":false,"visible":true,"helpText":"the length of subject","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host total mass","name":"host_total_mass","required":false,"visible":true,"helpText":"total mass of the host at collection, the unit depends on host","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"host description"},{"type":"text","label":"host phenotype","name":"host_phenotype","required":false,"visible":true,"helpText":"phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO","group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"host subspecific genetic lineage","name":"host_subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"host description"},{"type":"text","label":"link to climate information","name":"link_to_climate_information","required":false,"visible":true,"helpText":"link to climate resource","group":"link"},{"type":"text","label":"link to classification information","name":"link_to_classification_information","required":false,"visible":true,"helpText":"link to digitized soil maps or other soil classification information","group":"link"},{"type":"text","label":"climate environment","name":"climate_environment","required":false,"visible":true,"helpText":"treatment involving an exposure to a particular climate; can include multiple climates","group":"local environment conditions"},{"type":"text","label":"presence of pets, animals, or insects","name":"presence_of_pets_animals_or_insects","required":false,"visible":true,"helpText":"The type and number of animals or insects present in the sampling space.","group":"local environment conditions"},{"type":"text","label":"current vegetation","name":"current_vegetation","required":false,"visible":true,"helpText":"vegetation classification from one or more standard classification systems, or agricultural crop","group":"local environment conditions"},{"type":"text","label":"gaseous environment","name":"gaseous_environment","required":false,"visible":true,"helpText":"use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens","group":"local environment conditions"},{"type":"text","label":"humidity","name":"humidity","required":false,"visible":true,"helpText":"amount of water vapour in the air, at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/m3","label":"g/m3"},{"value":"%","label":"%"}],"group":"local environment conditions"},{"type":"text","label":"current vegetation method","name":"current_vegetation_method","required":false,"visible":true,"helpText":"reference or method used in vegetation classification","group":"local environment conditions"},{"type":"text","label":"seasonal environment","name":"seasonal_environment","required":false,"visible":true,"helpText":"treatment involving an exposure to a particular season (e.g. winter, summer, rabi, rainy etc.)","group":"local environment conditions"},{"type":"select","label":"soil horizon","name":"soil_horizon","required":false,"visible":true,"helpText":"specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath","options":[{"value":"A horizon","label":"A horizon"},{"value":"B horizon","label":"B horizon"},{"value":"E horizon","label":"E horizon"},{"value":"O horizon","label":"O horizon"},{"value":"Permafrost","label":"Permafrost"},{"value":"R layer","label":"R layer"}],"group":"local environment conditions"},{"type":"text","label":"solar irradiance","name":"solar_irradiance","required":false,"visible":true,"helpText":"the amount of solar energy that arrives at a specific area of a surface during a specific time interval","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"W/m2","label":"W/m2"}],"group":"local environment conditions"},{"type":"select","label":"drainage classification","name":"drainage_classification","required":false,"visible":true,"helpText":"drainage classification from a standard system such as the USDA system","options":[{"value":"excessively drained","label":"excessively drained"},{"value":"moderately well","label":"moderately well"},{"value":"poorly","label":"poorly"},{"value":"somewhat poorly","label":"somewhat poorly"},{"value":"very poorly","label":"very poorly"},{"value":"well","label":"well"}],"group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"pH method","name":"ph_method","required":false,"visible":true,"helpText":"reference or method used in determining pH","group":"local environment conditions"},{"type":"text","label":"slope gradient","name":"slope_gradient","required":false,"visible":true,"helpText":"commonly called slope. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"%","label":"%"}],"group":"local environment conditions"},{"type":"text","label":"slope aspect","name":"slope_aspect","required":false,"visible":true,"helpText":"the direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., NW or 315°. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.","group":"local environment conditions"},{"type":"select","label":"profile position","name":"profile_position","required":false,"visible":true,"helpText":"cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas","options":[{"value":"backslope","label":"backslope"},{"value":"footslope","label":"footslope"},{"value":"shoulder","label":"shoulder"},{"value":"summit","label":"summit"},{"value":"toeslope","label":"toeslope"}],"group":"local environment conditions"},{"type":"text","label":"total organic carbon method","name":"total_organic_carbon_method","required":false,"visible":true,"helpText":"Reference or method used in determining total organic carbon","group":"concentration measurement"},{"type":"text","label":"total nitrogen content method","name":"total_nitrogen_content_method","required":false,"visible":true,"helpText":"Reference or method used in determining the total nitrogen","group":"concentration measurement"},{"type":"text","label":"total phosphate","name":"total_phosphate","required":false,"visible":true,"helpText":"total amount or concentration of phosphate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen concentration","name":"total_nitrogen_concentration","required":false,"visible":true,"helpText":"Concentration of nitrogen (total). Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"total carbon","name":"total_carbon","required":false,"visible":true,"helpText":"total carbon content","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"total organic carbon","name":"total_organic_carbon","required":false,"visible":true,"helpText":"Definition for soil: total organic C content of the soil units of g C/kg soil. Definition otherwise: total organic carbon content","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/kg","label":"g/kg"}],"group":"concentration measurement"},{"type":"text","label":"water pH","name":"water_ph","required":false,"visible":true,"helpText":"pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid.","simpleValidation":{"pattern":"[\\d][0-4]?(\\.[\\d]{1,10})?","patternMessage":"Must match pattern: [\\d][0-4]?(\\.[\\d]{1,10})?"},"group":"concentration measurement"},{"type":"text","label":"photosynthetic activity method","name":"photosynthetic_activity_method","required":false,"visible":true,"helpText":"Reference or method used in measurement of photosythentic activity","group":"concentration measurement"},{"type":"text","label":"photosynthetic activity","name":"photosynthetic_activity","required":false,"visible":true,"helpText":"Measurement of photosythetic activity (i.e. leaf gas exchange / chlorophyll fluorescence emissions / reflectance / transpiration) Please also include the term method term detailing the method of activity measurement.","group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"history/previous land use","name":"historyprevious_land_use","required":false,"visible":true,"helpText":"previous land use and dates","group":"local environment history"},{"type":"text","label":"previous land use method","name":"previous_land_use_method","required":false,"visible":true,"helpText":"Reference or method used in determining previous land use and dates","group":"local environment history"},{"type":"text","label":"history/crop rotation","name":"historycrop_rotation","required":false,"visible":true,"helpText":"whether or not crop is rotated, and if yes, rotation schedule","group":"local environment history"},{"type":"text","label":"history/agrochemical additions","name":"historyagrochemical_additions","required":false,"visible":true,"helpText":"addition of fertilizers, pesticides, etc. - amount and time of applications","group":"local environment history"},{"type":"select","label":"history/tillage","name":"historytillage","required":false,"visible":true,"helpText":"note method(s) used for tilling","options":[{"value":"chisel","label":"chisel"},{"value":"cutting disc","label":"cutting disc"},{"value":"disc plough","label":"disc plough"},{"value":"drill","label":"drill"},{"value":"mouldboard","label":"mouldboard"},{"value":"ridge till","label":"ridge till"},{"value":"strip tillage","label":"strip tillage"},{"value":"tined","label":"tined"},{"value":"zonal tillage","label":"zonal tillage"}],"group":"local environment history"},{"type":"text","label":"history/fire","name":"historyfire","required":false,"visible":true,"helpText":"historical and/or physical evidence of fire","group":"local environment history"},{"type":"text","label":"history/flooding","name":"historyflooding","required":false,"visible":true,"helpText":"historical and/or physical evidence of flooding","group":"local environment history"},{"type":"text","label":"history/extreme events","name":"historyextreme_events","required":false,"visible":true,"helpText":"unusual physical events that may have affected microbial populations","group":"local environment history"},{"type":"text","label":"mean seasonal humidity","name":"mean_seasonal_humidity","required":false,"visible":true,"helpText":"Average humidity of the region throughout the growing season.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/m3","label":"g/m3"},{"value":"%","label":"%"}],"group":"local environment history"},{"type":"text","label":"mean seasonal temperature","name":"mean_seasonal_temperature","required":false,"visible":true,"helpText":"Mean seasonal temperature","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"local environment history"},{"type":"text","label":"mean seasonal precipitation","name":"mean_seasonal_precipitation","required":false,"visible":true,"helpText":"The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"}],"group":"local environment history"},{"type":"text","label":"season","name":"season","required":false,"visible":true,"helpText":"The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).","group":"local environment history"},{"type":"text","label":"mean annual precipitation","name":"mean_annual_precipitation","required":false,"visible":true,"helpText":"The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"}],"group":"local environment history"},{"type":"text","label":"mean annual temperature","name":"mean_annual_temperature","required":false,"visible":true,"helpText":"Mean annual temperature","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment history"},{"type":"text","label":"host genotype","name":"host_genotype","required":false,"visible":true,"helpText":"observed genotype","group":"host details"},{"type":"text","label":"host specificity or range","name":"host_specificity_or_range","required":false,"visible":true,"helpText":"The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier.","group":"host details"},{"type":"text","label":"host dry mass","name":"host_dry_mass","required":false,"visible":true,"helpText":"measurement of dry mass","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"mg","label":"mg"},{"value":"kg","label":"kg"}],"group":"host details"},{"type":"text","label":"spike-in microbial strain","name":"spikein_microbial_strain","required":false,"visible":true,"helpText":"Taxonomic information about the spike-in organism(s) at the strain level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes.","group":"treatment"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"genetic modification","name":"genetic_modification","required":false,"visible":true,"helpText":"A genetic modification of the genome of an organism which may occur naturally by spontaneous mutation, or be introduced by some experimental means. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection.","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"ancestral data","name":"ancestral_data","required":false,"visible":true,"helpText":"information about either pedigree or other description of ancestral information (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"plant growth medium","name":"plant_growth_medium","required":false,"visible":true,"helpText":"Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147).","group":"growth medium"},{"type":"text","label":"rooting medium macronutrients","name":"rooting_medium_macronutrients","required":false,"visible":true,"helpText":"measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L)","group":"growth medium"},{"type":"text","label":"rooting medium carbon","name":"rooting_medium_carbon","required":false,"visible":true,"helpText":"source of organic carbon in the culture rooting medium; e.g. sucrose","group":"growth medium"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sequencing location","name":"sequencing_location","required":false,"visible":true,"helpText":"The location the sequencing run was performed. Indicate the name of the lab or core facility where samples were sequenced.","group":"sample processing"},{"type":"text","label":"enrichment protocol","name":"enrichment_protocol","required":false,"visible":true,"helpText":"The microbiological workflow or protocol followed to test for the presence or enumeration of the target microbial analyte(s). Please provide a PubMed or DOI reference for published protocols.","group":"sample processing"},{"type":"text","label":"library preparation kit","name":"library_preparation_kit","required":false,"visible":true,"helpText":"Packaged kits (containing adapters, indexes, enzymes, buffers etc.), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids.","group":"sample processing"},{"type":"text","label":"sample pooling","name":"sample_pooling","required":false,"visible":true,"helpText":"Physical combination of several instances of like material, e.g. RNA extracted from samples or dishes of cell cultures into one big aliquot of cells. Please provide a short description of the samples that were pooled.","group":"sample processing"},{"type":"text","label":"lot number","name":"lot_number","required":false,"visible":true,"helpText":"A distinctive alpha-numeric identification code assigned by the manufacturer or distributor to a specific quantity of manufactured material or product within a batch. Synonym: Batch Number. The submitter should provide lot number of the item followed by the item name for which the lot number was provided.","group":"sample processing"},{"type":"select","label":"single cell or viral particle lysis approach","name":"single_cell_or_viral_particle_lysis_approach","required":false,"visible":true,"helpText":"Method used to free DNA from interior of the cell(s) or particle(s)","options":[{"value":"chemical","label":"chemical"},{"value":"combination","label":"combination"},{"value":"enzymatic","label":"enzymatic"},{"value":"physical","label":"physical"}],"group":"sample processing"},{"type":"text","label":"single cell or viral particle lysis kit protocol","name":"single_cell_or_viral_particle_lysis_kit_protocol","required":false,"visible":true,"helpText":"Name of the kit or standard protocol used for cell(s) or particle(s) lysis","group":"sample processing"},{"type":"text","label":"pooled DNA extract total","name":"pooled_dna_extract_total","required":false,"visible":true,"helpText":"Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given. [ENA version of MIxS term: pooling of DNA extracts (if done). ]","simpleValidation":{"pattern":"([0-9]*)","patternMessage":"Must match pattern: ([0-9]*)"},"group":"sample processing"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library construction method","name":"library_construction_method","required":false,"visible":true,"helpText":"Library construction method used for clone libraries","group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"food shipping transportation vehicle","name":"food_shipping_transportation_vehicle","required":false,"visible":true,"helpText":"A descriptor for the mobile machine which is used to transport food commodities along the food distribution system. This field accepts terms listed under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes.","group":"food and agriculture"},{"type":"text","label":"water source shared","name":"water_source_shared","required":false,"visible":true,"helpText":"Other users sharing access to the same water source. Multiple terms can be separated by one or more pipes.","group":"food and agriculture"},{"type":"text","label":"food source","name":"food_source","required":false,"visible":true,"helpText":"Type of plant or animal from which the food product or its major ingredient is derived or a chemical food source [FDA CFSAN 1995].","group":"food and agriculture"},{"type":"text","label":"food shipping transportation method","name":"food_shipping_transportation_method","required":false,"visible":true,"helpText":"A descriptor for the method of movement of food commodity along the food distribution system. This field accepts terms listed under travel mode (http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes.","group":"food and agriculture"},{"type":"text","label":"food product type","name":"food_product_type","required":false,"visible":true,"helpText":"A food product type is a class of food products that is differentiated by its food composition (e.g., single- or multi-ingredient), processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories. This field accepts terms under food product type (http://purl.obolibrary.org/obo/FOODON:03400361). For terms related to food product for an animal, consult food product for animal (http://purl.obolibrary.org/obo/FOODON_03309997). If the proper descriptor is not listed please use text to describe the food type. Multiple terms can be separated by one or more pipes.","group":"food and agriculture"},{"type":"text","label":"plant product","name":"plant_product","required":false,"visible":true,"helpText":"substance produced by the plant, where the sample was obtained from","group":"food and agriculture"},{"type":"text","label":"relative location of sample","name":"relative_location_of_sample","required":false,"visible":true,"helpText":"Location of sampled soil to other parts of the farm e.g. under crop plant, near irrigation ditch, from the dirt road.","group":"Environmental information"},{"type":"text","label":"porosity","name":"porosity","required":false,"visible":true,"helpText":"Porosity of deposited sediment is volume of voids divided by the total volume of sample","simpleValidation":{"pattern":"[0-9]+","patternMessage":"Must match pattern: [0-9]+"},"group":"Environmental information"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"environment adjacent to site","name":"environment_adjacent_to_site","required":false,"visible":true,"helpText":"Description of the environmental system or features that are adjacent to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes.","group":"Environmental information"},{"type":"text","label":"fungicide regimen","name":"fungicide_regimen","required":false,"visible":true,"helpText":"information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment duration, interval and total experimental duration; can include multiple fungicide regimens","group":"local environment conditions imposed"},{"type":"text","label":"herbicide regimen","name":"herbicide_regimen","required":false,"visible":true,"helpText":"information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment duration, interval and total experimental duration; can include multiple regimens","group":"local environment conditions imposed"},{"type":"text","label":"non-mineral nutrient regimen","name":"nonmineral_nutrient_regimen","required":false,"visible":true,"helpText":"information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment duration, interval and total experimental duration; can include multiple non-mineral nutrient regimens","group":"local environment conditions imposed"},{"type":"text","label":"pesticide regimen","name":"pesticide_regimen","required":false,"visible":true,"helpText":"information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment duration, interval and total experimental duration; can include multiple pesticide regimens","group":"local environment conditions imposed"},{"type":"text","label":"pH regimen","name":"ph_regimen","required":false,"visible":true,"helpText":"information about treatment involving exposure of plants to varying levels of pH of the growth media; can include multiple regimen","group":"local environment conditions imposed"},{"type":"text","label":"salt regimen","name":"salt_regimen","required":false,"visible":true,"helpText":"information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment duration, interval and total experimental duration; can include multiple salt regimens","group":"local environment conditions imposed"},{"type":"text","label":"standing water regimen","name":"standing_water_regimen","required":false,"visible":true,"helpText":"treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water; can include multiple regimens","group":"local environment conditions imposed"},{"type":"text","label":"watering regimen","name":"watering_regimen","required":false,"visible":true,"helpText":"information about treatment involving an exposure to watering frequencies; can include multiple regimens","group":"local environment conditions imposed"},{"type":"text","label":"water temperature regimen","name":"water_temperature_regimen","required":false,"visible":true,"helpText":"information about treatment involving an exposure to water with varying degree of temperature; can include multiple regimens","group":"local environment conditions imposed"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}]},{"name":"GSC MIxS Food and Production","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms. This package is a combination of the four food extensions (MIxS-food-animal and animal feed, MIxS-food-farm environment, MIxS-food-food production facility, MIxS-food-human foods).","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000056","category":"mixs","accession":"ERC000056","fields":[{"type":"text","label":"culture result","name":"culture_result","required":false,"visible":true,"helpText":"Any result of a bacterial culture experiment reported as a binary assessment such as positive/negative, active/inactive.","group":"investigation and results"},{"type":"text","label":"culture result organism","name":"culture_result_organism","required":false,"visible":true,"helpText":"Taxonomic information about the cultured organism(s).","group":"investigation and results"},{"type":"text","label":"culture target microbial analyte","name":"culture_target_microbial_analyte","required":false,"visible":true,"helpText":"The target microbial analyte in terms of investigation scope. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.","group":"investigation and results"},{"type":"text","label":"biological sample replicate","name":"biological_sample_replicate","required":false,"visible":true,"helpText":"Measurements of biologically distinct samples that show biological variation.","group":"investigation experiment design"},{"type":"text","label":"technical sample replicate","name":"technical_sample_replicate","required":false,"visible":true,"helpText":"Repeated measurements of the same sample that show independent measures of the noise associated with the equipment and the protocols.","group":"investigation experiment design"},{"type":"text","label":"purpose of sampling","name":"purpose_of_sampling","required":false,"visible":true,"helpText":"The reason that the sample was collected.","group":"investigation experiment design"},{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample transportation temperature","name":"sample_transportation_temperature","required":false,"visible":true,"helpText":"Temperature at which sample was transported, e.g. -20 or 4 degree Celsius.","units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample transport container","name":"sample_transport_container","required":false,"visible":true,"helpText":"Container in which the sample was stored during transport. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample transport duration","name":"sample_transport_duration","required":false,"visible":true,"helpText":"The duration of time from when the sample was collected until processed. Indicate the duration for which the sample was stored written in ISO 8601 format.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage device","name":"sample_storage_device","required":false,"visible":true,"helpText":"The container used to store the sample. This field accepts terms listed under container (http://purl.obolibrary.org/obo/NCIT_C43186). If the proper descriptor is not listed please use text to describe the storage device.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"size-fraction lower threshold","name":"sizefraction_lower_threshold","required":false,"visible":true,"helpText":"Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"mm","label":"mm"},{"value":"µm","label":"µm"},{"value":"nm","label":"nm"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"size-fraction upper threshold","name":"sizefraction_upper_threshold","required":false,"visible":true,"helpText":"Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"},{"value":"µm","label":"µm"},{"value":"nm","label":"nm"}],"group":"sample collection: methods, storage and transport"},{"type":"select","label":"soil type","name":"soil_type","required":false,"visible":true,"helpText":"Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.","options":[{"value":"Acrisol","label":"Acrisol"},{"value":"Albeluvisol","label":"Albeluvisol"},{"value":"Alisol","label":"Alisol"},{"value":"Andosol","label":"Andosol"},{"value":"Anthrosol","label":"Anthrosol"},{"value":"Arenosol","label":"Arenosol"},{"value":"Calcisol","label":"Calcisol"},{"value":"Cambisol","label":"Cambisol"},{"value":"Chernozem","label":"Chernozem"},{"value":"Cryosol","label":"Cryosol"},{"value":"Durisol","label":"Durisol"},{"value":"Ferralsol","label":"Ferralsol"},{"value":"Fluvisol","label":"Fluvisol"},{"value":"Gleysol","label":"Gleysol"},{"value":"Gypsisol","label":"Gypsisol"},{"value":"Histosol","label":"Histosol"},{"value":"Kastanozem","label":"Kastanozem"},{"value":"Leptosol","label":"Leptosol"},{"value":"Lixisol","label":"Lixisol"},{"value":"Luvisol","label":"Luvisol"},{"value":"Nitisol","label":"Nitisol"},{"value":"Phaeozem","label":"Phaeozem"},{"value":"Planosol","label":"Planosol"},{"value":"Plinthosol","label":"Plinthosol"},{"value":"Podzol","label":"Podzol"},{"value":"Regosol","label":"Regosol"},{"value":"Solonchak","label":"Solonchak"},{"value":"Solonetz","label":"Solonetz"},{"value":"Stagnosol","label":"Stagnosol"},{"value":"Technosol","label":"Technosol"},{"value":"Umbrisol","label":"Umbrisol"},{"value":"Vertisol","label":"Vertisol"}],"group":"local environment conditions: soil"},{"type":"text","label":"soil type method","name":"soil_type_method","required":false,"visible":true,"helpText":"reference or method used in determining soil series name or other lower-level classification","group":"local environment conditions: soil"},{"type":"text","label":"soil texture method","name":"soil_texture_method","required":false,"visible":true,"helpText":"reference or method used in determining soil texture","group":"local environment conditions: soil"},{"type":"text","label":"soil pH","name":"soil_ph","required":false,"visible":true,"helpText":"pH measurement of the soil; e.g. 6.2","group":"local environment conditions: soil"},{"type":"text","label":"soil cover","name":"soil_cover","required":false,"visible":true,"helpText":"Description of the material covering the sampled soil. This field accepts terms under ENVO:00010483, environmental material.","group":"local environment conditions: soil"},{"type":"text","label":"soil texture classification","name":"soil_texture_classification","required":false,"visible":true,"helpText":"One of the 12 soil texture classes use to describe soil texture based on the relative proportion of different grain sizes of mineral particles [sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um)] in a soil.","group":"local environment conditions: soil"},{"type":"text","label":"soil sediment porosity","name":"soil_sediment_porosity","required":false,"visible":true,"helpText":"Porosity of soil or deposited sediment is volume of voids divided by the total volume of sample.","group":"local environment conditions: soil"},{"type":"text","label":"soil conductivity","name":"soil_conductivity","required":false,"visible":true,"helpText":"Conductivity of soil at time of sampling.","group":"local environment conditions: soil"},{"type":"text","label":"facility type","name":"facility_type","required":false,"visible":true,"helpText":"Establishment details about the type of facility where the sample was taken. This is independent of the specific product(s) within the facility.","group":"sample collection: site related"},{"type":"text","label":"collection site geographic feature","name":"collection_site_geographic_feature","required":false,"visible":true,"helpText":"Text or terms that describe the geographic feature where the food sample was obtained by the researcher. This field accepts selected terms listed under the following ontologies: anthropogenic geographic feature (http://purl.obolibrary.org/obo/ENVO_00000002), for example agricultural fairground [ENVO:01000986]; garden [ENVO:00000011} or any of its subclasses; market [ENVO:01000987]; water well [ENVO:01000002]; or human construction (http://purl.obolibrary.org/obo/ENVO_00000070).","group":"sample collection: site related"},{"type":"text","label":"area sampled size","name":"area_sampled_size","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"m2","label":"m2"},{"value":"g","label":"g"},{"value":"ml","label":"ml"}],"group":"sample collection: core sample properties"},{"type":"text","label":"sample name","name":"sample_name","required":false,"visible":true,"helpText":"Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique.","group":"sample collection: core sample properties"},{"type":"text","label":"study design","name":"study_design","required":false,"visible":true,"helpText":"A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. This field accepts terms under study design (http://purl.obolibrary.org/obo/OBI_0500000). If the proper descriptor is not listed please use text to describe the study design. Multiple terms can be separated by pipes.","group":"non-sample terms: study or project"},{"type":"text","label":"project name","name":"project_name","required":false,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"farm equipment sanitization","name":"farm_equipment_sanitization","required":false,"visible":true,"helpText":"Method used to sanitize growing and harvesting equipment. This can including type and concentration of sanitizing solution. Multiple terms can be separated by one or more pipes.","group":"food and agriculture: farm"},{"type":"text","label":"equipment shared with other farms","name":"equipment_shared_with_other_farms","required":false,"visible":true,"helpText":"List of planting, growing or harvesting equipment shared with other farms. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes.","group":"food and agriculture: farm"},{"type":"text","label":"farm equipment used","name":"farm_equipment_used","required":false,"visible":true,"helpText":"List of equipment used for planting, fertilization, harvesting, irrigation, land levelling, residue management, weeding or transplanting during the growing season. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416). Multiple terms can be separated by pipes.","group":"food and agriculture: farm"},{"type":"text","label":"farm equipment sanitization frequency","name":"farm_equipment_sanitization_frequency","required":false,"visible":true,"helpText":"The number of times farm equipment is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.","group":"food and agriculture: farm"},{"type":"text","label":"farm watering water source","name":"farm_watering_water_source","required":false,"visible":true,"helpText":"Source of water used on the farm for irrigation of crops or watering of livestock.","group":"food and agriculture: farm"},{"type":"text","label":"food production system characteristics","name":"food_production_system_characteristics","required":false,"visible":true,"helpText":"Descriptors of the food production system or of the agricultural environment and growing conditions related to the farm production system, such as wild caught, organic, free-range, industrial, dairy, beef, domestic or cultivated food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206). Multiple terms may apply and can be separated by pipes.","group":"food and agriculture: farm"},{"type":"text","label":"animal water delivery method","name":"animal_water_delivery_method","required":false,"visible":true,"helpText":"Description of the equipment or method used to distribute water to livestock. This field accepts termed listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653). Multiple terms can be separated by pipes.","group":"food and agriculture: farm"},{"type":"text","label":"plant water delivery method","name":"plant_water_delivery_method","required":false,"visible":true,"helpText":"Description of the equipment or method used to distribute water to crops. This field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006). Multiple terms can be separated by pipes.","group":"food and agriculture: farm"},{"type":"text","label":"food harvesting process","name":"food_harvesting_process","required":false,"visible":true,"helpText":"A harvesting process is a process which takes in some food material from an individual or community of plant or animal organisms in a given context and time, and outputs a precursor or consumable food product. This may include a part of an organism or the whole, and may involve killing the organism.","group":"food and agriculture: farm"},{"type":"text","label":"food animal source diet","name":"food_animal_source_diet","required":false,"visible":true,"helpText":"If the isolate is from a food animal, the type of diet eaten by the food animal. Please list the main food staple and the setting, if appropriate. For a list of acceptable animal feed terms or categories, please see http://www.feedipedia.org. Multiple terms may apply and can be separated by pipes |Food product for animal covers foods intended for consumption by domesticated animals. Consult http://purl.obolibrary.org/obo/FOODON_03309997. If the proper descriptor is not listed please use text to describe the food type. Multiple terms can be separated by one or more pipes. If the proper descriptor is not listed please use text to describe the food product type.","group":"food and agriculture: farm"},{"type":"text","label":"food production characteristics","name":"food_production_characteristics","required":false,"visible":true,"helpText":"Descriptors of the food production system such as wild caught, free-range, organic, free-range, industrial, dairy, beef.","group":"food and agriculture: farm"},{"type":"text","label":"food animal group size","name":"food_animal_group_size","required":false,"visible":true,"helpText":"The number of food animals of the same species that are maintained together as a unit, i.e. a herd or flock.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"food and agriculture: farm"},{"type":"text","label":"fertilizer administration date","name":"fertilizer_administration_date","required":false,"visible":true,"helpText":"Date of administration of soil amendment or fertilizer. Multiple terms may apply and can be separated by pipes, listing in reverse chronological order.","group":"food and agriculture: farm"},{"type":"text","label":"animal feeding equipment","name":"animal_feeding_equipment","required":false,"visible":true,"helpText":"Description of the feeding equipment used for livestock. This field accepts terms listed under feed delivery (http://opendata.inra.fr/EOL/EOL_0001757). Multiple terms can be separated by one or more pipes.","group":"food and agriculture: farm"},{"type":"text","label":"crop yield","name":"crop_yield","required":false,"visible":true,"helpText":"Amount of crop produced per unit or area of land.","group":"food and agriculture: farm"},{"type":"text","label":"water delivery frequency","name":"water_delivery_frequency","required":false,"visible":true,"helpText":"Number of water delivery events within a given period of time.","group":"food and agriculture: farm"},{"type":"text","label":"animal housing system","name":"animal_housing_system","required":false,"visible":true,"helpText":"Description of the housing system of the livestock. This field accepts terms listed under terrestrial management housing system (http://opendata.inra.fr/EOL/EOL_0001605).","group":"food and agriculture: farm"},{"type":"text","label":"environmental feature adjacent water source","name":"environmental_feature_adjacent_water_source","required":false,"visible":true,"helpText":"Description of the environmental features that are adjacent to the farm water source. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes.","group":"food and agriculture: farm"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"select","label":"16s recovered","name":"16s_recovered","required":false,"visible":true,"helpText":"Can a 16S gene be recovered from the submitted bin, SAG or MAG?","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"non-sample terms"},{"type":"text","label":"16S recovery software","name":"16s_recovery_software","required":false,"visible":true,"helpText":"Tools used for 16S rRNA gene extraction. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"completeness score","name":"completeness_score","required":false,"visible":true,"helpText":"Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. Completeness score is one of 3 attributes which in combination reflect the standard quality of a MAG, see here for more information: https://ena-docs.readthedocs.io/en/latest/faq_metagenomes.html. Mandatory for all samples directly linked with SAGs or MAGs.","simpleValidation":{"pattern":"^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$","patternMessage":"Must match pattern: ^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$"},"units":[{"value":"%","label":"%"}],"group":"non-sample terms"},{"type":"text","label":"completeness software","name":"completeness_software","required":false,"visible":true,"helpText":"Tools used for completion estimate, i.e. checkm, anvi'o, busco. Mandatory for all samples directly linked with SAGs or MAGs.","group":"non-sample terms"},{"type":"text","label":"completeness approach","name":"completeness_approach","required":false,"visible":true,"helpText":"The approach used to determine the completeness of a given bin, SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome","group":"non-sample terms"},{"type":"select","label":"assembly quality","name":"assembly_quality","required":false,"visible":true,"helpText":"The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated.","options":[{"value":"Many fragments with little to no review of assembly other than reporting of standard assembly statistics","label":"Many fragments with little to no review of assembly other than reporting of standard assembly statistics"},{"value":"Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs","label":"Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs"},{"value":"Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better","label":"Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better"}],"group":"non-sample terms"},{"type":"text","label":"assembly name","name":"assembly_name","required":false,"visible":true,"helpText":"Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":false,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":false,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":false,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"culture isolation date","name":"culture_isolation_date","required":false,"visible":true,"helpText":"A culture isolation date is a date-time entity marking the end of a process in which a sample yields a positive result for the target microbial analyte(s) in the form of an isolated colony or colonies.","group":"Collection event information"},{"type":"text","label":"time course duration","name":"time_course_duration","required":false,"visible":true,"helpText":"For time-course research studies involving samples of the food commodity, indicate the total duration of the time-course study.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"},{"value":"minute","label":"minute"}],"group":"Collection event information"},{"type":"text","label":"number of samples collected","name":"number_of_samples_collected","required":false,"visible":true,"helpText":"The number of samples collected during the current sampling event.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"Collection event information"},{"type":"select","label":"surface material","name":"surface_material","required":false,"visible":true,"helpText":"surface materials at the point of sampling","options":[{"value":"adobe","label":"adobe"},{"value":"carpet","label":"carpet"},{"value":"concrete","label":"concrete"},{"value":"cinder blocks","label":"cinder blocks"},{"value":"epoxy resin","label":"epoxy resin"},{"value":"glass","label":"glass"},{"value":"hay bales","label":"hay bales"},{"value":"metal","label":"metal"},{"value":"paint","label":"paint"},{"value":"plastic","label":"plastic"},{"value":"stainless steel","label":"stainless steel"},{"value":"stone","label":"stone"},{"value":"stucco","label":"stucco"},{"value":"tile","label":"tile"},{"value":"vinyl","label":"vinyl"},{"value":"wood","label":"wood"}],"group":"internal environment"},{"type":"text","label":"ventilation rate","name":"ventilation_rate","required":false,"visible":true,"helpText":"ventilation rate of the system in the sampled premises","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"L/sec","label":"L/sec"},{"value":"m3/min","label":"m3/min"}],"group":"internal environment"},{"type":"select","label":"indoor surface","name":"indoor_surface","required":false,"visible":true,"helpText":"type of indoor surface","options":[{"value":"cabinet","label":"cabinet"},{"value":"ceiling","label":"ceiling"},{"value":"counter top","label":"counter top"},{"value":"door","label":"door"},{"value":"floor","label":"floor"},{"value":"shelving","label":"shelving"},{"value":"vent cover","label":"vent cover"},{"value":"wall","label":"wall"},{"value":"window","label":"window"}],"group":"internal environment"},{"type":"select","label":"ventilation type","name":"ventilation_type","required":false,"visible":true,"helpText":"The intentional movement of air from outside a building to the inside through forced or natural movement of air","options":[{"value":"forced ventilation","label":"forced ventilation"},{"value":"mechanical ventilation","label":"mechanical ventilation"},{"value":"natural ventilation","label":"natural ventilation"}],"group":"internal environment"},{"type":"text","label":"sampling room sterilization method","name":"sampling_room_sterilization_method","required":false,"visible":true,"helpText":"The method used to sterilize the sampling room. This field accepts terms listed under electromagnetic radiation (http://purl.obolibrary.org/obo/ENVO_01001026). If the proper descriptor is not listed, please use text to describe the sampling room sterilization method. Multiple terms can be separated by pipes.","group":"internal environment"},{"type":"text","label":"sampling floor","name":"sampling_floor","required":false,"visible":true,"helpText":"The floor of the building, where the sampling room is located","group":"internal environment"},{"type":"text","label":"average daily occupancy","name":"average_daily_occupancy","required":false,"visible":true,"helpText":"Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"internal environment"},{"type":"text","label":"sample surface moisture","name":"sample_surface_moisture","required":false,"visible":true,"helpText":"Degree of water held on a sampled surface. If present, user can state the degree of water held on surface (intermittent moisture, submerged). If no surface moisture is present indicate not present.","group":"internal environment"},{"type":"text","label":"sampling room id or name","name":"sampling_room_id_or_name","required":false,"visible":true,"helpText":"Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).","group":"internal environment"},{"type":"text","label":"fermentation relative humidity","name":"fermentation_relative_humidity","required":false,"visible":true,"helpText":"The relative humidity of the fermented food fermentation process.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"g/m3","label":"g/m3"},{"value":"%","label":"%"}],"group":"internal environment"},{"type":"text","label":"room dimensions","name":"room_dimensions","required":false,"visible":true,"helpText":"The length, width and height of sampling room","group":"internal environment"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sampling time point","name":"sampling_time_point","required":false,"visible":true,"helpText":"Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point. Indicate the timepoint written in ISO 8601 format.","group":"sample collection"},{"type":"select","label":"growth habit","name":"growth_habit","required":false,"visible":true,"helpText":"characteristic shape, appearance or growth form of a plant species","options":[{"value":"erect","label":"erect"},{"value":"prostrate","label":"prostrate"},{"value":"semi-erect","label":"semi-erect"},{"value":"spreading","label":"spreading"}],"group":"Organism characteristics"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"text","label":"sequencing kit","name":"sequencing_kit","required":false,"visible":true,"helpText":"Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications. Indicate name of the sequencing kit.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"text","label":"host taxid","name":"host_taxid","required":false,"visible":true,"helpText":"NCBI taxon id of the host, e.g. 9606","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"host description"},{"type":"text","label":"host height","name":"host_height","required":false,"visible":true,"helpText":"the height of subject","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host length","name":"host_length","required":false,"visible":true,"helpText":"the length of subject","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host total mass","name":"host_total_mass","required":false,"visible":true,"helpText":"total mass of the host at collection, the unit depends on host","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"host description"},{"type":"text","label":"host phenotype","name":"host_phenotype","required":false,"visible":true,"helpText":"phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO","group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"host subspecific genetic lineage","name":"host_subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"host description"},{"type":"text","label":"serovar or serotype","name":"serovar_or_serotype","required":false,"visible":true,"helpText":"A characterization of a cell or microorganism based on the antigenic properties of the molecules on its surface. Indicate the name of a serovar or serotype of interest. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.","group":"Serology detection"},{"type":"text","label":"humidity","name":"humidity","required":false,"visible":true,"helpText":"amount of water vapour in the air, at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/m3","label":"g/m3"},{"value":"%","label":"%"}],"group":"local environment conditions"},{"type":"text","label":"conductivity","name":"conductivity","required":false,"visible":true,"helpText":"electrical conductivity of water","simpleValidation":{"pattern":"[1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?"},"units":[{"value":"mS/cm","label":"mS/cm"}],"group":"local environment conditions"},{"type":"text","label":"solar irradiance","name":"solar_irradiance","required":false,"visible":true,"helpText":"the amount of solar energy that arrives at a specific area of a surface during a specific time interval","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"W/m2","label":"W/m2"}],"group":"local environment conditions"},{"type":"text","label":"wind direction","name":"wind_direction","required":false,"visible":true,"helpText":"wind direction is the direction from which a wind originates","group":"local environment conditions"},{"type":"text","label":"wind speed","name":"wind_speed","required":false,"visible":true,"helpText":"speed of wind measured at the time of sampling","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m/s","label":"m/s"},{"value":"km/h","label":"km/h"}],"group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"turbidity","name":"turbidity","required":false,"visible":true,"helpText":"turbidity measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"FTU","label":"FTU"},{"value":"NTU","label":"NTU"}],"group":"local environment conditions"},{"type":"text","label":"pH","name":"ph","required":false,"visible":true,"helpText":"pH measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"local environment conditions"},{"type":"text","label":"pH method","name":"ph_method","required":false,"visible":true,"helpText":"reference or method used in determining pH","group":"local environment conditions"},{"type":"text","label":"fermentation vessel","name":"fermentation_vessel","required":false,"visible":true,"helpText":"The type of vessel used for containment of the fermentation.","group":"local environment conditions"},{"type":"text","label":"fermentation headspace oxygen","name":"fermentation_headspace_oxygen","required":false,"visible":true,"helpText":"The amount of headspace oxygen in a fermentation vessel.","units":[{"value":"m2","label":"m2"}],"group":"local environment conditions"},{"type":"select","label":"frequency of cleaning","name":"frequency_of_cleaning","required":false,"visible":true,"helpText":"The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.","options":[{"value":"Annually","label":"Annually"},{"value":"Daily","label":"Daily"},{"value":"Monthly","label":"Monthly"},{"value":"Quarterly","label":"Quarterly"},{"value":"Weekly","label":"Weekly"}],"units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"},{"value":"minute","label":"minute"}],"group":"local environment conditions"},{"type":"text","label":"total organic carbon method","name":"total_organic_carbon_method","required":false,"visible":true,"helpText":"Reference or method used in determining total organic carbon","group":"concentration measurement"},{"type":"text","label":"air particulate matter concentration","name":"air_particulate_matter_concentration","required":false,"visible":true,"helpText":"Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/m3","label":"µg/m3"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen content method","name":"total_nitrogen_content_method","required":false,"visible":true,"helpText":"Reference or method used in determining the total nitrogen","group":"concentration measurement"},{"type":"text","label":"total nitrogen concentration","name":"total_nitrogen_concentration","required":false,"visible":true,"helpText":"Concentration of nitrogen (total). Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"total carbon","name":"total_carbon","required":false,"visible":true,"helpText":"total carbon content","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"total organic carbon","name":"total_organic_carbon","required":false,"visible":true,"helpText":"Definition for soil: total organic C content of the soil units of g C/kg soil. Definition otherwise: total organic carbon content","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/kg","label":"g/kg"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen content","name":"total_nitrogen_content","required":false,"visible":true,"helpText":"Total nitrogen content of the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"water pH","name":"water_ph","required":false,"visible":true,"helpText":"pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid.","simpleValidation":{"pattern":"[\\d][0-4]?(\\.[\\d]{1,10})?","patternMessage":"Must match pattern: [\\d][0-4]?(\\.[\\d]{1,10})?"},"group":"concentration measurement"},{"type":"text","label":"fermentation ph","name":"fermentation_ph","required":false,"visible":true,"helpText":"The pH of the fermented food fermentation process.","simpleValidation":{"pattern":"[\\d][0-4]?(\\.[\\d]{1,10})?","patternMessage":"Must match pattern: [\\d][0-4]?(\\.[\\d]{1,10})?"},"group":"concentration measurement"},{"type":"text","label":"bacteria density","name":"bacteria_density","required":false,"visible":true,"helpText":"Number of bacteria in sample, as defined by bacteria density (http://purl.obolibrary.org/obo/GENEPIO_0000043).","units":[{"value":"g/m3","label":"g/m3"},{"value":"%","label":"%"}],"group":"concentration measurement"},{"type":"text","label":"salinity method","name":"salinity_method","required":false,"visible":true,"helpText":"reference or method used in determining salinity","group":"concentration measurement"},{"type":"text","label":"bio_material","name":"bio_material","required":false,"visible":true,"helpText":"Unique identifier that references the biological material from which the sample was obtained and that ideally exists in a curated collection (e.g. stock centres, seed banks, DNA banks). The ID should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). Please note institution codes and collection codes are taken from a controlled vocabulary maintained by the INSDC: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/","group":"Pointer to physical material"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"sample source material category","name":"sample_source_material_category","required":false,"visible":true,"helpText":"This is the scientific role or category that the subject organism or material has with respect to an investigation. This field accepts terms listed under specimen source material category (http://purl.obolibrary.org/obo/GENEPIO_0001237 or http://purl.obolibrary.org/obo/OBI_0100051).","group":"Pointer to physical material"},{"type":"text","label":"history/previous land use","name":"historyprevious_land_use","required":false,"visible":true,"helpText":"previous land use and dates","group":"local environment history"},{"type":"text","label":"history/crop rotation","name":"historycrop_rotation","required":false,"visible":true,"helpText":"whether or not crop is rotated, and if yes, rotation schedule","group":"local environment history"},{"type":"select","label":"history/tillage","name":"historytillage","required":false,"visible":true,"helpText":"note method(s) used for tilling","options":[{"value":"chisel","label":"chisel"},{"value":"cutting disc","label":"cutting disc"},{"value":"disc plough","label":"disc plough"},{"value":"drill","label":"drill"},{"value":"mouldboard","label":"mouldboard"},{"value":"ridge till","label":"ridge till"},{"value":"strip tillage","label":"strip tillage"},{"value":"tined","label":"tined"},{"value":"zonal tillage","label":"zonal tillage"}],"group":"local environment history"},{"type":"text","label":"mean seasonal humidity","name":"mean_seasonal_humidity","required":false,"visible":true,"helpText":"Average humidity of the region throughout the growing season.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/m3","label":"g/m3"},{"value":"%","label":"%"}],"group":"local environment history"},{"type":"text","label":"mean seasonal temperature","name":"mean_seasonal_temperature","required":false,"visible":true,"helpText":"Mean seasonal temperature","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"local environment history"},{"type":"text","label":"mean seasonal precipitation","name":"mean_seasonal_precipitation","required":false,"visible":true,"helpText":"The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"}],"group":"local environment history"},{"type":"text","label":"extreme weather date","name":"extreme_weather_date","required":false,"visible":true,"helpText":"Date of unusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order.","group":"local environment history"},{"type":"text","label":"extreme weather event","name":"extreme_weather_event","required":false,"visible":true,"helpText":"Unusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order.","group":"local environment history"},{"type":"text","label":"season","name":"season","required":false,"visible":true,"helpText":"The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).","group":"local environment history"},{"type":"text","label":"host genotype","name":"host_genotype","required":false,"visible":true,"helpText":"observed genotype","group":"host details"},{"type":"text","label":"host specificity or range","name":"host_specificity_or_range","required":false,"visible":true,"helpText":"The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier.","group":"host details"},{"type":"text","label":"host dry mass","name":"host_dry_mass","required":false,"visible":true,"helpText":"measurement of dry mass","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"mg","label":"mg"},{"value":"kg","label":"kg"}],"group":"host details"},{"type":"select","label":"host prediction approach","name":"host_prediction_approach","required":false,"visible":true,"helpText":"Tool or approach used for host prediction","options":[{"value":"CRISPR spacer match","label":"CRISPR spacer match"},{"value":"co-occurrence","label":"co-occurrence"},{"value":"combination","label":"combination"},{"value":"host sequence similarity","label":"host sequence similarity"},{"value":"kmer similarity","label":"kmer similarity"},{"value":"other","label":"other"},{"value":"provirus","label":"provirus"}],"group":"host details"},{"type":"text","label":"host prediction estimated accuracy","name":"host_prediction_estimated_accuracy","required":false,"visible":true,"helpText":"For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature","group":"host details"},{"type":"text","label":"spike-in microbial strain","name":"spikein_microbial_strain","required":false,"visible":true,"helpText":"Taxonomic information about the spike-in organism(s) at the strain level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes.","group":"treatment"},{"type":"text","label":"fermentation chemical additives","name":"fermentation_chemical_additives","required":false,"visible":true,"helpText":"Any chemicals that are added to the fermentation process to achieve the desired final product.","group":"treatment"},{"type":"text","label":"fermentation chemical additives percentage","name":"fermentation_chemical_additives_percentage","required":false,"visible":true,"helpText":"The amount of chemical added to the fermentation process.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*)))","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*)))"},"units":[{"value":"%","label":"%"}],"group":"treatment"},{"type":"text","label":"study treatment","name":"study_treatment","required":false,"visible":true,"helpText":"A process in which the act is intended to modify or alter some other material entity. From the study design, each treatment is comprised of one level of one or multiple factors. This field accepts terms listed under treatment (http://purl.obolibrary.org/obo/MCO_0000866). If the proper descriptor is not listed please use text to describe the study treatment. Multiple terms can be separated by one or more pipes.","group":"treatment"},{"type":"text","label":"spike-in organism","name":"spikein_organism","required":false,"visible":true,"helpText":"Taxonomic information about the spike-in organism(s). This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes.","group":"treatment"},{"type":"text","label":"spike-in organism count","name":"spikein_organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) should also be provided (example: total prokaryotes; 3.5e7 cells per ml; qPCR).","group":"treatment"},{"type":"text","label":"fermentation temperature","name":"fermentation_temperature","required":false,"visible":true,"helpText":"The temperature of the fermented food fermentation process.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"treatment"},{"type":"text","label":"spike-in with heavy metals","name":"spikein_with_heavy_metals","required":false,"visible":true,"helpText":"Heavy metals used in research study to assess effects of exposure on microbiome of a specific site. Please list heavy metals and concentration used for spike-in.","group":"treatment"},{"type":"text","label":"microbial starter inoculation","name":"microbial_starter_inoculation","required":false,"visible":true,"helpText":"The amount of starter culture used to inoculate a new batch.","group":"treatment"},{"type":"text","label":"microbial starter source","name":"microbial_starter_source","required":false,"visible":true,"helpText":"The source from which the microbial starter culture was sourced. If commercially supplied, list supplier.","group":"treatment"},{"type":"text","label":"microbial starter preparation","name":"microbial_starter_preparation","required":false,"visible":true,"helpText":"Information about the protocol or method used to prepare the starter inoculum.","group":"treatment"},{"type":"text","label":"spike-in bacterial serovar or serotype","name":"spikein_bacterial_serovar_or_serotype","required":false,"visible":true,"helpText":"Taxonomic information about the spike-in organism(s) at the serovar or serotype level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes.","group":"treatment"},{"type":"text","label":"antimicrobial phenotype of spike-in bacteria","name":"antimicrobial_phenotype_of_spikein_bacteria","required":false,"visible":true,"helpText":"Qualitative description of a microbial response to antimicrobial agents. Bacteria may be susceptible or resistant to a broad range of antibiotic drugs or drug classes, with several intermediate states or phases. This field accepts terms under antimicrobial phenotype (http://purl.obolibrary.org/obo/ARO_3004299).","group":"treatment"},{"type":"text","label":"fermentation time","name":"fermentation_time","required":false,"visible":true,"helpText":"The time duration of the fermented food fermentation process.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"},{"value":"minute","label":"minute"}],"group":"treatment"},{"type":"text","label":"microbial starter organism count","name":"microbial_starter_organism_count","required":false,"visible":true,"helpText":"Total cell count of starter culture per gram, volume or area of sample and the method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) should also be provided. (example : total prokaryotes; 3.5e7 cells per ml; qPCR).","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"treatment"},{"type":"text","label":"spike-in with antibiotics","name":"spikein_with_antibiotics","required":false,"visible":true,"helpText":"Antimicrobials used in research study to assess effects of exposure on microbiome of a specific site. Please list antimicrobial, common name and/or class and concentration used for spike-in.","group":"treatment"},{"type":"text","label":"study incubation temperature","name":"study_incubation_temperature","required":false,"visible":true,"helpText":"Sample incubation temperature if unpublished or unvalidated method is used.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"°C","label":"°C"}],"group":"treatment"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"study incubation duration","name":"study_incubation_duration","required":false,"visible":true,"helpText":"Sample incubation duration if unpublished or unvalidated method is used. Indicate the timepoint written in ISO 8601 format.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"},{"value":"minute","label":"minute"}],"group":"treatment"},{"type":"text","label":"biocide","name":"biocide","required":false,"visible":true,"helpText":"Substance intended for preventing, neutralizing, destroying, repelling, or mitigating the effects of any pest or microorganism; that inhibits the growth, reproduction, and activity of organisms, including fungal cells; decreases the number of fungi or pests present; deters microbial growth and degradation of other ingredients in the formulation. Indicate the biocide used on the location where the sample was taken. Multiple terms can be separated by pipes.","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"genetic modification","name":"genetic_modification","required":false,"visible":true,"helpText":"A genetic modification of the genome of an organism which may occur naturally by spontaneous mutation, or be introduced by some experimental means. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection.","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"ancestral data","name":"ancestral_data","required":false,"visible":true,"helpText":"information about either pedigree or other description of ancestral information (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"plant growth medium","name":"plant_growth_medium","required":false,"visible":true,"helpText":"Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147).","group":"growth medium"},{"type":"text","label":"rooting conditions","name":"rooting_conditions","required":false,"visible":true,"helpText":"relevant rooting conditions, such as field plot size, sowing density, container dimensions, number of plants per container","group":"growth medium"},{"type":"text","label":"rooting medium macronutrients","name":"rooting_medium_macronutrients","required":false,"visible":true,"helpText":"measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L)","group":"growth medium"},{"type":"text","label":"rooting medium micronutrients","name":"rooting_medium_micronutrients","required":false,"visible":true,"helpText":"measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L)","group":"growth medium"},{"type":"text","label":"rooting medium carbon","name":"rooting_medium_carbon","required":false,"visible":true,"helpText":"source of organic carbon in the culture rooting medium; e.g. sucrose","group":"growth medium"},{"type":"text","label":"rooting medium pH","name":"rooting_medium_ph","required":false,"visible":true,"helpText":"pH measurement of the culture rooting medium; e.g. 5.5","group":"growth medium"},{"type":"text","label":"microbiological culture medium","name":"microbiological_culture_medium","required":false,"visible":true,"helpText":"A culture medium used to select for, grow, and maintain prokaryotic microorganisms. Can be in either liquid (broth) or solidified (e.g. with agar) forms. This field accepts terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). If the proper descriptor is not listed please use text to describe the culture medium.","group":"growth medium"},{"type":"text","label":"spike-in growth medium","name":"spikein_growth_medium","required":false,"visible":true,"helpText":"A liquid or gel containing nutrients, salts, and other factors formulated to support the growth of microorganisms, cells, or plants (National Cancer Institute Thesaurus). A growth medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment. In this case, list the culture medium used to propagate the spike-in bacteria during preparation of spike-in inoculum. This field accepts terms listed under microbiological culture medium (http://purl.obolibrary.org/obo/MICRO_0000067). If the proper descriptor is not listed please use text to describe the spike in growth media.","group":"growth medium"},{"type":"text","label":"fermentation medium","name":"fermentation_medium","required":false,"visible":true,"helpText":"The growth medium used for the fermented food fermentation process, which supplies the required nutrients. Usually this includes a carbon and nitrogen source, water, micronutrients and chemical additives.","group":"growth medium"},{"type":"text","label":"growth medium","name":"growth_medium","required":false,"visible":true,"helpText":"A liquid or gel containing nutrients, salts, and other factors formulated to support the growth of microorganisms, cells, or plants (National Cancer Institute Thesaurus). The name of the medium used to grow the microorganism.","group":"growth medium"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sequencing location","name":"sequencing_location","required":false,"visible":true,"helpText":"The location the sequencing run was performed. Indicate the name of the lab or core facility where samples were sequenced.","group":"sample processing"},{"type":"text","label":"enrichment protocol","name":"enrichment_protocol","required":false,"visible":true,"helpText":"The microbiological workflow or protocol followed to test for the presence or enumeration of the target microbial analyte(s). Please provide a PubMed or DOI reference for published protocols.","group":"sample processing"},{"type":"text","label":"library preparation kit","name":"library_preparation_kit","required":false,"visible":true,"helpText":"Packaged kits (containing adapters, indexes, enzymes, buffers etc.), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids.","group":"sample processing"},{"type":"text","label":"nucleic acid extraction kit","name":"nucleic_acid_extraction_kit","required":false,"visible":true,"helpText":"The name of the extraction kit used to recover the nucleic acid fraction of an input material is performed.","group":"sample processing"},{"type":"text","label":"sample pooling","name":"sample_pooling","required":false,"visible":true,"helpText":"Physical combination of several instances of like material, e.g. RNA extracted from samples or dishes of cell cultures into one big aliquot of cells. Please provide a short description of the samples that were pooled.","group":"sample processing"},{"type":"text","label":"lot number","name":"lot_number","required":false,"visible":true,"helpText":"A distinctive alpha-numeric identification code assigned by the manufacturer or distributor to a specific quantity of manufactured material or product within a batch. Synonym: Batch Number. The submitter should provide lot number of the item followed by the item name for which the lot number was provided.","group":"sample processing"},{"type":"select","label":"single cell or viral particle lysis approach","name":"single_cell_or_viral_particle_lysis_approach","required":false,"visible":true,"helpText":"Method used to free DNA from interior of the cell(s) or particle(s)","options":[{"value":"chemical","label":"chemical"},{"value":"combination","label":"combination"},{"value":"enzymatic","label":"enzymatic"},{"value":"physical","label":"physical"}],"group":"sample processing"},{"type":"text","label":"single cell or viral particle lysis kit protocol","name":"single_cell_or_viral_particle_lysis_kit_protocol","required":false,"visible":true,"helpText":"Name of the kit or standard protocol used for cell(s) or particle(s) lysis","group":"sample processing"},{"type":"text","label":"pooled DNA extract total","name":"pooled_dna_extract_total","required":false,"visible":true,"helpText":"Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given. [ENA version of MIxS term: pooling of DNA extracts (if done). ]","simpleValidation":{"pattern":"([0-9]*)","patternMessage":"Must match pattern: ([0-9]*)"},"group":"sample processing"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"assembly software","name":"assembly_software","required":false,"visible":true,"helpText":"Tool(s) used for assembly, including version number and parameters in the format {software};{version};{parameters} e.g. metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"food animal antimicrobial","name":"food_animal_antimicrobial","required":false,"visible":true,"helpText":"The name(s) (generic or brand) of the antimicrobial(s) given to the food animal within the last 30 days.","group":"food and agriculture"},{"type":"text","label":"food shipping transportation vehicle","name":"food_shipping_transportation_vehicle","required":false,"visible":true,"helpText":"A descriptor for the mobile machine which is used to transport food commodities along the food distribution system. This field accepts terms listed under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes.","group":"food and agriculture"},{"type":"text","label":"water source shared","name":"water_source_shared","required":false,"visible":true,"helpText":"Other users sharing access to the same water source. Multiple terms can be separated by one or more pipes.","group":"food and agriculture"},{"type":"text","label":"food source","name":"food_source","required":false,"visible":true,"helpText":"Type of plant or animal from which the food product or its major ingredient is derived or a chemical food source [FDA CFSAN 1995].","group":"food and agriculture"},{"type":"text","label":"food shipping transportation method","name":"food_shipping_transportation_method","required":false,"visible":true,"helpText":"A descriptor for the method of movement of food commodity along the food distribution system. This field accepts terms listed under travel mode (http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is not listed please use text to describe the mode of travel. Multiple terms can be separated by one or more pipes.","group":"food and agriculture"},{"type":"text","label":"material of contact prior to food packaging","name":"material_of_contact_prior_to_food_packaging","required":false,"visible":true,"helpText":"The material the food contacted (e.g., was processed in) prior to packaging. This field accepts terms listed under material of contact prior to food packaging (http://purl.obolibrary.org/obo/FOODON_03530077). If the proper descriptor is not listed please use text to describe the material of contact prior to food packaging.","group":"food and agriculture"},{"type":"text","label":"food product name legal status","name":"food_product_name_legal_status","required":false,"visible":true,"helpText":"A datum indicating that use of a food product name is regulated in some legal jurisdiction. This field accepts terms listed under food product name legal status (http://purl.obolibrary.org/obo/FOODON_03530087).","group":"food and agriculture"},{"type":"text","label":"food quality date","name":"food_quality_date","required":false,"visible":true,"helpText":"The date recommended for the use of the product while at peak quality, this date is not a reflection of safety unless used on infant formula this date is not a reflection of safety and is typically labeled on a food product as \"best if used by,\" best by,\" \"use by,\" or \"freeze by.\"","group":"food and agriculture"},{"type":"text","label":"food cleaning process","name":"food_cleaning_process","required":false,"visible":true,"helpText":"The process of cleaning food to separate other environmental materials from the food source. Multiple terms can be separated by pipes.","group":"food and agriculture"},{"type":"text","label":"hygienic food production area","name":"hygienic_food_production_area","required":false,"visible":true,"helpText":"The subdivision of areas within a food production facility according to hygienic requirements. This field accepts terms listed under hygienic food production area (http://purl.obolibrary.org/obo/ENVO). Please add a term that most accurately indicates the hygienic area your sample was taken from according to the definitions provided.","units":[{"value":"W/m2","label":"W/m2"},{"value":"kg s−3","label":"kg s−3"}],"group":"food and agriculture"},{"type":"text","label":"food contact surface","name":"food_contact_surface","required":false,"visible":true,"helpText":"The specific container or coating materials in direct contact with the food. Multiple values can be assigned. This field accepts terms listed under food contact surface (http://purl.obolibrary.org/obo/FOODON_03500010).","group":"food and agriculture"},{"type":"text","label":"food cooking process","name":"food_cooking_process","required":false,"visible":true,"helpText":"The transformation of raw food by the application of heat. This field accepts terms listed under food cooking (http://purl.obolibrary.org/obo/FOODON_03450002).","group":"food and agriculture"},{"type":"text","label":"food product by quality","name":"food_product_by_quality","required":false,"visible":true,"helpText":"Descriptors for describing food visually or via other senses, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like \"food (frozen)\" are both a quality descriptor and the output of a process. This field accepts terms listed under food product by quality (http://purl.obolibrary.org/obo/FOODON_00002454).","group":"food and agriculture"},{"type":"text","label":"food animal antimicrobial route of administration","name":"food_animal_antimicrobial_route_of_administration","required":false,"visible":true,"helpText":"The route by which the antimicrobial is administered into the body of the food animal.","group":"food and agriculture"},{"type":"text","label":"food allergen labeling","name":"food_allergen_labeling","required":false,"visible":true,"helpText":"A label indication that the product contains a recognized allergen. This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510213).","group":"food and agriculture"},{"type":"text","label":"food product type","name":"food_product_type","required":false,"visible":true,"helpText":"A food product type is a class of food products that is differentiated by its food composition (e.g., single- or multi-ingredient), processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories. This field accepts terms under food product type (http://purl.obolibrary.org/obo/FOODON:03400361). For terms related to food product for an animal, consult food product for animal (http://purl.obolibrary.org/obo/FOODON_03309997). If the proper descriptor is not listed please use text to describe the food type. Multiple terms can be separated by one or more pipes.","group":"food and agriculture"},{"type":"text","label":"food animal source sex category","name":"food_animal_source_sex_category","required":false,"visible":true,"helpText":"The sex and reproductive status of the food animal.","group":"food and agriculture"},{"type":"text","label":"animal intrusion near sample source","name":"animal_intrusion_near_sample_source","required":false,"visible":true,"helpText":"Identification of animals intruding on the sample or sample site including invertebrates (such as pests or pollinators) and vertebrates (such as wildlife or domesticated animals). This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250). This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy. Multiple terms can be separated by pipes.","group":"food and agriculture"},{"type":"text","label":"food packing medium integrity","name":"food_packing_medium_integrity","required":false,"visible":true,"helpText":"A term label and term id to describe the state of the packing material and text to explain the exact condition. This field accepts terms listed under food packing medium integrity (http://purl.obolibrary.org/obo/FOODON_03530218).","group":"food and agriculture"},{"type":"text","label":"microbial starter","name":"microbial_starter","required":false,"visible":true,"helpText":"Any type of microorganisms used in food production. This field accepts terms listed under live organisms for food production (http://purl.obolibrary.org/obo/FOODON_0344453).","group":"food and agriculture"},{"type":"text","label":"food treatment process","name":"food_treatment_process","required":false,"visible":true,"helpText":"Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. Multiple values can be assigned. This fields accepts terms listed under food treatment process (http://purl.obolibrary.org/obo/FOODON_03460111).","group":"food and agriculture"},{"type":"text","label":"food preservation process","name":"food_preservation_process","required":false,"visible":true,"helpText":"The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. This field accepts terms listed under food preservation process (http://purl.obolibrary.org/obo/FOODON_03470107).","group":"food and agriculture"},{"type":"text","label":"microbial starter ncbi taxonomy id","name":"microbial_starter_ncbi_taxonomy_id","required":false,"visible":true,"helpText":"Please include Genus species and strain ID, if known of microorganisms used in food production. For complex communities, pipes can be used to separate two or more microbes.","group":"food and agriculture"},{"type":"text","label":"interagency food safety analytics collaboration (ifsac) category","name":"interagency_food_safety_analytics_collaboration_ifsac_category","required":false,"visible":true,"helpText":"The IFSAC food categorization scheme has five distinct levels to which foods can be assigned, depending upon the type of food. First, foods are assigned to one of four food groups (aquatic animals, land animals, plants, and other). Food groups include increasingly specific food categories; dairy, eggs, meat and poultry, and game are in the land animal food group, and the category meat and poultry is further subdivided into more specific categories of meat (beef, pork, other meat) and poultry (chicken, turkey, other poultry). Finally, foods are differentiated by differences in food processing (such as pasteurized fluid dairy products, unpasteurized fluid dairy products, pasteurized solid and semi-solid dairy products, and unpasteurized solid and semi-solid dairy products. An IFSAC food category chart is available from https://www.cdc.gov/foodsafety/ifsac/projects/food-categorization-scheme.html PMID: 28926300.","group":"food and agriculture"},{"type":"text","label":"food animal body condition","name":"food_animal_body_condition","required":false,"visible":true,"helpText":"Body condition scoring is a production management tool used to evaluate overall health and nutritional needs of a food animal. Because there are different scoring systems, this field is restricted to three categories.","group":"food and agriculture"},{"type":"text","label":"food product synonym","name":"food_product_synonym","required":false,"visible":true,"helpText":"Other names by which the food product is known by (e.g., regional or non-English names).","group":"food and agriculture"},{"type":"text","label":"food ingredient","name":"food_ingredient","required":false,"visible":true,"helpText":"In this field, please list individual ingredients for multi-component food [FOODON:00002501] and simple foods that is not captured in food_type. Please use terms that are present in FoodOn. Multiple terms can be separated by one or more pipes |, but please consider limiting this list to the top 5 ingredients listed in order as on the food label. See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors.","group":"food and agriculture"},{"type":"text","label":"food stored by consumer (storage duration)","name":"food_stored_by_consumer_storage_duration","required":false,"visible":true,"helpText":"The storage duration of the food commodity by the consumer, prior to onset of illness or sample collection. Indicate the timepoint written in ISO 8601 format.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"},{"value":"minute","label":"minute"}],"group":"food and agriculture"},{"type":"text","label":"food animal antimicrobial duration","name":"food_animal_antimicrobial_duration","required":false,"visible":true,"helpText":"The duration of time (days) that the antimicrobial was administered to the food animal.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"},{"value":"minute","label":"minute"}],"group":"food and agriculture"},{"type":"text","label":"part of plant or animal","name":"part_of_plant_or_animal","required":false,"visible":true,"helpText":"The anatomical part of the organism being involved in food production or consumption; e.g., a carrot is the root of the plant (root vegetable). This field accepts terms listed under part of plant or animal (http://purl.obolibrary.org/obo/FOODON_03420116).","group":"food and agriculture"},{"type":"text","label":"hazard analysis critical control points (haccp) guide food safety term","name":"hazard_analysis_critical_control_points_haccp_guide_food_safety_term","required":false,"visible":true,"helpText":"Hazard Analysis Critical Control Points (HACCP) food safety terms; This field accepts terms listed under HACCP guide food safety term (http://purl.obolibrary.org/obo/FOODON_03530221).","group":"food and agriculture"},{"type":"text","label":"dietary claim or use","name":"dietary_claim_or_use","required":false,"visible":true,"helpText":"These descriptors are used either for foods intended for special dietary use as defined in 21 CFR 105 or for foods that have special characteristics indicated in the name or labeling. This field accepts terms listed under dietary claim or use (http://purl.obolibrary.org/obo/FOODON_03510023). Multiple terms can be separated by one or more pipes, but please consider limiting this list to the most prominent dietary claim or use.","group":"food and agriculture"},{"type":"text","label":"degree of plant part maturity","name":"degree_of_plant_part_maturity","required":false,"visible":true,"helpText":"A description of the stage of development of a plant or plant part based on maturity or ripeness. This field accepts terms listed under degree of plant maturity (http://purl.obolibrary.org/obo/FOODON_03530050).","group":"food and agriculture"},{"type":"text","label":"food production environmental monitoring zone","name":"food_production_environmental_monitoring_zone","required":false,"visible":true,"helpText":"An environmental monitoring zone is a formal designation as part of an environmental monitoring program, in which areas of a food production facility are categorized, commonly as zones 1-4, based on likelihood or risk of foodborne pathogen contamination. This field accepts terms listed under food production environmental monitoring zone (http://purl.obolibrary.org/obo/ENVO). Please add a term to indicate the environmental monitoring zone the sample was taken from.","group":"food and agriculture"},{"type":"text","label":"plant reproductive part","name":"plant_reproductive_part","required":false,"visible":true,"helpText":"Plant reproductive part used in the field during planting to start the crop.","group":"food and agriculture"},{"type":"text","label":"food traceability list category","name":"food_traceability_list_category","required":false,"visible":true,"helpText":"The FDA is proposing to establish additional traceability recordkeeping requirements (beyond what is already required in existing regulations) for persons who manufacture, process, pack, or hold foods the Agency has designated for inclusion on the Food Traceability List. The Food Traceability List (FTL) identifies the foods for which the additional traceability records described in the proposed rule would be required. The term “Food Traceability List” (FTL) refers not only to the foods specifically listed (https://www.fda.gov/media/142303/download), but also to any foods that contain listed foods as ingredients.","group":"food and agriculture"},{"type":"text","label":"food animal antimicrobial frequency","name":"food_animal_antimicrobial_frequency","required":false,"visible":true,"helpText":"The frequency per day that the antimicrobial was administered to the food animal.","units":[{"value":"day","label":"day"}],"group":"food and agriculture"},{"type":"text","label":"intended consumer","name":"intended_consumer","required":false,"visible":true,"helpText":"Food consumer type, human or animal, for which the food product is produced and marketed. This field accepts terms listed under food consumer group (http://purl.obolibrary.org/obo/FOODON_03510136) or NCBI taxid.","group":"food and agriculture"},{"type":"text","label":"quantity purchased","name":"quantity_purchased","required":false,"visible":true,"helpText":"The quantity of food purchased by consumer.","group":"food and agriculture"},{"type":"text","label":"food container or wrapping","name":"food_container_or_wrapping","required":false,"visible":true,"helpText":"Type of container or wrapping defined by the main container material, the container form, and the material of the liner lids or ends. Also type of container or wrapping by form; prefer description by material first, then by form. This field accepts terms listed under food container or wrapping (http://purl.obolibrary.org/obo/FOODON_03490100).","group":"food and agriculture"},{"type":"text","label":"food additive","name":"food_additive","required":false,"visible":true,"helpText":"A substance or substances added to food to maintain or improve safety and freshness, to improve or maintain nutritional value, or improve taste, texture and appearance. This field accepts terms listed under food additive (http://purl.obolibrary.org/obo/FOODON_03412972). Multiple terms can be separated by one or more pipes, but please consider limiting this list to the top 5 ingredients listed in order as on the food label. See also, https://www.fda.gov/food/food-ingredients-packaging/overview-food-ingredients-additives-colors.","group":"food and agriculture"},{"type":"text","label":"food source age","name":"food_source_age","required":false,"visible":true,"helpText":"The age of the food source host organism. Depending on the type of host organism, age may be more appropriate to report in days, weeks, or years.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"week","label":"week"},{"value":"year","label":"year"},{"value":"day","label":"day"}],"group":"food and agriculture"},{"type":"text","label":"food animal antimicrobial intended use","name":"food_animal_antimicrobial_intended_use","required":false,"visible":true,"helpText":"The prescribed intended use of or the condition treated by the antimicrobial given to the food animal by any route of administration.","group":"food and agriculture"},{"type":"text","label":"food packing medium","name":"food_packing_medium","required":false,"visible":true,"helpText":"The medium in which the food is packed for preservation and handling or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup. The packing medium may provide a controlled environment for the food. It may also serve to improve palatability and consumer appeal. This includes edible packing media (e.g. fruit juice), gas other than air (e.g. carbon dioxide), vacuum packed, or packed with aerosol propellant. This field accepts terms under food packing medium (http://purl.obolibrary.org/obo/FOODON_03480020). Multiple terms may apply and can be separated by pipes.","group":"food and agriculture"},{"type":"text","label":"specific intended consumer","name":"specific_intended_consumer","required":false,"visible":true,"helpText":"Food consumer type, human or animal, for which the food product is produced and marketed. This field accepts terms listed under food consumer group (http://purl.obolibrary.org/obo/FOODON_03510136).","group":"food and agriculture"},{"type":"text","label":"purchase date","name":"purchase_date","required":false,"visible":true,"helpText":"The date a food product was purchased by consumer.","group":"food and agriculture"},{"type":"text","label":"food stored by consumer (storage temperature)","name":"food_stored_by_consumer_storage_temperature","required":false,"visible":true,"helpText":"Temperature at which food commodity was stored by the consumer, prior to onset of illness or sample collection.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"°C","label":"°C"}],"group":"food and agriculture"},{"type":"text","label":"food package capacity","name":"food_package_capacity","required":false,"visible":true,"helpText":"The maximum number of product units within a package","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"food and agriculture"},{"type":"text","label":"food distribution point geographic location (city)","name":"food_distribution_point_geographic_location_city","required":false,"visible":true,"helpText":"A reference to a place on the Earth, by its name or by its geographical location that refers to a distribution point along the food chain. This field accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448). Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012.","group":"food and agriculture"},{"type":"text","label":"food product origin geographic location","name":"food_product_origin_geographic_location","required":false,"visible":true,"helpText":"A reference to a place on the Earth, by its name or by its geographical location that describes the origin of the food commodity, either in terms of its cultivation or production. This field accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448).","group":"food and agriculture"},{"type":"text","label":"food distribution point geographic location","name":"food_distribution_point_geographic_location","required":false,"visible":true,"helpText":"A reference to a place on the Earth, by its name or by its geographical location that refers to a distribution point along the food chain. This field accepts terms listed under geographic location (http://purl.obolibrary.org/obo/GAZ_00000448). Reference: Adam Diamond, James Barham. Moving Food Along the Value Chain: Innovations in Regional Food Distribution. U.S. Dept. of Agriculture, Agricultural Marketing Service. Washington, DC. March 2012. http://dx.doi.org/10.9752/MS045.03-2012.","group":"food and agriculture"},{"type":"text","label":"production labeling claims","name":"production_labeling_claims","required":false,"visible":true,"helpText":"Labeling claims containing descriptors such as wild caught, free-range, organic, free-range, industrial, hormone-free, antibiotic free, cage free. Can include more than one term, separated by \";\"","group":"food and agriculture"},{"type":"text","label":"relative location of sample","name":"relative_location_of_sample","required":false,"visible":true,"helpText":"Location of sampled soil to other parts of the farm e.g. under crop plant, near irrigation ditch, from the dirt road.","group":"Environmental information"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"environment adjacent to site","name":"environment_adjacent_to_site","required":false,"visible":true,"helpText":"Description of the environmental system or features that are adjacent to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110) and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple terms can be separated by pipes.","group":"Environmental information"},{"type":"text","label":"fertilizer administration","name":"fertilizer_administration","required":false,"visible":true,"helpText":"Type of fertilizer or amendment added to the soil or water for the purpose of improving substrate health and quality for plant growth. This field accepts terms listed under agronomic fertilizer (http://purl.obolibrary.org/obo/AGRO_00002062). Multiple terms may apply and can be separated by pipes, listing in reverse chronological order. N.B. Old ENA definition as \"fertilizer regimen\": information about treatment involving the use of fertilizers; should include the name fertilizer, amount administered, treatment duration, interval and total experimental duration; can include multiple fertilizer regimens","group":"local environment conditions imposed"},{"type":"text","label":"biotic regimen","name":"biotic_regimen","required":false,"visible":true,"helpText":"information about treatment involving use of biotic factors, such as bacteria, viruses or fungi","group":"local environment conditions imposed"},{"type":"text","label":"mechanical damage","name":"mechanical_damage","required":false,"visible":true,"helpText":"information about any mechanical damage exerted on the plant; can include multiple damages and sites","group":"local environment conditions imposed"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}]},{"name":"GSC MIxS Symbiont","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000057","category":"mixs","accession":"ERC000057","fields":[{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"host of the symbiont role","name":"host_of_the_symbiont_role","required":false,"visible":true,"helpText":"Role of the host in the life cycle of the symbiotic organism.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample symbiont of","name":"sample_symbiont_of","required":false,"visible":true,"helpText":"Reference to host sample from symbiont. The referenced sample should already be registered in INSDC. E.g. ERSxxxxxx","simpleValidation":{"pattern":"(^[ESD]RS\\d{6,}$)|(^SAM[END][AG]?\\d+$)|(^EGAN\\d{11}$)","patternMessage":"Must match pattern: (^[ESD]RS\\d{6,}$)|(^SAM[END][AG]?\\d+$)|(^EGAN\\d{11}$)"},"group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage solution","name":"sample_storage_solution","required":false,"visible":true,"helpText":"Solution within which sample was stored, if any.","group":"sample collection: methods, storage and transport"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":false,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"select","label":"16s recovered","name":"16s_recovered","required":false,"visible":true,"helpText":"Can a 16S gene be recovered from the submitted bin, SAG or MAG?","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"non-sample terms"},{"type":"text","label":"16S recovery software","name":"16s_recovery_software","required":false,"visible":true,"helpText":"Tools used for 16S rRNA gene extraction. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":false,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":false,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":false,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host of the symbiotic host disease status","name":"host_of_the_symbiotic_host_disease_status","required":false,"visible":true,"helpText":"List of diseases with which the host of the symbiotic host organism has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text.","group":"host disorder"},{"type":"text","label":"host common name","name":"host_common_name","required":false,"visible":true,"helpText":"common name of the host, e.g. human","group":"host description"},{"type":"text","label":"host subject id","name":"host_subject_id","required":false,"visible":true,"helpText":"a unique identifier by which each subject can be referred to, de-identified, e.g. #131","group":"host description"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"text","label":"host taxid","name":"host_taxid","required":false,"visible":true,"helpText":"NCBI taxon id of the host, e.g. 9606","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"host description"},{"type":"text","label":"host body habitat","name":"host_body_habitat","required":false,"visible":true,"helpText":"original body habitat where the sample was obtained from","group":"host description"},{"type":"text","label":"host body site","name":"host_body_site","required":false,"visible":true,"helpText":"name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host description"},{"type":"text","label":"host life stage","name":"host_life_stage","required":false,"visible":true,"helpText":"description of life stage of host","group":"host description"},{"type":"text","label":"host height","name":"host_height","required":false,"visible":true,"helpText":"the height of subject","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$))"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host length","name":"host_length","required":false,"visible":true,"helpText":"the length of subject","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"},{"value":"cm","label":"cm"},{"value":"m","label":"m"}],"group":"host description"},{"type":"text","label":"host growth conditions","name":"host_growth_conditions","required":false,"visible":true,"helpText":"literature reference giving growth conditions of the host","group":"host description"},{"type":"text","label":"host substrate","name":"host_substrate","required":false,"visible":true,"helpText":"the growth substrate of the host","group":"host description"},{"type":"text","label":"host total mass","name":"host_total_mass","required":false,"visible":true,"helpText":"total mass of the host at collection, the unit depends on host","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"kg","label":"kg"}],"group":"host description"},{"type":"text","label":"host infra-specific name","name":"host_infraspecific_name","required":false,"visible":true,"helpText":"taxonomic information about the host below subspecies level","group":"host description"},{"type":"text","label":"host infra-specific rank","name":"host_infraspecific_rank","required":false,"visible":true,"helpText":"taxonomic rank information about the host below subspecies level, such as variety, form, rank etc.","group":"host description"},{"type":"text","label":"host phenotype","name":"host_phenotype","required":false,"visible":true,"helpText":"phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO","group":"host description"},{"type":"text","label":"host color","name":"host_color","required":false,"visible":true,"helpText":"the color of host","group":"host description"},{"type":"text","label":"host shape","name":"host_shape","required":false,"visible":true,"helpText":"morphological shape of host","group":"host description"},{"type":"select","label":"host sex","name":"host_sex","required":false,"visible":true,"helpText":"Gender or sex of the host.","options":[{"value":"female","label":"female"},{"value":"hermaphrodite","label":"hermaphrodite"},{"value":"male","label":"male"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"neuter","label":"neuter"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"other","label":"other"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"host of the symbiotic host subject id","name":"host_of_the_symbiotic_host_subject_id","required":false,"visible":true,"helpText":"A unique identifier by which each host of the symbiotic host organism subject can be referred to, de-identified, e.g. #H14.","group":"host description"},{"type":"text","label":"host of the symbiotic host taxon id","name":"host_of_the_symbiotic_host_taxon_id","required":false,"visible":true,"helpText":"NCBI taxon id of the host of the symbiotic host organism.","group":"Host association"},{"type":"text","label":"duration of association with the host","name":"duration_of_association_with_the_host","required":false,"visible":true,"helpText":"Time spent in host of the symbiotic organism at the time of sampling; relevant scale depends on symbiotic organism and study.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"},{"value":"minute","label":"minute"}],"group":"Host association"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"sample salinity","name":"sample_salinity","required":false,"visible":true,"helpText":"Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"host family relationship","name":"host_family_relationship","required":false,"visible":true,"helpText":"Familial relationships to other hosts in the same study; can include multiple relationships","group":"host details"},{"type":"text","label":"host genotype","name":"host_genotype","required":false,"visible":true,"helpText":"observed genotype","group":"host details"},{"type":"text","label":"gravidity","name":"gravidity","required":false,"visible":true,"helpText":"Whether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.","group":"host details"},{"type":"text","label":"host specificity or range","name":"host_specificity_or_range","required":false,"visible":true,"helpText":"The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier.","group":"host details"},{"type":"text","label":"host of the symbiotic host phenotype","name":"host_of_the_symbiotic_host_phenotype","required":false,"visible":true,"helpText":"Phenotype of the host of the symbiotic host organism. For phenotypic quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato.","group":"host details"},{"type":"text","label":"mode of transmission","name":"mode_of_transmission","required":false,"visible":true,"helpText":"The process through which the symbiotic host organism entered the host from which it was sampled.","group":"host details"},{"type":"text","label":"symbiotic host organism life cycle type","name":"symbiotic_host_organism_life_cycle_type","required":false,"visible":true,"helpText":"Type of life cycle of the symbiotic host species (the thing being sampled). Simple life cycles occur within a single host, complex ones within multiple different hosts over the course of their normal life cycle.","group":"host details"},{"type":"text","label":"host dependence","name":"host_dependence","required":false,"visible":true,"helpText":"Type of host dependence for the symbiotic host organism to its host.","group":"host details"},{"type":"text","label":"host specificity","name":"host_specificity","required":false,"visible":true,"helpText":"Level of specificity of symbiont-host interaction: e.g. generalist (symbiont able to establish associations with distantly related hosts) or species-specific.","group":"host details"},{"type":"text","label":"host cellular location","name":"host_cellular_location","required":false,"visible":true,"helpText":"The localization of the symbiotic host organism within the host from which it was sampled: e.g. intracellular if the symbiotic host organism is localized within the cells or extracellular if the symbiotic host organism is localized outside of cells.","group":"host details"},{"type":"text","label":"host of the symbiotic host infra-specific rank","name":"host_of_the_symbiotic_host_infraspecific_rank","required":false,"visible":true,"helpText":"Taxonomic rank information about the host of the symbiotic host organism below subspecies level, such as variety, form, rank etc.","group":"host details"},{"type":"text","label":"type of symbiosis","name":"type_of_symbiosis","required":false,"visible":true,"helpText":"Type of biological interaction established between the symbiotic host organism being sampled and its respective host","group":"host details"},{"type":"text","label":"observed coinfecting organisms in host of host","name":"observed_coinfecting_organisms_in_host_of_host","required":false,"visible":true,"helpText":"The taxonomic name of any coinfecting organism observed in a symbiotic relationship with the host of the sampled host organism. e.g. where a sample collected from a host trematode species (A) which was collected from a host_of_host fish (B) that was also infected with a nematode (C), the value here would be (C) the nematode {species name} or {common name}. Multiple co-infecting species may be added in a comma-separated list. For listing symbiotic organisms associated with the host (A) use the term Observed host symbiont.","group":"host details"},{"type":"text","label":"host of the symbiotic host infra-specific name","name":"host_of_the_symbiotic_host_infraspecific_name","required":false,"visible":true,"helpText":"Taxonomic name information of the host of the symbiotic host organism below subspecies level.","group":"host details"},{"type":"text","label":"host of the symbiotic host total mass","name":"host_of_the_symbiotic_host_total_mass","required":false,"visible":true,"helpText":"Total mass of the host of the symbiotic host organism at collection, the unit depends on the host.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"µg","label":"µg"},{"value":"g","label":"g"},{"value":"pg","label":"pg"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"kg","label":"kg"}],"group":"host details"},{"type":"text","label":"host of the symbiotic host local environmental context","name":"host_of_the_symbiotic_host_local_environmental_context","required":false,"visible":true,"helpText":"For a symbiotic host organism the local anatomical environment within its host may have causal influences. Report the anatomical entity(s) which are in the direct environment of the symbiotic host organism being sampled and which you believe have significant causal influences on your sample or specimen. For example, if the symbiotic host organism being sampled is an intestinal worm, its local environmental context will be the term for intestine from UBERON (http://uberon.github.io/).","group":"host details"},{"type":"text","label":"host of the symbiotic host common name","name":"host_of_the_symbiotic_host_common_name","required":false,"visible":true,"helpText":"Common name of the host of the symbiotic host organism.","group":"host details"},{"type":"text","label":"host of the symbiotic host genotype","name":"host_of_the_symbiotic_host_genotype","required":false,"visible":true,"helpText":"Observed genotype of the host of the symbiotic host organism.","group":"host details"},{"type":"text","label":"route of transmission","name":"route_of_transmission","required":false,"visible":true,"helpText":"Description of path taken by the symbiotic host organism being sampled in order to establish a symbiotic relationship with the host (with which it was observed at the time of sampling) via a mode of transmission (specified in mode_transmission).","group":"host details"},{"type":"text","label":"host dry mass","name":"host_dry_mass","required":false,"visible":true,"helpText":"measurement of dry mass","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"mg","label":"mg"},{"value":"kg","label":"kg"}],"group":"host details"},{"type":"text","label":"host body product","name":"host_body_product","required":false,"visible":true,"helpText":"substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA","group":"host details"},{"type":"text","label":"host number individual","name":"host_number_individual","required":false,"visible":true,"helpText":"Number of symbiotic host individuals pooled at the time of collection.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"host details"},{"type":"text","label":"perturbation","name":"perturbation","required":false,"visible":true,"helpText":"type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"select","label":"single cell or viral particle lysis approach","name":"single_cell_or_viral_particle_lysis_approach","required":false,"visible":true,"helpText":"Method used to free DNA from interior of the cell(s) or particle(s)","options":[{"value":"chemical","label":"chemical"},{"value":"combination","label":"combination"},{"value":"enzymatic","label":"enzymatic"},{"value":"physical","label":"physical"}],"group":"sample processing"},{"type":"text","label":"single cell or viral particle lysis kit protocol","name":"single_cell_or_viral_particle_lysis_kit_protocol","required":false,"visible":true,"helpText":"Name of the kit or standard protocol used for cell(s) or particle(s) lysis","group":"sample processing"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"chemical administration","name":"chemical_administration","required":false,"visible":true,"helpText":"list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v111), please see http://purl.bioontology.org/ontology/CHEBI","group":"local environment conditions imposed"}]},{"name":"GSC MIxS Hydrocarbon","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000058","category":"mixs","accession":"ERC000058","fields":[{"type":"text","label":"sample true vertical depth subsea","name":"sample_true_vertical_depth_subsea","required":false,"visible":true,"helpText":"Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m","group":"Marine Sample"},{"type":"select","label":"trophic level","name":"trophic_level","required":false,"visible":true,"helpText":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)","options":[{"value":"autotroph","label":"autotroph"},{"value":"carboxydotroph","label":"carboxydotroph"},{"value":"chemoautotroph","label":"chemoautotroph"},{"value":"chemoheterotroph","label":"chemoheterotroph"},{"value":"chemolithoautotroph","label":"chemolithoautotroph"},{"value":"chemolithotroph","label":"chemolithotroph"},{"value":"chemoorganoheterotroph","label":"chemoorganoheterotroph"},{"value":"chemoorganotroph","label":"chemoorganotroph"},{"value":"chemosynthetic","label":"chemosynthetic"},{"value":"chemotroph","label":"chemotroph"},{"value":"copiotroph","label":"copiotroph"},{"value":"diazotroph","label":"diazotroph"},{"value":"facultative autotroph","label":"facultative autotroph"},{"value":"heterotroph","label":"heterotroph"},{"value":"lithoautotroph","label":"lithoautotroph"},{"value":"lithoheterotroph","label":"lithoheterotroph"},{"value":"lithotroph","label":"lithotroph"},{"value":"methanotroph","label":"methanotroph"},{"value":"methylotroph","label":"methylotroph"},{"value":"mixotroph","label":"mixotroph"},{"value":"obligate chemoautolithotroph","label":"obligate chemoautolithotroph"},{"value":"oligotroph","label":"oligotroph"},{"value":"organoheterotroph","label":"organoheterotroph"},{"value":"organotroph","label":"organotroph"},{"value":"photoautotroph","label":"photoautotroph"},{"value":"photoheterotroph","label":"photoheterotroph"},{"value":"photolithoautotroph","label":"photolithoautotroph"},{"value":"photolithotroph","label":"photolithotroph"},{"value":"photosynthetic","label":"photosynthetic"},{"value":"phototroph","label":"phototroph"}],"group":"Organism characteristics: ecosystem"},{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"propagation","name":"propagation","required":false,"visible":true,"helpText":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample transport conditions","name":"sample_transport_conditions","required":false,"visible":true,"helpText":"Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 °C)","units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"day","label":"day"},{"value":"minute","label":"minute"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage temperature","name":"sample_storage_temperature","required":false,"visible":true,"helpText":"temperature at which sample was stored, e.g. -80","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"°C","label":"°C"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage location","name":"sample_storage_location","required":false,"visible":true,"helpText":"Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"source rock depositional environment","name":"source_rock_depositional_environment","required":false,"visible":true,"helpText":"Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field","group":"local environment conditions: soil"},{"type":"text","label":"sample measured depth","name":"sample_measured_depth","required":false,"visible":true,"helpText":"In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"},{"value":"km","label":"km"},{"value":"m","label":"m"}],"group":"sample collection: site related"},{"type":"text","label":"corrosion rate at sample location","name":"corrosion_rate_at_sample_location","required":false,"visible":true,"helpText":"Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays","group":"sample collection: site related"},{"type":"text","label":"sample collection point","name":"sample_collection_point","required":false,"visible":true,"helpText":"Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field","group":"sample collection: site related"},{"type":"text","label":"depth (tvdss) of hydrocarbon resource temperature","name":"depth_tvdss_of_hydrocarbon_resource_temperature","required":false,"visible":true,"helpText":"True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m","label":"m"}],"group":"sample collection: site related"},{"type":"select","label":"oxygenation status of sample","name":"oxygenation_status_of_sample","required":false,"visible":true,"helpText":"oxygenation status of sample","options":[{"value":"aerobic","label":"aerobic"},{"value":"anaerobic","label":"anaerobic"}],"group":"sample collection: core sample properties"},{"type":"text","label":"density","name":"density","required":false,"visible":true,"helpText":"density of sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g/m3","label":"g/m3"}],"group":"sample collection: core sample properties"},{"type":"text","label":"sample well name","name":"sample_well_name","required":false,"visible":true,"helpText":"Name of the well (e.g. BXA1123) where sample was taken","group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":false,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"ploidy","name":"ploidy","required":false,"visible":true,"helpText":"The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO","group":"non-sample terms"},{"type":"text","label":"number of replicons","name":"number_of_replicons","required":false,"visible":true,"helpText":"Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"extrachromosomal elements","name":"extrachromosomal_elements","required":false,"visible":true,"helpText":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"target gene","name":"target_gene","required":false,"visible":true,"helpText":"Targeted gene or locus name for marker gene studies","group":"non-sample terms"},{"type":"text","label":"target subfragment","name":"target_subfragment","required":false,"visible":true,"helpText":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA","group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"select","label":"sequence quality check","name":"sequence_quality_check","required":false,"visible":true,"helpText":"Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA","options":[{"value":"manual","label":"manual"},{"value":"none","label":"none"},{"value":"software","label":"software"}],"group":"non-sample terms"},{"type":"text","label":"chimera check software","name":"chimera_check_software","required":false,"visible":true,"helpText":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"select","label":"16s recovered","name":"16s_recovered","required":false,"visible":true,"helpText":"Can a 16S gene be recovered from the submitted bin, SAG or MAG?","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"non-sample terms"},{"type":"text","label":"well identification number","name":"well_identification_number","required":false,"visible":true,"helpText":"A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)","group":"non-sample terms"},{"type":"text","label":"water cut","name":"water_cut","required":false,"visible":true,"helpText":"Current amount of water (%) in a produced fluid stream; or the average of the combined streams","units":[{"value":"%","label":"%"}],"group":"non-sample terms"},{"type":"text","label":"production rate","name":"production_rate","required":false,"visible":true,"helpText":"Oil and/or gas production rates per well (e.g. 524 m3 / day)","group":"non-sample terms"},{"type":"text","label":"field name","name":"field_name","required":false,"visible":true,"helpText":"Name of the hydrocarbon field (e.g. Albacora)","group":"non-sample terms"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":false,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":false,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":false,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"secondary and tertiary recovery methods and start date","name":"secondary_and_tertiary_recovery_methods_and_start_date","required":false,"visible":true,"helpText":"Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field.","group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"organism count","name":"organism_count","required":false,"visible":true,"helpText":"Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","group":"sample collection"},{"type":"text","label":"organism count qpcr information","name":"organism_count_qpcr_information","required":false,"visible":true,"helpText":"If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)","group":"sample collection"},{"type":"text","label":"hydrocarbon type produced","name":"hydrocarbon_type_produced","required":false,"visible":true,"helpText":"Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field","group":"unusual properties"},{"type":"text","label":"api gravity","name":"api_gravity","required":false,"visible":true,"helpText":"API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1API)","group":"unusual properties"},{"type":"text","label":"sample storage duration","name":"sample_storage_duration","required":false,"visible":true,"helpText":"Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host disease status","name":"host_disease_status","required":false,"visible":true,"helpText":"list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text","group":"host disorder"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"pressure","name":"pressure","required":false,"visible":true,"helpText":"pressure to which the sample is subject, in atmospheres","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"bar","label":"bar"},{"value":"atm","label":"atm"}],"group":"local environment conditions"},{"type":"text","label":"temperature","name":"temperature","required":false,"visible":true,"helpText":"temperature of the sample at time of sampling","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"local environment conditions"},{"type":"text","label":"pH","name":"ph","required":false,"visible":true,"helpText":"pH measurement","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"local environment conditions"},{"type":"text","label":"viscosity","name":"viscosity","required":false,"visible":true,"helpText":"A measure of oil's resistance to gradual deformation by shear stress or tensile stress (e.g. 3.5 cp; 100 C)","group":"local environment conditions"},{"type":"text","label":"permeability","name":"permeability","required":false,"visible":true,"helpText":"Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))","group":"local environment conditions"},{"type":"text","label":"oil water contact depth","name":"oil_water_contact_depth","required":false,"visible":true,"helpText":"Depth of the original oil water contact (OWC) zone (average) (m TVDSS)","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*)))","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*)))"},"units":[{"value":"m","label":"m"}],"group":"local environment conditions"},{"type":"text","label":"hydrocarbon resource original pressure","name":"hydrocarbon_resource_original_pressure","required":false,"visible":true,"helpText":"Original pressure of the hydrocarbon resource","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*)))","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*)))"},"units":[{"value":"Pa","label":"Pa"},{"value":"N/m2","label":"N/m2"}],"group":"local environment conditions"},{"type":"text","label":"source rock geological age","name":"source_rock_geological_age","required":false,"visible":true,"helpText":"Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field","group":"local environment conditions"},{"type":"text","label":"ammonium","name":"ammonium","required":false,"visible":true,"helpText":"concentration of ammonium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"sample salinity","name":"sample_salinity","required":false,"visible":true,"helpText":"Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"calcium","name":"calcium","required":false,"visible":true,"helpText":"concentration of calcium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"chloride","name":"chloride","required":false,"visible":true,"helpText":"concentration of chloride","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"suspended solids","name":"suspended_solids","required":false,"visible":true,"helpText":"concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter, etc,; can include multiple substances","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"mol/L","label":"mol/L"},{"value":"g/L","label":"g/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved carbon dioxide","name":"dissolved_carbon_dioxide","required":false,"visible":true,"helpText":"concentration of dissolved carbon dioxide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved inorganic carbon","name":"dissolved_inorganic_carbon","required":false,"visible":true,"helpText":"dissolved inorganic carbon concentration","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved inorganic phosphorus","name":"dissolved_inorganic_phosphorus","required":false,"visible":true,"helpText":"concentration of dissolved inorganic phosphorus","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"dissolved organic carbon","name":"dissolved_organic_carbon","required":false,"visible":true,"helpText":"concentration of dissolved organic carbon","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"magnesium","name":"magnesium","required":false,"visible":true,"helpText":"concentration of magnesium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"mol/L","label":"mol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"nitrate","name":"nitrate","required":false,"visible":true,"helpText":"concentration of nitrate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"nitrite","name":"nitrite","required":false,"visible":true,"helpText":"concentration of nitrite","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"total nitrogen concentration","name":"total_nitrogen_concentration","required":false,"visible":true,"helpText":"Concentration of nitrogen (total). Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"potassium","name":"potassium","required":false,"visible":true,"helpText":"concentration of potassium","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"salinity","name":"salinity","required":false,"visible":true,"helpText":"The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"concentration measurement"},{"type":"text","label":"sodium","name":"sodium","required":false,"visible":true,"helpText":"sodium concentration","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"parts/million","label":"parts/million"},{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"sulfate","name":"sulfate","required":false,"visible":true,"helpText":"concentration of sulfate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"sulfide","name":"sulfide","required":false,"visible":true,"helpText":"concentration of sulfide","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"}],"group":"concentration measurement"},{"type":"text","label":"total phosphorus","name":"total_phosphorus","required":false,"visible":true,"helpText":"total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"concentration measurement"},{"type":"text","label":"total iron","name":"total_iron","required":false,"visible":true,"helpText":"Concentration of total iron in the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"concentration measurement"},{"type":"text","label":"volatile fatty acids","name":"volatile_fatty_acids","required":false,"visible":true,"helpText":"Concentration of Volatile Fatty Acids in the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"concentration measurement"},{"type":"text","label":"dissolved iron","name":"dissolved_iron","required":false,"visible":true,"helpText":"Concentration of dissolved iron in the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"},{"value":"µl/L","label":"µl/L"}],"group":"concentration measurement"},{"type":"text","label":"resins wt%","name":"resins_wt","required":false,"visible":true,"helpText":"Saturate, Aromatic, Resin and Asphaltene(SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)","group":"concentration measurement"},{"type":"text","label":"dissolved oxygen in fluids","name":"dissolved_oxygen_in_fluids","required":false,"visible":true,"helpText":"Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgyen-corrosion and microbial activity (e.g. Mic).","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/kg","label":"µmol/kg"},{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"total sulfur","name":"total_sulfur","required":false,"visible":true,"helpText":"Concentration of total sulfur in the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"injection water fraction","name":"injection_water_fraction","required":false,"visible":true,"helpText":"Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"%","label":"%"}],"group":"concentration measurement"},{"type":"text","label":"ethylbenzene","name":"ethylbenzene","required":false,"visible":true,"helpText":"Concentration of ethylbenzene in the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"},{"value":"mg/L","label":"mg/L"},{"value":"µg/L","label":"µg/L"}],"group":"concentration measurement"},{"type":"text","label":"vfa in formation water","name":"vfa_in_formation_water","required":false,"visible":true,"helpText":"Original volatile fatty acid concentration in the hydrocarbon resource","group":"concentration measurement"},{"type":"text","label":"total acid number","name":"total_acid_number","required":false,"visible":true,"helpText":"Total Acid Number(TAN) is a measurement of acidity that is determined by the amount of potassium hydroxide in milligrams that is needed to neutralize the acids in one gram of oil. It is an important quality measurement of crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"group":"concentration measurement"},{"type":"text","label":"sulfate in formation water","name":"sulfate_in_formation_water","required":false,"visible":true,"helpText":"Original sulfate concentration in the hydrocarbon resource","units":[{"value":"week","label":"week"},{"value":"hour","label":"hour"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"},{"value":"minute","label":"minute"}],"group":"concentration measurement"},{"type":"text","label":"toluene","name":"toluene","required":false,"visible":true,"helpText":"Concentration of toluene in the sample","group":"concentration measurement"},{"type":"text","label":"asphaltenes wt%","name":"asphaltenes_wt","required":false,"visible":true,"helpText":"Saturate, Aromatic, Resin and Asphaltene(SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"%","label":"%"}],"group":"concentration measurement"},{"type":"text","label":"xylene","name":"xylene","required":false,"visible":true,"helpText":"Concentration of xylene in the sample","group":"concentration measurement"},{"type":"text","label":"alkalinity method","name":"alkalinity_method","required":false,"visible":true,"helpText":"Method used for alkalinity measurement","units":[{"value":"m2","label":"m2"}],"group":"concentration measurement"},{"type":"text","label":"benzene","name":"benzene","required":false,"visible":true,"helpText":"Concentration of benzene in the sample","group":"concentration measurement"},{"type":"text","label":"alkalinity","name":"alkalinity","required":false,"visible":true,"helpText":"alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mEq/L","label":"mEq/L"}],"group":"concentration measurement"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"source rock lithology","name":"source_rock_lithology","required":false,"visible":true,"helpText":"Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field","group":"local environment history"},{"type":"text","label":"sample material type","name":"sample_material_type","required":false,"visible":true,"helpText":"The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).","group":"other"},{"type":"text","label":"host of the symbiotic host phenotype","name":"host_of_the_symbiotic_host_phenotype","required":false,"visible":true,"helpText":"Phenotype of the host of the symbiotic host organism. For phenotypic quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato.","group":"host details"},{"type":"text","label":"biocide administration method","name":"biocide_administration_method","required":false,"visible":true,"helpText":"Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)","group":"treatment"},{"type":"text","label":"chemical treatment","name":"chemical_treatment","required":false,"visible":true,"helpText":"List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included","group":"treatment"},{"type":"text","label":"biocide administration","name":"biocide_administration","required":false,"visible":true,"helpText":"List of biocides (commercial name of product and supplier) and date of administration","group":"treatment"},{"type":"text","label":"chemical treatment method","name":"chemical_treatment_method","required":false,"visible":true,"helpText":"Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)","group":"treatment"},{"type":"text","label":"negative control type","name":"negative_control_type","required":false,"visible":true,"helpText":"The substance or equipment used as a negative control in an investigation","group":"experimental factor and block"},{"type":"text","label":"positive control type","name":"positive_control_type","required":false,"visible":true,"helpText":"The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.","group":"experimental factor and block"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"encoded traits","name":"encoded_traits","required":false,"visible":true,"helpText":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage","group":"Organism characteristics: genetic"},{"type":"text","label":"subspecific genetic lineage","name":"subspecific_genetic_lineage","required":false,"visible":true,"helpText":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.","group":"Organism characteristics: genetic"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"isolation and growth condition","name":"isolation_and_growth_condition","required":false,"visible":true,"helpText":"Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.","group":"Reference"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample subtype","name":"sample_subtype","required":false,"visible":true,"helpText":"Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field","group":"Reference"},{"type":"text","label":"preservative added to sample","name":"preservative_added_to_sample","required":false,"visible":true,"helpText":"Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)","group":"sample processing"},{"type":"select","label":"single cell or viral particle lysis approach","name":"single_cell_or_viral_particle_lysis_approach","required":false,"visible":true,"helpText":"Method used to free DNA from interior of the cell(s) or particle(s)","options":[{"value":"chemical","label":"chemical"},{"value":"combination","label":"combination"},{"value":"enzymatic","label":"enzymatic"},{"value":"physical","label":"physical"}],"group":"sample processing"},{"type":"text","label":"single cell or viral particle lysis kit protocol","name":"single_cell_or_viral_particle_lysis_kit_protocol","required":false,"visible":true,"helpText":"Name of the kit or standard protocol used for cell(s) or particle(s) lysis","group":"sample processing"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"sample volume or weight for DNA extraction","name":"sample_volume_or_weight_for_dna_extraction","required":false,"visible":true,"helpText":"Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"g","label":"g"},{"value":"ng","label":"ng"},{"value":"mg","label":"mg"},{"value":"mL","label":"mL"}],"group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"pcr conditions","name":"pcr_conditions","required":false,"visible":true,"helpText":"Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'","group":"sample processing"},{"type":"text","label":"pcr primers","name":"pcr_primers","required":false,"visible":true,"helpText":"PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"production start date","name":"production_start_date","required":false,"visible":true,"helpText":"Date of field's first production","group":"food and agriculture"},{"type":"text","label":"aromatics wt%","name":"aromatics_wt","required":false,"visible":true,"helpText":"Saturate, Aromatic, Resin and Asphaltene(SARA) is an analysis method that divides crude oil components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"group":"food and agriculture"},{"type":"text","label":"saturates wt%","name":"saturates_wt","required":false,"visible":true,"helpText":"Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"%","label":"%"}],"group":"food and agriculture"},{"type":"text","label":"porosity","name":"porosity","required":false,"visible":true,"helpText":"Porosity of deposited sediment is volume of voids divided by the total volume of sample","simpleValidation":{"pattern":"[0-9]+","patternMessage":"Must match pattern: [0-9]+"},"group":"Environmental information"},{"type":"text","label":"formation water salinity","name":"formation_water_salinity","required":false,"visible":true,"helpText":"Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg/L","label":"mg/L"},{"value":"ppm","label":"ppm"}],"group":"Environmental information"},{"type":"text","label":"basin name","name":"basin_name","required":false,"visible":true,"helpText":"Name of the basin (e.g. Campos)","group":"Environmental information"},{"type":"text","label":"pour point","name":"pour_point","required":false,"visible":true,"helpText":"Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high pour point is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (source: https://en.wikipedia.org/wiki/pour_point)","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"°C","label":"°C"}],"group":"Environmental information"},{"type":"text","label":"reservoir name","name":"reservoir_name","required":false,"visible":true,"helpText":"Name of the reservoir (e.g. Carapebus)","group":"Environmental information"},{"type":"text","label":"hydrocarbon resource geological age","name":"hydrocarbon_resource_geological_age","required":false,"visible":true,"helpText":"Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field","group":"Environmental information"},{"type":"text","label":"depositional environment","name":"depositional_environment","required":false,"visible":true,"helpText":"Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field","group":"Environmental information"},{"type":"text","label":"source rock kerogen type","name":"source_rock_kerogen_type","required":false,"visible":true,"helpText":"Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field","group":"Environmental information"},{"type":"text","label":"hydrocarbon resource type","name":"hydrocarbon_resource_type","required":false,"visible":true,"helpText":"Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field","group":"Environmental information"},{"type":"text","label":"water production rate","name":"water_production_rate","required":false,"visible":true,"helpText":"Water production rates per well (e.g. 987 m3 / day)","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m3/day","label":"m3/day"}],"group":"Environmental information"},{"type":"text","label":"lithology","name":"lithology","required":false,"visible":true,"helpText":"Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field","group":"Environmental information"},{"type":"text","label":"hydrocarbon resource original temperature","name":"hydrocarbon_resource_original_temperature","required":false,"visible":true,"helpText":"Original temperature of the hydrocarbon resource","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"°C","label":"°C"}],"group":"Environmental information"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"},{"type":"text","label":"injection water breakthrough date of specific well","name":"injection_water_breakthrough_date_of_specific_well","required":false,"visible":true,"helpText":"Injection water breakthrough date per well following a secondary and/or tertiary recovery","group":"local environment conditions imposed"}]},{"name":"GSC MISAGS","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000048","category":"mixs","accession":"ERC000048","fields":[{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"metagenomic source","name":"metagenomic_source","required":true,"visible":true,"helpText":"The metagenomic source of the sample. This value should contain “metagenome” and be in the taxonomy database e.g. wastewater metagenome or human gut metagenome. Please note “metagenome” alone will not be accepted. Check here for more details on metagenome taxonomy: https://ena-docs.readthedocs.io/en/latest/faq_taxonomy.html#environmental-taxonomic-classifications","group":"sample collection: core sample properties"},{"type":"text","label":"sample derived from","name":"sample_derived_from","required":true,"visible":true,"helpText":"Reference to parental sample(s) or original run(s) that the assembly is derived from. The referenced samples or runs should already be registered in INSDC. This should be formatted as one of the following. A single sample/run e.g. ERSxxxxxx OR a comma separated list e.g. ERSxxxxxx,ERSxxxxxx OR a range e.g. ERSxxxxxx-ERSxxxxxx","simpleValidation":{"pattern":"(^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)","patternMessage":"Must match pattern: (^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)"},"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"number of standard tRNAs extracted","name":"number_of_standard_trnas_extracted","required":false,"visible":true,"helpText":"The total number of tRNAs identified from the bin, SAG or MAG","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"feature prediction","name":"feature_prediction","required":false,"visible":true,"helpText":"Method used to predict UViGs features such as ORFs, integration site, etc. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"similarity search method","name":"similarity_search_method","required":false,"visible":true,"helpText":"Tool used to compare ORFs with database, along with version and cutoffs used. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"select","label":"16s recovered","name":"16s_recovered","required":false,"visible":true,"helpText":"Can a 16S gene be recovered from the submitted bin, SAG or MAG?","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"non-sample terms"},{"type":"text","label":"16S recovery software","name":"16s_recovery_software","required":false,"visible":true,"helpText":"Tools used for 16S rRNA gene extraction. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"tRNA extraction software","name":"trna_extraction_software","required":false,"visible":true,"helpText":"Tools used for tRNA identification. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"completeness score","name":"completeness_score","required":false,"visible":true,"helpText":"Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. Completeness score is one of 3 attributes which in combination reflect the standard quality of a MAG, see here for more information: https://ena-docs.readthedocs.io/en/latest/faq_metagenomes.html. Mandatory for all samples directly linked with SAGs or MAGs.","simpleValidation":{"pattern":"^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$","patternMessage":"Must match pattern: ^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$"},"units":[{"value":"%","label":"%"}],"group":"non-sample terms"},{"type":"text","label":"completeness software","name":"completeness_software","required":false,"visible":true,"helpText":"Tools used for completion estimate, i.e. checkm, anvi'o, busco. Mandatory for all samples directly linked with SAGs or MAGs.","group":"non-sample terms"},{"type":"text","label":"completeness approach","name":"completeness_approach","required":false,"visible":true,"helpText":"The approach used to determine the completeness of a given bin, SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome","group":"non-sample terms"},{"type":"text","label":"contamination score","name":"contamination_score","required":false,"visible":true,"helpText":"The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. Contamination score is one of 3 attributes which in combination reflect the standard quality of a MAG, see here for more information: https://ena-docs.readthedocs.io/en/latest/faq_metagenomes.html. If contamination ≥ 10% then please submit as a binned assembly. In SAGs, contamination score is mandatory for prokaryotes and optional for eukaryotes.","simpleValidation":{"pattern":"^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$","patternMessage":"Must match pattern: ^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$"},"units":[{"value":"%","label":"%"}],"group":"non-sample terms"},{"type":"select","label":"contamination screening input","name":"contamination_screening_input","required":false,"visible":true,"helpText":"The type of sequence data used as input","options":[{"value":"contigs","label":"contigs"},{"value":"reads","label":"reads"}],"group":"non-sample terms"},{"type":"text","label":"contamination screening parameters","name":"contamination_screening_parameters","required":false,"visible":true,"helpText":"Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer","group":"non-sample terms"},{"type":"text","label":"decontamination software","name":"decontamination_software","required":false,"visible":true,"helpText":"Tool(s) used in contamination screening","group":"non-sample terms"},{"type":"select","label":"assembly quality","name":"assembly_quality","required":false,"visible":true,"helpText":"The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated.","options":[{"value":"Many fragments with little to no review of assembly other than reporting of standard assembly statistics","label":"Many fragments with little to no review of assembly other than reporting of standard assembly statistics"},{"value":"Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs","label":"Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs"},{"value":"Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better","label":"Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better"}],"group":"non-sample terms"},{"type":"text","label":"taxonomic identity marker","name":"taxonomic_identity_marker","required":false,"visible":true,"helpText":"The phylogenetic marker(s) used to assign an organism name to the bin, SAG or MAG. Examples are 16S gene, multi-marker approach or other e.g. rpoB gene. Mandatory for all samples directly linked with SAGs or MAGs.","group":"non-sample terms"},{"type":"text","label":"isolation_source","name":"isolation_source","required":true,"visible":true,"helpText":"describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived","group":"Collection event information"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"size fraction selected","name":"size_fraction_selected","required":false,"visible":true,"helpText":"Filtering pore size used in sample preparation e.g. 0-0.22 micrometer","group":"sample collection"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"reference database(s)","name":"reference_databases","required":false,"visible":true,"helpText":"List of database(s) used for ORF annotation, along with version number and reference to website or publication","group":"Reference"},{"type":"select","label":"single cell or viral particle lysis approach","name":"single_cell_or_viral_particle_lysis_approach","required":true,"visible":true,"helpText":"Method used to free DNA from interior of the cell(s) or particle(s)","options":[{"value":"chemical","label":"chemical"},{"value":"combination","label":"combination"},{"value":"enzymatic","label":"enzymatic"},{"value":"physical","label":"physical"}],"group":"sample processing"},{"type":"text","label":"single cell or viral particle lysis kit protocol","name":"single_cell_or_viral_particle_lysis_kit_protocol","required":false,"visible":true,"helpText":"Name of the kit or standard protocol used for cell(s) or particle(s) lysis","group":"sample processing"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"assembly software","name":"assembly_software","required":false,"visible":true,"helpText":"Tool(s) used for assembly, including version number and parameters in the format {software};{version};{parameters} e.g. metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise","group":"sample processing"},{"type":"select","label":"WGA amplification approach","name":"wga_amplification_approach","required":true,"visible":true,"helpText":"Method used to amplify genomic DNA in preparation for sequencing","options":[{"value":"mda based","label":"mda based"},{"value":"pcr based","label":"pcr based"}],"group":"sample processing"},{"type":"text","label":"WGA amplification kit","name":"wga_amplification_kit","required":false,"visible":true,"helpText":"Kit used to amplify genomic DNA in preparation for sequencing","group":"sample processing"},{"type":"select","label":"sorting technology","name":"sorting_technology","required":true,"visible":true,"helpText":"Method used to sort/isolate cells or particles of interest","options":[{"value":"flow cytometric cell sorting","label":"flow cytometric cell sorting"},{"value":"lazer-tweezing","label":"lazer-tweezing"},{"value":"microfluidics","label":"microfluidics"},{"value":"micromanipulation","label":"micromanipulation"},{"value":"optical manipulation","label":"optical manipulation"},{"value":"other","label":"other"}],"group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"}]},{"name":"GSC MIUVIGS","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000049","category":"mixs","accession":"ERC000049","fields":[{"type":"select","label":"observed biotic relationship","name":"observed_biotic_relationship","required":false,"visible":true,"helpText":"Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.","options":[{"value":"commensal","label":"commensal"},{"value":"free living","label":"free living"},{"value":"mutualism","label":"mutualism"},{"value":"parasite","label":"parasite"},{"value":"symbiont","label":"symbiont"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"known pathogenicity","name":"known_pathogenicity","required":false,"visible":true,"helpText":"To what is the entity pathogenic, for instance plant, fungi, bacteria","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"metagenomic source","name":"metagenomic_source","required":true,"visible":true,"helpText":"The metagenomic source of the sample. This value should contain “metagenome” and be in the taxonomy database e.g. wastewater metagenome or human gut metagenome. Please note “metagenome” alone will not be accepted. Check here for more details on metagenome taxonomy: https://ena-docs.readthedocs.io/en/latest/faq_taxonomy.html#environmental-taxonomic-classifications","group":"sample collection: core sample properties"},{"type":"text","label":"sample derived from","name":"sample_derived_from","required":true,"visible":true,"helpText":"Reference to parental sample(s) or original run(s) that the assembly is derived from. The referenced samples or runs should already be registered in INSDC. This should be formatted as one of the following. A single sample/run e.g. ERSxxxxxx OR a comma separated list e.g. ERSxxxxxx,ERSxxxxxx OR a range e.g. ERSxxxxxx-ERSxxxxxx","simpleValidation":{"pattern":"(^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)","patternMessage":"Must match pattern: (^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)"},"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"estimated size","name":"estimated_size","required":false,"visible":true,"helpText":"The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"number of standard tRNAs extracted","name":"number_of_standard_trnas_extracted","required":false,"visible":true,"helpText":"The total number of tRNAs identified from the bin, SAG or MAG","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"non-sample terms"},{"type":"text","label":"feature prediction","name":"feature_prediction","required":false,"visible":true,"helpText":"Method used to predict UViGs features such as ORFs, integration site, etc. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"similarity search method","name":"similarity_search_method","required":false,"visible":true,"helpText":"Tool used to compare ORFs with database, along with version and cutoffs used. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"tRNA extraction software","name":"trna_extraction_software","required":false,"visible":true,"helpText":"Tools used for tRNA identification. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"completeness score","name":"completeness_score","required":false,"visible":true,"helpText":"Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. Completeness score is one of 3 attributes which in combination reflect the standard quality of a MAG, see here for more information: https://ena-docs.readthedocs.io/en/latest/faq_metagenomes.html. Mandatory for all samples directly linked with SAGs or MAGs.","simpleValidation":{"pattern":"^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$","patternMessage":"Must match pattern: ^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$"},"units":[{"value":"%","label":"%"}],"group":"non-sample terms"},{"type":"text","label":"completeness software","name":"completeness_software","required":false,"visible":true,"helpText":"Tools used for completion estimate, i.e. checkm, anvi'o, busco. Mandatory for all samples directly linked with SAGs or MAGs.","group":"non-sample terms"},{"type":"text","label":"completeness approach","name":"completeness_approach","required":false,"visible":true,"helpText":"The approach used to determine the completeness of a given bin, SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome","group":"non-sample terms"},{"type":"text","label":"binning software","name":"binning_software","required":false,"visible":true,"helpText":"Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used. E.g. MetaCluster-TA (RRID:SCR_004599) or MaxBin (biotools:maxbin)","group":"non-sample terms"},{"type":"select","label":"reassembly post binning","name":"reassembly_post_binning","required":false,"visible":true,"helpText":"Has an assembly been performed on a genome bin extracted from a metagenomic assembly?","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"units":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"non-sample terms"},{"type":"text","label":"MAG coverage software","name":"mag_coverage_software","required":false,"visible":true,"helpText":"Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets e.g. bwa, bbmap, bowtie, other","group":"non-sample terms"},{"type":"text","label":"binning parameters","name":"binning_parameters","required":false,"visible":true,"helpText":"The parameters that have been applied during the extraction of genomes from metagenomic datasets e.g. coverage and kmer","group":"non-sample terms"},{"type":"text","label":"taxonomic identity marker","name":"taxonomic_identity_marker","required":false,"visible":true,"helpText":"The phylogenetic marker(s) used to assign an organism name to the bin, SAG or MAG. Examples are 16S gene, multi-marker approach or other e.g. rpoB gene. Mandatory for all samples directly linked with SAGs or MAGs.","group":"non-sample terms"},{"type":"select","label":"source of UViGs","name":"source_of_uvigs","required":true,"visible":true,"helpText":"Type of dataset from which the UViG was obtained","options":[{"value":"isolate microbial genome","label":"isolate microbial genome"},{"value":"metagenome (not viral targeted)","label":"metagenome (not viral targeted)"},{"value":"metatranscriptome (not viral targeted)","label":"metatranscriptome (not viral targeted)"},{"value":"microbial single amplified genome (SAG)","label":"microbial single amplified genome (SAG)"},{"value":"other","label":"other"},{"value":"sequence-targeted RNA metagenome","label":"sequence-targeted RNA metagenome"},{"value":"sequence-targeted metagenome","label":"sequence-targeted metagenome"},{"value":"viral fraction RNA metagenome (RNA virome)","label":"viral fraction RNA metagenome (RNA virome)"},{"value":"viral fraction metagenome (virome)","label":"viral fraction metagenome (virome)"},{"value":"viral single amplified genome (vSAG)","label":"viral single amplified genome (vSAG)"}],"group":"non-sample terms"},{"type":"select","label":"predicted genome type","name":"predicted_genome_type","required":true,"visible":true,"helpText":"Type of genome predicted for the UViG","options":[{"value":"DNA","label":"DNA"},{"value":"RNA","label":"RNA"},{"value":"dsDNA","label":"dsDNA"},{"value":"dsRNA","label":"dsRNA"},{"value":"mixed","label":"mixed"},{"value":"ssDNA","label":"ssDNA"},{"value":"ssRNA","label":"ssRNA"},{"value":"ssRNA (+)","label":"ssRNA (+)"},{"value":"ssRNA (-)","label":"ssRNA (-)"},{"value":"uncharacterized","label":"uncharacterized"}],"group":"non-sample terms"},{"type":"select","label":"predicted genome structure","name":"predicted_genome_structure","required":true,"visible":true,"helpText":"Expected structure of the viral genome","options":[{"value":"non-segmented","label":"non-segmented"},{"value":"segmented","label":"segmented"},{"value":"undetermined","label":"undetermined"}],"group":"non-sample terms"},{"type":"select","label":"detection type","name":"detection_type","required":true,"visible":true,"helpText":"Type of UViG detection","options":[{"value":"independent sequence (UViG)","label":"independent sequence (UViG)"},{"value":"provirus (UpViG)","label":"provirus (UpViG)"}],"group":"non-sample terms"},{"type":"text","label":"viral identification software","name":"viral_identification_software","required":true,"visible":true,"helpText":"Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used formatted {software};{version};{parameters} e.g. VirSorter; 1.0.4; Virome database, category 2","group":"non-sample terms"},{"type":"text","label":"OTU classification approach","name":"otu_classification_approach","required":false,"visible":true,"helpText":"Cutoffs and approach used when clustering “species-level” OTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside OTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis. This should be formatted {ANI cutoff};{AF cutoff};{clustering method} e.g. 95% ANI;85% AF; greedy incremental clustering","group":"non-sample terms"},{"type":"text","label":"OTU sequence comparison approach","name":"otu_sequence_comparison_approach","required":false,"visible":true,"helpText":"Tool and thresholds used to compare sequences when computing \"species-level\" OTUs formatted: {software};{version};{parameters} e.g. gblastn;2.6.0+;e-value cutoff: 0.001","group":"non-sample terms"},{"type":"text","label":"OTU database","name":"otu_database","required":false,"visible":true,"helpText":"Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in \"species-level\" OTUs, if any. This should be formatted: {database};{version} e.g. NCBI Viral RefSeq;83","group":"non-sample terms"},{"type":"select","label":"UViG assembly quality","name":"uvig_assembly_quality","required":true,"visible":true,"helpText":"UViG assembly quality is one of 3 attributes which in combination reflect the standard quality of a UViG, see here for more information: https://ena-docs.readthedocs.io/en/latest/faq_metagenomes.html.","options":[{"value":"One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete","label":"One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete"},{"value":"One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated","label":"One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated"},{"value":"Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units","label":"Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units"}],"group":"non-sample terms"},{"type":"text","label":"isolation_source","name":"isolation_source","required":true,"visible":true,"helpText":"describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived","group":"Collection event information"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"m2","label":"m2"},{"value":"m3","label":"m3"},{"value":"g","label":"g"},{"value":"L","label":"L"},{"value":"kg","label":"kg"}],"group":"sample collection"},{"type":"text","label":"size fraction selected","name":"size_fraction_selected","required":false,"visible":true,"helpText":"Filtering pore size used in sample preparation e.g. 0-0.22 micrometer","group":"sample collection"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"select","label":"host prediction approach","name":"host_prediction_approach","required":false,"visible":true,"helpText":"Tool or approach used for host prediction","options":[{"value":"CRISPR spacer match","label":"CRISPR spacer match"},{"value":"co-occurrence","label":"co-occurrence"},{"value":"combination","label":"combination"},{"value":"host sequence similarity","label":"host sequence similarity"},{"value":"kmer similarity","label":"kmer similarity"},{"value":"other","label":"other"},{"value":"provirus","label":"provirus"}],"group":"host details"},{"type":"text","label":"host prediction estimated accuracy","name":"host_prediction_estimated_accuracy","required":false,"visible":true,"helpText":"For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature","group":"host details"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"reference database(s)","name":"reference_databases","required":false,"visible":true,"helpText":"List of database(s) used for ORF annotation, along with version number and reference to website or publication","group":"Reference"},{"type":"select","label":"single cell or viral particle lysis approach","name":"single_cell_or_viral_particle_lysis_approach","required":false,"visible":true,"helpText":"Method used to free DNA from interior of the cell(s) or particle(s)","options":[{"value":"chemical","label":"chemical"},{"value":"combination","label":"combination"},{"value":"enzymatic","label":"enzymatic"},{"value":"physical","label":"physical"}],"group":"sample processing"},{"type":"text","label":"single cell or viral particle lysis kit protocol","name":"single_cell_or_viral_particle_lysis_kit_protocol","required":false,"visible":true,"helpText":"Name of the kit or standard protocol used for cell(s) or particle(s) lysis","group":"sample processing"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"sample processing"},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"assembly software","name":"assembly_software","required":true,"visible":true,"helpText":"Tool(s) used for assembly, including version number and parameters in the format {software};{version};{parameters} e.g. metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise","group":"sample processing"},{"type":"select","label":"WGA amplification approach","name":"wga_amplification_approach","required":false,"visible":true,"helpText":"Method used to amplify genomic DNA in preparation for sequencing","options":[{"value":"mda based","label":"mda based"},{"value":"pcr based","label":"pcr based"}],"group":"sample processing"},{"type":"text","label":"WGA amplification kit","name":"wga_amplification_kit","required":false,"visible":true,"helpText":"Kit used to amplify genomic DNA in preparation for sequencing","group":"sample processing"},{"type":"select","label":"sorting technology","name":"sorting_technology","required":false,"visible":true,"helpText":"Method used to sort/isolate cells or particles of interest","options":[{"value":"flow cytometric cell sorting","label":"flow cytometric cell sorting"},{"value":"lazer-tweezing","label":"lazer-tweezing"},{"value":"microfluidics","label":"microfluidics"},{"value":"micromanipulation","label":"micromanipulation"},{"value":"optical manipulation","label":"optical manipulation"},{"value":"other","label":"other"}],"group":"sample processing"},{"type":"select","label":"virus enrichment approach","name":"virus_enrichment_approach","required":true,"visible":true,"helpText":"List of approaches used to enrich the sample for viruses, if any","options":[{"value":"CsCl density gradient","label":"CsCl density gradient"},{"value":"DNAse","label":"DNAse"},{"value":"FeCl Precipitation","label":"FeCl Precipitation"},{"value":"PEG Precipitation","label":"PEG Precipitation"},{"value":"RNAse","label":"RNAse"},{"value":"centrifugation","label":"centrifugation"},{"value":"filtration","label":"filtration"},{"value":"none","label":"none"},{"value":"other","label":"other"},{"value":"targeted sequence capture","label":"targeted sequence capture"},{"value":"ultracentrifugation","label":"ultracentrifugation"},{"value":"ultrafiltration","label":"ultrafiltration"}],"group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"}]},{"name":"ENA prokaryotic pathogen minimal sample checklist","description":"Minimum information required for a prokaryotic pathogen sample","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000028","category":"mixs","accession":"ERC000028","fields":[{"type":"text","label":"isolation_source","name":"isolation_source","required":true,"visible":true,"helpText":"describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived","group":"Collection event information"},{"type":"text","label":"lat_lon","name":"lat_lon","required":false,"visible":true,"helpText":"geographical coordinates of the location where the specimen was collected","group":"Collection event information"},{"type":"text","label":"collected_by","name":"collected_by","required":false,"visible":true,"helpText":"name of persons or institute who collected the specimen","group":"Collection event information"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"identified_by","name":"identified_by","required":false,"visible":true,"helpText":"name of the expert who identified the specimen taxonomically","group":"Collection event information"},{"type":"select","label":"environmental_sample","name":"environmental_sample","required":false,"visible":true,"helpText":"identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"group":"sample collection"},{"type":"text","label":"mating_type","name":"mating_type","required":false,"visible":true,"helpText":"mating type of the organism from which the sequence was obtained; mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"select","label":"host health state","name":"host_health_state","required":true,"visible":true,"helpText":"Health status of the host at the time of sample collection.","options":[{"value":"diseased","label":"diseased"},{"value":"healthy","label":"healthy"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"text","label":"lab_host","name":"lab_host","required":false,"visible":true,"helpText":"scientific name of the laboratory host used to propagate the source organism from which the sample was obtained","group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":true,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"bio_material","name":"bio_material","required":false,"visible":true,"helpText":"Unique identifier that references the biological material from which the sample was obtained and that ideally exists in a curated collection (e.g. stock centres, seed banks, DNA banks). The ID should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). Please note institution codes and collection codes are taken from a controlled vocabulary maintained by the INSDC: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/","group":"Pointer to physical material"},{"type":"text","label":"culture_collection","name":"culture_collection","required":false,"visible":true,"helpText":"Unique identifier that references the culture (e.g. live microbial and viral cultures and cell lines) from which the sample has been obtained and that have been deposited in curated culture collections. The ID needs to provide an institution code and the culture id, with optional collection code, in the following structure: (-institution_code:(collection_code):voucher_id. Please note institution codes (and optional collection codes) are taken from a controlled vocabulary maintained by the INSDC: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/","group":"Pointer to physical material"},{"type":"text","label":"specimen_voucher","name":"specimen_voucher","required":false,"visible":true,"helpText":"Unique identifier that references the physical specimen that remains after the sequence has been obtained and that ideally exists in a curated collection. The ID should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). Please note institution codes and collection codes are taken from a controlled vocabulary maintained by the INSDC: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/","group":"Pointer to physical material"},{"type":"text","label":"isolate","name":"isolate","required":true,"visible":true,"helpText":"individual isolate from which the sample was obtained","group":"Infraspecies information"},{"type":"text","label":"sub_species","name":"sub_species","required":false,"visible":true,"helpText":"name of sub-species of organism from which sample was obtained","group":"Infraspecies information"},{"type":"text","label":"sub_strain","name":"sub_strain","required":false,"visible":true,"helpText":"name or identifier of a genetically or otherwise modified strain from which sample was obtained, derived from a parental strain (which should be annotated in the strain field; sub_strain from which sample was obtained","group":"Infraspecies information"},{"type":"text","label":"serovar","name":"serovar","required":false,"visible":true,"helpText":"serological variety of a species (usually a prokaryote) characterized by its antigenic properties","group":"Infraspecies information"},{"type":"text","label":"strain","name":"strain","required":false,"visible":true,"helpText":"Name of the strain from which the sample was obtained.","group":"Infraspecies information"}]},{"name":"ENA Influenza virus reporting standard checklist","description":"Minimum information about an Influenza virus sample. A checklist for reporting metadata of Influenza virus samples associated with genomic data. This minimum metadata standard supports submission of avian, human and mammalian surveillance data as well as serology and viruse isolate information (where available). The ENA Influenza sample checklist is based on standards in use at the Influenza Research Database.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000032","category":"mixs","accession":"ERC000032","fields":[{"type":"text","label":"number of inoculated individuals","name":"number_of_inoculated_individuals","required":false,"visible":true,"helpText":"Number of host individuals inoculated for the experiment.","group":"Host inoculation"},{"type":"text","label":"inoculation route","name":"inoculation_route","required":false,"visible":true,"helpText":"Brief description of the protocol inoculation route.","group":"Host inoculation"},{"type":"text","label":"inoculation dose","name":"inoculation_dose","required":false,"visible":true,"helpText":"Dose used for the inoculoation experiment.","group":"Host inoculation"},{"type":"select","label":"inoculation stock availability","name":"inoculation_stock_availability","required":false,"visible":true,"helpText":"Is the virus stock used for the inoculation available?","options":[{"value":"no","label":"no"},{"value":"yes","label":"yes"}],"group":"Host inoculation"},{"type":"text","label":"sample storage conditions","name":"sample_storage_conditions","required":false,"visible":true,"helpText":"Conditions at which sample was stored, usually storage temperature, duration and location. In soil context: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"subject exposure","name":"subject_exposure","required":false,"visible":true,"helpText":"Exposure of the subject to infected human or animals, such as poultry, wild bird or swine. If multiple exposures are applicable, please state them separated by semicolon. Example: poultry; wild bird","group":"Human surveillance data"},{"type":"text","label":"type exposure","name":"type_exposure","required":false,"visible":true,"helpText":"Setting within which the subject is exposed to animals, such as farm, slaughterhouse, food preparation. If multiple exposures are applicable, please state their type in the same order in which you reported the exposure in the field 'subject exposure'. Example: backyard flock; confined animal feeding operation","group":"Human surveillance data"},{"type":"text","label":"personal protective equipment","name":"personal_protective_equipment","required":false,"visible":true,"helpText":"Use of personal protective equipment, such as gloves, gowns, during any type of exposure. Example: mask","group":"Human surveillance data"},{"type":"select","label":"hospitalisation","name":"hospitalisation","required":false,"visible":true,"helpText":"Was the subject confined to a hospital as a result of virus infection or problems occurring secondary to virus infection?","options":[{"value":"no","label":"no"},{"value":"yes","label":"yes"}],"group":"Human surveillance data"},{"type":"text","label":"antiviral treatment","name":"antiviral_treatment","required":false,"visible":true,"helpText":"Antiviral treatment used for this subject, such as Zanamavir Oseltamivir, Amantadine. Example: Rimantadine","group":"Human surveillance data"},{"type":"text","label":"antiviral treatment initiation","name":"antiviral_treatment_initiation","required":false,"visible":true,"helpText":"Initiation of antiviral treatment after onset of clinical symptoms in days. Example: 2.5","group":"Human surveillance data"},{"type":"text","label":"antiviral treatment dosage","name":"antiviral_treatment_dosage","required":false,"visible":true,"helpText":"Dosage of the treatment taken by the subject. Example: 0.05 mg","group":"Human surveillance data"},{"type":"text","label":"antiviral treatment duration","name":"antiviral_treatment_duration","required":false,"visible":true,"helpText":"Duration of antiviral treatment after onset of clinical symptoms in days.Example: 5","group":"Human surveillance data"},{"type":"text","label":"influenza vaccination type","name":"influenza_vaccination_type","required":false,"visible":true,"helpText":"Influenza vaccinations that have been administered to the subject over the last year. Example: 2009 H1N1 Flumist","group":"Human surveillance data"},{"type":"text","label":"influenza vaccination date","name":"influenza_vaccination_date","required":false,"visible":true,"helpText":"Date that the influenza vaccination was administered to the subject over the past year. Format: YYYY-MM-DD. Example: 2007-05-12","simpleValidation":{"pattern":"^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$","patternMessage":"Must match pattern: ^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$"},"group":"Human surveillance data"},{"type":"select","label":"source of vaccination information","name":"source_of_vaccination_information","required":false,"visible":true,"helpText":"Designation of information related to vaccination history as self reported or documented.","options":[{"value":"documented","label":"documented"},{"value":"self reported","label":"self reported"}],"group":"Human surveillance data"},{"type":"text","label":"vaccine lot number","name":"vaccine_lot_number","required":false,"visible":true,"helpText":"Lot number of the vaccine.","group":"Human surveillance data"},{"type":"text","label":"vaccine manufacturer","name":"vaccine_manufacturer","required":false,"visible":true,"helpText":"Manufacturer of the vaccine.","group":"Human surveillance data"},{"type":"text","label":"vaccine dosage","name":"vaccine_dosage","required":false,"visible":true,"helpText":"Dosage of the vaccine taken by the subject. Example: 0.05 mL","group":"Human surveillance data"},{"type":"select","label":"influenza-like illness at the time of sample collection","name":"influenzalike_illness_at_the_time_of_sample_collection","required":false,"visible":true,"helpText":"Is the subject at the time of sample collection considered to have influenza like illness?","options":[{"value":"no","label":"no"},{"value":"yes","label":"yes"}],"group":"Human surveillance data"},{"type":"text","label":"illness onset date","name":"illness_onset_date","required":false,"visible":true,"helpText":"Date the subject showed an onset of symptoms. Format: YYYY-MM-DD. Example: 2011-10-20","simpleValidation":{"pattern":"^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$","patternMessage":"Must match pattern: ^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$"},"group":"Human surveillance data"},{"type":"text","label":"illness duration","name":"illness_duration","required":false,"visible":true,"helpText":"The number of days the illness lasted. Example: 4","group":"Human surveillance data"},{"type":"text","label":"illness symptoms","name":"illness_symptoms","required":false,"visible":true,"helpText":"The symptoms that have been reported in relation to the illness, such as cough, diarrhea, fever, headache, malaise, myalgia, nausea, runny_nose, shortness_of_breath, sore_throat. If multiple exposures are applicable, please state them separated by semicolon.","group":"Human surveillance data"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"subject exposure duration","name":"subject_exposure_duration","required":false,"visible":true,"helpText":"Duration of the exposure of the subject to an infected human or animal. If multiple exposures are applicable, please state their duration in the same order in which you reported the exposure in the field 'subject exposure'. Example: 1 day; 0.33 days","units":[{"value":"week","label":"week"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"}],"group":"internal environment"},{"type":"select","label":"sample capture status","name":"sample_capture_status","required":false,"visible":true,"helpText":"Reason for the sample collection.","options":[{"value":"active surveillance in response to outbreak","label":"active surveillance in response to outbreak"},{"value":"active surveillance not initiated by an outbreak","label":"active surveillance not initiated by an outbreak"},{"value":"farm sample","label":"farm sample"},{"value":"market sample","label":"market sample"},{"value":"other","label":"other"},{"value":"pet sample","label":"pet sample"},{"value":"zoo sample","label":"zoo sample"}],"group":"sample collection"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"select","label":"host disease outcome","name":"host_disease_outcome","required":false,"visible":true,"helpText":"Disease outcome in the host.","options":[{"value":"dead","label":"dead"},{"value":"recovered","label":"recovered"},{"value":"recovered with sequelae","label":"recovered with sequelae"}],"group":"host disorder"},{"type":"text","label":"host common name","name":"host_common_name","required":true,"visible":true,"helpText":"common name of the host, e.g. human","group":"host description"},{"type":"text","label":"host subject id","name":"host_subject_id","required":true,"visible":true,"helpText":"a unique identifier by which each subject can be referred to, de-identified, e.g. #131","group":"host description"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"select","label":"host health state","name":"host_health_state","required":true,"visible":true,"helpText":"Health status of the host at the time of sample collection.","options":[{"value":"diseased","label":"diseased"},{"value":"healthy","label":"healthy"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"select","label":"host sex","name":"host_sex","required":true,"visible":true,"helpText":"Gender or sex of the host.","options":[{"value":"female","label":"female"},{"value":"hermaphrodite","label":"hermaphrodite"},{"value":"male","label":"male"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"neuter","label":"neuter"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"other","label":"other"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":true,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"influenza test method","name":"influenza_test_method","required":true,"visible":true,"helpText":"Method by which the current assessment of a sample as flu positive/negative is made. If multiple test were performed, please state them separated by semicolon. Example: RT-PCR; antigen ELISA","group":"Pathogen testing"},{"type":"text","label":"influenza test result","name":"influenza_test_result","required":true,"visible":true,"helpText":"Classification of a sample as flu positive or negative based on the test performed and reported. If multiple tests were performed, please state the results in the same order in which you reported the tests in the field 'influenza test method'. Format: P(ositive)/N(egative). Example: P; P","group":"Pathogen testing"},{"type":"text","label":"other pathogens tested","name":"other_pathogens_tested","required":true,"visible":true,"helpText":"Classification of pathogenic organisms other than influenza virus tested in the current assessment of a sample. If multiple tests were performed, please state them separated by semicolon. If no other pathogens test was performed, please state 'none'. Example: Newcastle","group":"Pathogen testing"},{"type":"text","label":"other pathogens test result","name":"other_pathogens_test_result","required":true,"visible":true,"helpText":"Classification of a sample as positive or negative based on the test performed and reported. If tests for multiple pathogenic organisms were performed, please state the results in the same order in which you reported the tests in the field 'other pathogens tested'. Format: P(ositive)/N(egative)/not applicable. Example: N","group":"Pathogen testing"},{"type":"select","label":"influenza virus type","name":"influenza_virus_type","required":false,"visible":true,"helpText":"One of the three influenza virus classification types.","options":[{"value":"A","label":"A"},{"value":"B","label":"B"},{"value":"C","label":"C"}],"group":"Virus isolate information"},{"type":"text","label":"virus identifier","name":"virus_identifier","required":false,"visible":true,"helpText":"Unique laboratory identifier assigned to the virus by the investigator. Strain name is not sufficient since it might not be unique due to various passsages of the same virus. Format: up to 50 alphanumeric characters","group":"Virus isolate information"},{"type":"text","label":"influenza strain unique number","name":"influenza_strain_unique_number","required":false,"visible":true,"helpText":"Unique number of the strain which is reported as a part of the influenza strain name, such as A/chicken/Fujian/411/2002(HxN1). Format: integer number, Example: 411","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"},"group":"Virus isolate information"},{"type":"text","label":"WHO/OIE/FAO clade (required for HPAI H5N1 viruses)","name":"whooiefao_clade_required_for_hpai_h5n1_viruses","required":false,"visible":true,"helpText":"WHO/OIE/FAO clade should be included for highly pathogenic H5N1 viruses. Example: 2.2","group":"Virus isolate information"},{"type":"select","label":"lineage:swl (required for H1N1 viruses)","name":"lineageswl_required_for_h1n1_viruses","required":false,"visible":true,"helpText":"Does the H1N1 influenza virus originate from a swine-like outbreak (as opposed to a seasonal flu)?","options":[{"value":"no","label":"no"},{"value":"yes","label":"yes"}],"group":"Virus isolate information"},{"type":"text","label":"collector name","name":"collector_name","required":true,"visible":true,"helpText":"Name of the person who collected the specimen. Example: John Smith","group":"General collection event information"},{"type":"text","label":"collecting institution","name":"collecting_institution","required":true,"visible":true,"helpText":"Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address","group":"General collection event information"},{"type":"text","label":"receipt date","name":"receipt_date","required":false,"visible":true,"helpText":"Date on which the sample was received. Format:YYYY-MM-DD. Please provide the highest precision possible. If the sample was received by the institution and not collected, the 'receipt date' must be provided instead. Either the 'collection date' or 'receipt date' must be provided. If available, provide both dates.","simpleValidation":{"pattern":"^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$","patternMessage":"Must match pattern: ^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$"},"group":"General collection event information"},{"type":"text","label":"definition for seropositive sample","name":"definition_for_seropositive_sample","required":false,"visible":true,"helpText":"The cut off value used by an investigatior in determining that a sample was seropositive.","group":"Serology detection"},{"type":"text","label":"meaning of cut off value","name":"meaning_of_cut_off_value","required":false,"visible":true,"helpText":"Description helping to explain what the cut off value means.","group":"Serology detection"},{"type":"text","label":"serotype (required for a seropositive sample)","name":"serotype_required_for_a_seropositive_sample","required":false,"visible":true,"helpText":"Serological variety of a species characterised by its antigenic properties. For Influenza, HA subtype should be the letter H followed by a number between 1-16 unless novel subtype is identified and the NA subtype should be the letter N followed by a number between 1-9 unless novel subtype is identified. If only one of the subtypes have been tested then use the format H5Nx or HxN1. Example: H1N1","group":"Serology detection"},{"type":"text","label":"strain","name":"strain","required":false,"visible":true,"helpText":"Name of the strain from which the sample was obtained.","group":"Infraspecies information"},{"type":"select","label":"host habitat","name":"host_habitat","required":false,"visible":true,"helpText":"Natural habitat of the avian or mammalian host.","options":[{"value":"domestic:free-range farm","label":"domestic:free-range farm"},{"value":"domestic:indoor farm","label":"domestic:indoor farm"},{"value":"domestic:live market","label":"domestic:live market"},{"value":"domestic:semi-enclosed housing","label":"domestic:semi-enclosed housing"},{"value":"other","label":"other"},{"value":"wild:migratory","label":"wild:migratory"},{"value":"wild:resident","label":"wild:resident"}],"group":"Associated host information"},{"type":"text","label":"isolation source host-associated","name":"isolation_source_hostassociated","required":false,"visible":true,"helpText":"Name of host tissue or organ sampled for analysis. Example: tracheal tissue","group":"Associated host information"},{"type":"text","label":"host description","name":"host_description","required":false,"visible":true,"helpText":"Other descriptive information relating to the host.","group":"Associated host information"},{"type":"text","label":"gravidity","name":"gravidity","required":false,"visible":true,"helpText":"Whether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.","group":"host details"},{"type":"select","label":"host behaviour","name":"host_behaviour","required":false,"visible":true,"helpText":"Natural behaviour of the host.","options":[{"value":"captive-wild (e.g. at zoo)","label":"captive-wild (e.g. at zoo)"},{"value":"domestic","label":"domestic"},{"value":"other","label":"other"},{"value":"wild","label":"wild"}],"group":"host details"},{"type":"text","label":"isolation source non-host-associated","name":"isolation_source_nonhostassociated","required":false,"visible":true,"helpText":"Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. Example: soil","group":"Environmental information"}]},{"name":"ENA virus pathogen reporting standard checklist","description":"Minimum information about a virus pathogen. A checklist for reporting metadata of virus pathogen samples associated with genomic data. This minimum metadata standard was developed by the COMPARE platform for submission of virus surveillance and outbreak data (such as Ebola) as well as virus isolate information.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000033","category":"mixs","accession":"ERC000033","fields":[{"type":"text","label":"sample storage conditions","name":"sample_storage_conditions","required":false,"visible":true,"helpText":"Conditions at which sample was stored, usually storage temperature, duration and location. In soil context: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"subject exposure","name":"subject_exposure","required":false,"visible":true,"helpText":"Exposure of the subject to infected human or animals, such as poultry, wild bird or swine. If multiple exposures are applicable, please state them separated by semicolon. Example: poultry; wild bird","group":"Human surveillance data"},{"type":"text","label":"type exposure","name":"type_exposure","required":false,"visible":true,"helpText":"Setting within which the subject is exposed to animals, such as farm, slaughterhouse, food preparation. If multiple exposures are applicable, please state their type in the same order in which you reported the exposure in the field 'subject exposure'. Example: backyard flock; confined animal feeding operation","group":"Human surveillance data"},{"type":"text","label":"personal protective equipment","name":"personal_protective_equipment","required":false,"visible":true,"helpText":"Use of personal protective equipment, such as gloves, gowns, during any type of exposure. Example: mask","group":"Human surveillance data"},{"type":"select","label":"hospitalisation","name":"hospitalisation","required":false,"visible":true,"helpText":"Was the subject confined to a hospital as a result of virus infection or problems occurring secondary to virus infection?","options":[{"value":"no","label":"no"},{"value":"yes","label":"yes"}],"group":"Human surveillance data"},{"type":"text","label":"illness duration","name":"illness_duration","required":false,"visible":true,"helpText":"The number of days the illness lasted. Example: 4","group":"Human surveillance data"},{"type":"text","label":"illness symptoms","name":"illness_symptoms","required":false,"visible":true,"helpText":"The symptoms that have been reported in relation to the illness, such as cough, diarrhea, fever, headache, malaise, myalgia, nausea, runny_nose, shortness_of_breath, sore_throat. If multiple exposures are applicable, please state them separated by semicolon.","group":"Human surveillance data"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"subject exposure duration","name":"subject_exposure_duration","required":false,"visible":true,"helpText":"Duration of the exposure of the subject to an infected human or animal. If multiple exposures are applicable, please state their duration in the same order in which you reported the exposure in the field 'subject exposure'. Example: 1 day; 0.33 days","units":[{"value":"week","label":"week"},{"value":"month","label":"month"},{"value":"year","label":"year"},{"value":"day","label":"day"}],"group":"internal environment"},{"type":"select","label":"sample capture status","name":"sample_capture_status","required":false,"visible":true,"helpText":"Reason for the sample collection.","options":[{"value":"active surveillance in response to outbreak","label":"active surveillance in response to outbreak"},{"value":"active surveillance not initiated by an outbreak","label":"active surveillance not initiated by an outbreak"},{"value":"farm sample","label":"farm sample"},{"value":"market sample","label":"market sample"},{"value":"other","label":"other"},{"value":"pet sample","label":"pet sample"},{"value":"zoo sample","label":"zoo sample"}],"group":"sample collection"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"select","label":"host disease outcome","name":"host_disease_outcome","required":false,"visible":true,"helpText":"Disease outcome in the host.","options":[{"value":"dead","label":"dead"},{"value":"recovered","label":"recovered"},{"value":"recovered with sequelae","label":"recovered with sequelae"}],"group":"host disorder"},{"type":"text","label":"host common name","name":"host_common_name","required":true,"visible":true,"helpText":"common name of the host, e.g. human","group":"host description"},{"type":"text","label":"host subject id","name":"host_subject_id","required":true,"visible":true,"helpText":"a unique identifier by which each subject can be referred to, de-identified, e.g. #131","group":"host description"},{"type":"text","label":"host age","name":"host_age","required":false,"visible":true,"helpText":"age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"centuries","label":"centuries"},{"value":"hours","label":"hours"},{"value":"seconds","label":"seconds"},{"value":"months","label":"months"},{"value":"weeks","label":"weeks"},{"value":"minutes","label":"minutes"},{"value":"days","label":"days"},{"value":"decades","label":"decades"},{"value":"years","label":"years"}],"group":"host description"},{"type":"select","label":"host health state","name":"host_health_state","required":true,"visible":true,"helpText":"Health status of the host at the time of sample collection.","options":[{"value":"diseased","label":"diseased"},{"value":"healthy","label":"healthy"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"select","label":"host sex","name":"host_sex","required":true,"visible":true,"helpText":"Gender or sex of the host.","options":[{"value":"female","label":"female"},{"value":"hermaphrodite","label":"hermaphrodite"},{"value":"male","label":"male"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"neuter","label":"neuter"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"other","label":"other"},{"value":"restricted access","label":"restricted access"}],"group":"host description"},{"type":"text","label":"lab_host","name":"lab_host","required":false,"visible":true,"helpText":"scientific name of the laboratory host used to propagate the source organism from which the sample was obtained","group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":true,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"virus identifier","name":"virus_identifier","required":false,"visible":true,"helpText":"Unique laboratory identifier assigned to the virus by the investigator. Strain name is not sufficient since it might not be unique due to various passsages of the same virus. Format: up to 50 alphanumeric characters","group":"Virus isolate information"},{"type":"text","label":"collector name","name":"collector_name","required":true,"visible":true,"helpText":"Name of the person who collected the specimen. Example: John Smith","group":"General collection event information"},{"type":"text","label":"collecting institution","name":"collecting_institution","required":true,"visible":true,"helpText":"Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address","group":"General collection event information"},{"type":"text","label":"receipt date","name":"receipt_date","required":false,"visible":true,"helpText":"Date on which the sample was received. Format:YYYY-MM-DD. Please provide the highest precision possible. If the sample was received by the institution and not collected, the 'receipt date' must be provided instead. Either the 'collection date' or 'receipt date' must be provided. If available, provide both dates.","simpleValidation":{"pattern":"^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$","patternMessage":"Must match pattern: ^[0-9]{4}(-[0-9]{2}(-[0-9]{2})?)?$"},"group":"General collection event information"},{"type":"text","label":"definition for seropositive sample","name":"definition_for_seropositive_sample","required":false,"visible":true,"helpText":"The cut off value used by an investigatior in determining that a sample was seropositive.","group":"Serology detection"},{"type":"text","label":"serotype (required for a seropositive sample)","name":"serotype_required_for_a_seropositive_sample","required":false,"visible":true,"helpText":"Serological variety of a species characterised by its antigenic properties. For Influenza, HA subtype should be the letter H followed by a number between 1-16 unless novel subtype is identified and the NA subtype should be the letter N followed by a number between 1-9 unless novel subtype is identified. If only one of the subtypes have been tested then use the format H5Nx or HxN1. Example: H1N1","group":"Serology detection"},{"type":"text","label":"isolate","name":"isolate","required":true,"visible":true,"helpText":"individual isolate from which the sample was obtained","group":"Infraspecies information"},{"type":"text","label":"strain","name":"strain","required":false,"visible":true,"helpText":"Name of the strain from which the sample was obtained.","group":"Infraspecies information"},{"type":"select","label":"host habitat","name":"host_habitat","required":false,"visible":true,"helpText":"Natural habitat of the avian or mammalian host.","options":[{"value":"domestic:free-range farm","label":"domestic:free-range farm"},{"value":"domestic:indoor farm","label":"domestic:indoor farm"},{"value":"domestic:live market","label":"domestic:live market"},{"value":"domestic:semi-enclosed housing","label":"domestic:semi-enclosed housing"},{"value":"other","label":"other"},{"value":"wild:migratory","label":"wild:migratory"},{"value":"wild:resident","label":"wild:resident"}],"group":"Associated host information"},{"type":"text","label":"isolation source host-associated","name":"isolation_source_hostassociated","required":false,"visible":true,"helpText":"Name of host tissue or organ sampled for analysis. Example: tracheal tissue","group":"Associated host information"},{"type":"text","label":"host description","name":"host_description","required":false,"visible":true,"helpText":"Other descriptive information relating to the host.","group":"Associated host information"},{"type":"text","label":"gravidity","name":"gravidity","required":false,"visible":true,"helpText":"Whether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.","group":"host details"},{"type":"select","label":"host behaviour","name":"host_behaviour","required":false,"visible":true,"helpText":"Natural behaviour of the host.","options":[{"value":"captive-wild (e.g. at zoo)","label":"captive-wild (e.g. at zoo)"},{"value":"domestic","label":"domestic"},{"value":"other","label":"other"},{"value":"wild","label":"wild"}],"group":"host details"},{"type":"text","label":"isolation source non-host-associated","name":"isolation_source_nonhostassociated","required":false,"visible":true,"helpText":"Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. Example: soil","group":"Environmental information"}]},{"name":"ENA Tara Oceans","description":"Minimum information about a Tara Oceans sample. A checklist for reporting metadata of oceanic plankton samples associated with genomics data from the Tara Oceans Expedition.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000030","category":"mixs","accession":"ERC000030","fields":[{"type":"text","label":"event label","name":"event_label","required":false,"visible":true,"helpText":"An Event corresponds to the deployment of a sampling device. It is bound in space and time. The Event Label is a unique identifier composed of the project prefix \"TARA\", sampling date/time \"yyyymmddThh:mm:ssZ\", station number \"000\" and a short label to indicate the sampling device used, e.g. \"EVENT_CAST\", \"EVENT_NET\", \"EVENT_PUMP\". Example: TARA_20110416T1508Z_100_EVENT_CAST.","group":"Marine Event"},{"type":"text","label":"Event Date/Time Start","name":"event_datetime_start","required":false,"visible":true,"helpText":"Date and time in UTC when the sampling event started, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: yyyy-mm-ddThh:mm:ssZ. Example: 2011-04-16T15:05:30Z.","simpleValidation":{"pattern":"^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?$","patternMessage":"Must match pattern: ^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?$"},"group":"Marine Event"},{"type":"text","label":"Event Date/Time End","name":"event_datetime_end","required":false,"visible":true,"helpText":"Date and time in UTC when the sampling event ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: yyyy-mm-ddThh:mm:ssZ. Example: 2011-04-16T15:38:00Z.","simpleValidation":{"pattern":"^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?$","patternMessage":"Must match pattern: ^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?$"},"group":"Marine Event"},{"type":"text","label":"Latitude Start","name":"latitude_start","required":true,"visible":true,"helpText":"Latitude of the location where the sampling event started, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ##.####, Decimal degrees; North= +, South= -; Use WGS 84 for GPS data. Example: -24.6666.","simpleValidation":{"pattern":"[+-]?[0-9]+.?[0-9]*","patternMessage":"Must match pattern: [+-]?[0-9]+.?[0-9]*"},"units":[{"value":"DD","label":"DD"}],"group":"Marine Event"},{"type":"text","label":"Longitude Start","name":"longitude_start","required":true,"visible":true,"helpText":"Longitude of the location where the sampling event started, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ###.####, Decimal degrees; East= +, West= -; Use WGS 84 for GPS data. Example: -096.1012.","simpleValidation":{"pattern":"[+-]?[0-9]+.?[0-9]*","patternMessage":"Must match pattern: [+-]?[0-9]+.?[0-9]*"},"units":[{"value":"DD","label":"DD"}],"group":"Marine Event"},{"type":"text","label":"Latitude End","name":"latitude_end","required":false,"visible":true,"helpText":"Latitude of the location where the sampling event ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ##.####, Decimal degrees; North= +, South= -; Use WGS 84 for GPS data. Example: -24.6643.","simpleValidation":{"pattern":"[+-]?[0-9]+.?[0-9]*","patternMessage":"Must match pattern: [+-]?[0-9]+.?[0-9]*"},"units":[{"value":"DD","label":"DD"}],"group":"Marine Event"},{"type":"text","label":"Longitude End","name":"longitude_end","required":false,"visible":true,"helpText":"Longitude of the location where the sampling event ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ###.####, Decimal degrees; East= +, West= -; Use WGS 84 for GPS data. Example: -096.1171.","simpleValidation":{"pattern":"[+-]?[0-9]+.?[0-9]*","patternMessage":"Must match pattern: [+-]?[0-9]+.?[0-9]*"},"units":[{"value":"DD","label":"DD"}],"group":"Marine Event"},{"type":"text","label":"Protocol Label","name":"protocol_label","required":true,"visible":true,"helpText":"Identifies the protocol used to produce the sample, e.g. filtration and preservation. Example: BACT_NUC_W0.22-1.6.","group":"Marine Sample"},{"type":"text","label":"Sample Status","name":"sample_status","required":false,"visible":true,"helpText":"Refers to the completness of sample metadata validation. Example: preliminary but can be used to provide data discovery services.","group":"Marine Sample"},{"type":"text","label":"Last Update Date","name":"last_update_date","required":false,"visible":true,"helpText":"Date of the last update of this sample in the SAMPLES REGISTRY. Example: 2014-03-01Z.","group":"Marine Sample"},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample storage device","name":"sample_storage_device","required":false,"visible":true,"helpText":"The container used to store the sample. This field accepts terms listed under container (http://purl.obolibrary.org/obo/NCIT_C43186). If the proper descriptor is not listed please use text to describe the storage device.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"size-fraction lower threshold","name":"sizefraction_lower_threshold","required":false,"visible":true,"helpText":"Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)"},"units":[{"value":"mm","label":"mm"},{"value":"µm","label":"µm"},{"value":"nm","label":"nm"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"size-fraction upper threshold","name":"sizefraction_upper_threshold","required":false,"visible":true,"helpText":"Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mm","label":"mm"},{"value":"µm","label":"µm"},{"value":"nm","label":"nm"}],"group":"sample collection: methods, storage and transport"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"select","label":"environmental package","name":"environmental_package","required":true,"visible":true,"helpText":"MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported","options":[{"value":"water","label":"water"}],"group":"Collection event information"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broadscale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"Sampling Campaign","name":"sampling_campaign","required":true,"visible":true,"helpText":"Refers to a finite or indefinite activity aiming at collecting data/samples, e.g. a cruise, a time series, a mesocosm experiment. Example: TARA_20110401Z.","group":"Marine Sampling"},{"type":"text","label":"Sampling Station","name":"sampling_station","required":true,"visible":true,"helpText":"Refers to the site/station where data/sample collection is performed. Example: TARA_100.","group":"Marine Sampling"},{"type":"text","label":"Sampling Platform","name":"sampling_platform","required":true,"visible":true,"helpText":"Refers to the unique stage from which the sampling device has been deployed. Includes Platform category from SDN:L06, http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=L06, and Platform name. Example: Research Vessel Tara.","group":"Marine Sampling"},{"type":"text","label":"Marine Region","name":"marine_region","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by the marine region name chosen from the Marine Regions vocabulary at http://www.marineregions.org/. Example: Aegean Sea.","group":"Marine Environment"},{"type":"text","label":"Salinity Sensor","name":"salinity_sensor","required":true,"visible":true,"helpText":"Salinity of water at the time of taking the sample. Format: ##.####, SDN:P02:75:PSAL, SDN:P06:46:UGKG for PSU. Example: 39.2268.","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"psu","label":"psu"}],"group":"Marine Environment"},{"type":"text","label":"Oxygen Sensor","name":"oxygen_sensor","required":false,"visible":true,"helpText":"Oxygen concentration parameters in the water column measured in volts and converted to micromoles per kilogrammes. Format: ###.####, SDN:P02:75:DOXY, SDN:P06:46:KGUM for µmol/kg. Example: 217.7895.","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/kg","label":"µmol/kg"}],"group":"Marine Environment"},{"type":"text","label":"Nitrate Sensor","name":"nitrate_sensor","required":false,"visible":true,"helpText":"Nitrate concentration parameters in the water column measured in volts and converted to micromoles per litres. Format: ##.####, SDN:P02:75:NTRA, SDN:P06:46:UPOX for µmol/L. Example: 0.2259.","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"µmol/L","label":"µmol/L"}],"group":"Marine Environment"},{"type":"text","label":"water temperature","name":"water_temperature","required":true,"visible":true,"helpText":"Temperature of water at the time of taking the sample. Format: ##.####, SDN:P02:75:TEMP, SDN:P06:46:UPAA for °C. Example: 17.7122.","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"ºC","label":"ºC"}],"group":"Marine Environment"},{"type":"text","label":"Chlorophyll Sensor","name":"chlorophyll_sensor","required":false,"visible":true,"helpText":"Fluorescence of the water measured in volts and converted to milligrammes of chlorophyll per cubic metre. Format: ##.####, SDN:P02:75:CPWC, SDN:P06:46:UMMC for mg Chl/m3. Example: 0.066.","simpleValidation":{"pattern":"[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: [+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"mg Chl/m3","label":"mg Chl/m3"}],"group":"Marine Environment"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"Citation","name":"citation","required":false,"visible":true,"helpText":"Citation of the Sample Registry (HTML version) at the PANGAEA. Example: doi.pangaea.de/10.1594/PANGAEA.76752.","group":"Reference"},{"type":"text","label":"Further Details","name":"further_details","required":false,"visible":true,"helpText":"Reference details related to a sample in form of an URI.","group":"Reference"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"}]},{"name":"Tree of Life Checklist","description":"Minimum information required for reporting samples associated with the Tree of Life Programme (https://www.sanger.ac.uk/programme/tree-of-life/).","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000053","category":"mixs","accession":"ERC000053","fields":[{"type":"text","label":"Latitude Start","name":"latitude_start","required":false,"visible":true,"helpText":"Latitude of the location where the sampling event started, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ##.####, Decimal degrees; North= +, South= -; Use WGS 84 for GPS data. Example: -24.6666.","simpleValidation":{"pattern":"[+-]?[0-9]+.?[0-9]*","patternMessage":"Must match pattern: [+-]?[0-9]+.?[0-9]*"},"units":[{"value":"DD","label":"DD"}],"group":"Marine Event"},{"type":"text","label":"Longitude Start","name":"longitude_start","required":false,"visible":true,"helpText":"Longitude of the location where the sampling event started, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ###.####, Decimal degrees; East= +, West= -; Use WGS 84 for GPS data. Example: -096.1012.","simpleValidation":{"pattern":"[+-]?[0-9]+.?[0-9]*","patternMessage":"Must match pattern: [+-]?[0-9]+.?[0-9]*"},"units":[{"value":"DD","label":"DD"}],"group":"Marine Event"},{"type":"text","label":"Latitude End","name":"latitude_end","required":false,"visible":true,"helpText":"Latitude of the location where the sampling event ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ##.####, Decimal degrees; North= +, South= -; Use WGS 84 for GPS data. Example: -24.6643.","simpleValidation":{"pattern":"[+-]?[0-9]+.?[0-9]*","patternMessage":"Must match pattern: [+-]?[0-9]+.?[0-9]*"},"units":[{"value":"DD","label":"DD"}],"group":"Marine Event"},{"type":"text","label":"Longitude End","name":"longitude_end","required":false,"visible":true,"helpText":"Longitude of the location where the sampling event ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event. Format: ###.####, Decimal degrees; East= +, West= -; Use WGS 84 for GPS data. Example: -096.1171.","simpleValidation":{"pattern":"[+-]?[0-9]+.?[0-9]*","patternMessage":"Must match pattern: [+-]?[0-9]+.?[0-9]*"},"units":[{"value":"DD","label":"DD"}],"group":"Marine Event"},{"type":"text","label":"organism part","name":"organism_part","required":true,"visible":true,"helpText":"The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells.","group":"Part and developmental stage of organism"},{"type":"select","label":"lifestage","name":"lifestage","required":true,"visible":true,"helpText":"the age class or life stage of the organism at the time of collection.","options":[{"value":"adult","label":"adult"},{"value":"egg","label":"egg"},{"value":"embryo","label":"embryo"},{"value":"gametophyte","label":"gametophyte"},{"value":"juvenile","label":"juvenile"},{"value":"larva","label":"larva"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"pupa","label":"pupa"},{"value":"spore-bearing structure","label":"spore-bearing structure"},{"value":"sporophyte","label":"sporophyte"},{"value":"vegetative cell","label":"vegetative cell"},{"value":"vegetative structure","label":"vegetative structure"},{"value":"zygote","label":"zygote"}],"group":"Part and developmental stage of organism"},{"type":"text","label":"relationship","name":"relationship","required":false,"visible":true,"helpText":"indicates if the specimen has a known relationship to another specimen (e.g. parental, child, sibling or other kind of relationship)","group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample symbiont of","name":"sample_symbiont_of","required":false,"visible":true,"helpText":"Reference to host sample from symbiont. The referenced sample should already be registered in INSDC. E.g. ERSxxxxxx","simpleValidation":{"pattern":"(^[ESD]RS\\d{6,}$)|(^SAM[END][AG]?\\d+$)|(^EGAN\\d{11}$)","patternMessage":"Must match pattern: (^[ESD]RS\\d{6,}$)|(^SAM[END][AG]?\\d+$)|(^EGAN\\d{11}$)"},"group":"Organism characteristics: ecosystem"},{"type":"select","label":"symbiont","name":"symbiont","required":false,"visible":true,"helpText":"Used to separate host and symbiont metadata within a symbiont system where the host species are indicated as 'N' and symbionts are indicated as 'Y'","options":[{"value":"N","label":"N"},{"value":"Y","label":"Y"}],"group":"Organism characteristics: ecosystem"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample coordinator affiliation","name":"sample_coordinator_affiliation","required":false,"visible":true,"helpText":"The university, institution, or society affiliation of the sample coordinator.","group":"sample collection: site related"},{"type":"text","label":"sample same as","name":"sample_same_as","required":false,"visible":true,"helpText":"Reference to sample(s) that are equivalent. The referenced sample(s) should already be registered in INSDC. This should be formatted as one of the following. A single sample e.g. ERSxxxxxx OR a comma separated list e.g. ERSxxxxxx,ERSxxxxxx","simpleValidation":{"pattern":"(^[ESD]RS\\d{6,}(,[ESD]RS\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGAN\\d{11}(,EGAN\\d{11})*$)","patternMessage":"Must match pattern: (^[ESD]RS\\d{6,}(,[ESD]RS\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGAN\\d{11}(,EGAN\\d{11})*$)"},"group":"sample collection: core sample properties"},{"type":"text","label":"sample derived from","name":"sample_derived_from","required":false,"visible":true,"helpText":"Reference to parental sample(s) or original run(s) that the assembly is derived from. The referenced samples or runs should already be registered in INSDC. This should be formatted as one of the following. A single sample/run e.g. ERSxxxxxx OR a comma separated list e.g. ERSxxxxxx,ERSxxxxxx OR a range e.g. ERSxxxxxx-ERSxxxxxx","simpleValidation":{"pattern":"(^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)","patternMessage":"Must match pattern: (^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)"},"group":"sample collection: core sample properties"},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"barcoding center","name":"barcoding_center","required":false,"visible":true,"helpText":"Center where DNA barcoding was/will be performed.","group":"non-sample terms"},{"type":"text","label":"tolid","name":"tolid","required":false,"visible":true,"helpText":"A ToLID (Tree of Life ID) is a unique and easy to communicate sample identifier that provides species recognition, differentiates between specimen of the same species and adds taxonomic context. ToLIDs are issued by id.tol.sanger.ac.uk. They are endorsed by the EarthBioGenome Project (EBP) and should be assigned to any sample with association to the EBP.","group":"non-sample terms"},{"type":"text","label":"collected_by","name":"collected_by","required":true,"visible":true,"helpText":"name of persons or institute who collected the specimen","group":"Collection event information"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"group":"Collection event information"},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"identified_by","name":"identified_by","required":false,"visible":true,"helpText":"name of the expert who identified the specimen taxonomically","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}],"group":"Collection event information"},{"type":"text","label":"habitat","name":"habitat","required":true,"visible":true,"helpText":"description of the location of the sample material. please use EnvO terms where possible: https://www.ebi.ac.uk/ols/ontologies/envo","group":"Collection event information"},{"type":"text","label":"identifier_affiliation","name":"identifier_affiliation","required":false,"visible":true,"helpText":"the university, institution, or society responsible for identifying the specimen.","group":"Collection event information"},{"type":"text","label":"original collection date","name":"original_collection_date","required":false,"visible":true,"helpText":"For use if the specimen is from a zoo, botanic garden, culture collection etc. and has a known original date of collection. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","simpleValidation":{"pattern":"^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$","patternMessage":"Must match pattern: ^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$"},"group":"Collection event information"},{"type":"text","label":"original geographic location","name":"original_geographic_location","required":false,"visible":true,"helpText":"For use if the specimen is from a zoo, botanic garden or culture collection etc. and has a known origin elsewhere. Please record the general description of the original collection location. This should be formatted as a country and optionally include more specific locations ranging from least to most specific separated by a | character, e.g. “United Kingdom | East Anglia | Norfolk | Norwich | University of East Anglia | UEA Broad\".","group":"Collection event information"},{"type":"text","label":"original geographic location (latitude)","name":"original_geographic_location_latitude","required":false,"visible":true,"helpText":"For use if the specimen is from a zoo, botanic garden or culture collection etc. and has a known origin elsewhere. Please record the geographic location where the specimen or sample was originally taken as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"original geographic location (longitude)","name":"original_geographic_location_longitude","required":false,"visible":true,"helpText":"For use if the specimen is from a zoo, botanic garden or culture collection etc. and has a known origin elsewhere. Please record the geographic location where the specimen or sample was originally taken as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)"},"units":[{"value":"DD","label":"DD"}],"group":"Collection event information"},{"type":"text","label":"sample coordinator","name":"sample_coordinator","required":false,"visible":true,"helpText":"The name of the sample coordinator.","group":"sample collection"},{"type":"text","label":"sex","name":"sex","required":true,"visible":true,"helpText":"sex of the organism from which the sample was obtained","group":"Organism characteristics"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_andor_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d'Ivoire","label":"Cote d'Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Eswatini","label":"Eswatini"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Line Islands","label":"Line Islands"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia, Federated States of","label":"Micronesia, Federated States of"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Macedonia","label":"North Macedonia"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Barthelemy","label":"Saint Barthelemy"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Saint Martin","label":"Saint Martin"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"South Sudan","label":"South Sudan"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"State of Palestine","label":"State of Palestine"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Timor-Leste","label":"Timor-Leste"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Wake Island","label":"Wake Island"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}],"group":"Organism characteristics"},{"type":"text","label":"collecting institution","name":"collecting_institution","required":true,"visible":true,"helpText":"Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address","group":"General collection event information"},{"type":"select","label":"GAL","name":"gal","required":false,"visible":true,"helpText":"the name (or acronym) of the genome acquisition lab responsible for the sample.","options":[{"value":"Australian Genomic Research Facility","label":"Australian Genomic Research Facility"},{"value":"Biology Centre of the Academy of Sciences of the Czech Republic","label":"Biology Centre of the Academy of Sciences of the Czech Republic"},{"value":"Biomolecular Research Facility, Australian National University","label":"Biomolecular Research Facility, Australian National University"},{"value":"Centro Nacional de Análisis Genómico","label":"Centro Nacional de Análisis Genómico"},{"value":"DNA Sequencing and Genomics Laboratory, Helsinki Genomics Core Facility","label":"DNA Sequencing and Genomics Laboratory, Helsinki Genomics Core Facility"},{"value":"Dalhousie University","label":"Dalhousie University"},{"value":"Dresden-concept","label":"Dresden-concept"},{"value":"Earlham Institute","label":"Earlham Institute"},{"value":"Functional Genomics Center Zurich","label":"Functional Genomics Center Zurich"},{"value":"GIGA-Genomics Core Facility, University of Liege","label":"GIGA-Genomics Core Facility, University of Liege"},{"value":"Genomics Western Australia, University of Western Australia","label":"Genomics Western Australia, University of Western Australia"},{"value":"Genoscope","label":"Genoscope"},{"value":"Geomar Helmholtz Centre","label":"Geomar Helmholtz Centre"},{"value":"Grigore Antipa National Museum of Natural History","label":"Grigore Antipa National Museum of Natural History"},{"value":"Hansen Lab, Denmark","label":"Hansen Lab, Denmark"},{"value":"Institut de Biologia Evolutiva, CSIC-UPF","label":"Institut de Biologia Evolutiva, CSIC-UPF"},{"value":"Lausanne Genomic Technologies Facility","label":"Lausanne Genomic Technologies Facility"},{"value":"Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn","label":"Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn"},{"value":"Lund University","label":"Lund University"},{"value":"Marine Biological Association","label":"Marine Biological Association"},{"value":"NGS Bern","label":"NGS Bern"},{"value":"NGS Competence Center Tübingen","label":"NGS Competence Center Tübingen"},{"value":"Natural History Museum","label":"Natural History Museum"},{"value":"Neuromics Support Facility, UAntwerp, VIB","label":"Neuromics Support Facility, UAntwerp, VIB"},{"value":"Norwegian Sequencing Centre","label":"Norwegian Sequencing Centre"},{"value":"Nova Southeastern University","label":"Nova Southeastern University"},{"value":"Portland State University","label":"Portland State University"},{"value":"Queen Mary University of London","label":"Queen Mary University of London"},{"value":"Ramaciotti Centre for Genomics, Garvan","label":"Ramaciotti Centre for Genomics, Garvan"},{"value":"Ramaciotti Centre for Genomics, University of New South Wales","label":"Ramaciotti Centre for Genomics, University of New South Wales"},{"value":"Royal Botanic Garden Edinburgh","label":"Royal Botanic Garden Edinburgh"},{"value":"Royal Botanic Gardens Kew","label":"Royal Botanic Gardens Kew"},{"value":"Sanger Institute","label":"Sanger Institute"},{"value":"SciLifeLab","label":"SciLifeLab"},{"value":"Senckenberg Research Institute","label":"Senckenberg Research Institute"},{"value":"South Australian Genomics Centre","label":"South Australian Genomics Centre"},{"value":"Svardal Lab, Antwerp","label":"Svardal Lab, Antwerp"},{"value":"The Sainsbury Laboratory","label":"The Sainsbury Laboratory"},{"value":"University of Bari","label":"University of Bari"},{"value":"University of British Columbia","label":"University of British Columbia"},{"value":"University of California","label":"University of California"},{"value":"University of Cambridge","label":"University of Cambridge"},{"value":"University of Derby","label":"University of Derby"},{"value":"University of Edinburgh","label":"University of Edinburgh"},{"value":"University of Florence","label":"University of Florence"},{"value":"University of Neuchatel","label":"University of Neuchatel"},{"value":"University of Oulu","label":"University of Oulu"},{"value":"University of Oregon","label":"University of Oregon"},{"value":"University of Oxford","label":"University of Oxford"},{"value":"University of Rhode Island","label":"University of Rhode Island"},{"value":"University of Vienna (Cephalopod)","label":"University of Vienna (Cephalopod)"},{"value":"University of Vienna (Mollusc)","label":"University of Vienna (Mollusc)"},{"value":"West German Genome Centre","label":"West German Genome Centre"},{"value":"industry partner","label":"industry partner"},{"value":"other ERGA associated GAL","label":"other ERGA associated GAL"}],"group":"General collection event information"},{"type":"text","label":"specimen_id","name":"specimen_id","required":false,"visible":true,"helpText":"Unique identifier used to link all data for the recorded specimen.","group":"Pointer to physical material"},{"type":"text","label":"GAL_sample_id","name":"gal_sample_id","required":false,"visible":true,"helpText":"unique name assigned to the sample by the genome acquisition lab.","group":"Pointer to physical material"},{"type":"text","label":"proxy voucher","name":"proxy_voucher","required":false,"visible":true,"helpText":"For use if voucher material needs to be made from a specimen that is different than the one submitted for sequencing. Please record the unique identifier that references the physical specimen and that ideally exists in a curated collection. The ID should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). Please note institution codes and collection codes are taken from a controlled vocabulary maintained by the INSDC: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/","group":"Pointer to physical material"},{"type":"text","label":"proxy biomaterial","name":"proxy_biomaterial","required":false,"visible":true,"helpText":"For use if voucher material needs to be made from a material that is different from the one submitted for sequencing. Please record the unique identifier that references the biomaterial and that ideally exists in a curated collection (e.g. stock centres, seed banks, DNA banks). The ID should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the material id (institution_code:collection_code:material_id). Please note institution codes and collection codes are taken from a controlled vocabulary maintained by the INSDC: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/","group":"Pointer to physical material"},{"type":"text","label":"bio_material","name":"bio_material","required":false,"visible":true,"helpText":"Unique identifier that references the biological material from which the sample was obtained and that ideally exists in a curated collection (e.g. stock centres, seed banks, DNA banks). The ID should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). Please note institution codes and collection codes are taken from a controlled vocabulary maintained by the INSDC: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/","group":"Pointer to physical material"},{"type":"text","label":"specimen_voucher","name":"specimen_voucher","required":false,"visible":true,"helpText":"Unique identifier that references the physical specimen that remains after the sequence has been obtained and that ideally exists in a curated collection. The ID should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). Please note institution codes and collection codes are taken from a controlled vocabulary maintained by the INSDC: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/","group":"Pointer to physical material"},{"type":"text","label":"culture_or_strain_id","name":"culture_or_strain_id","required":false,"visible":true,"helpText":"living, culturable, named laboratory strain that sequenced material is derived from.","group":"Infraspecies information"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"mm","label":"mm"},{"value":"m","label":"m"}],"group":"Environmental information"}]},{"name":"ENA default sample checklist","description":"Minimum information required for the sample","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000011","category":"mixs","accession":"ERC000011","fields":[{"type":"text","label":"cell_type","name":"cell_type","required":false,"visible":true,"helpText":"cell type from which the sample was obtained","group":"Part and developmental stage of organism"},{"type":"text","label":"dev_stage","name":"dev_stage","required":false,"visible":true,"helpText":"if the sample was obtained from an organism in a specific developmental stage, it is specified with this qualifier","group":"Part and developmental stage of organism"},{"type":"text","label":"germline","name":"germline","required":false,"visible":true,"helpText":"the sample described presented in the entry has not undergone somatic genomic rearrangement as part of an adaptive immune response; it is the unrearranged molecule that was inherited from the parental germline","group":"Part and developmental stage of organism"},{"type":"text","label":"tissue_lib","name":"tissue_lib","required":false,"visible":true,"helpText":"tissue library from which sample was obtained","group":"Part and developmental stage of organism"},{"type":"text","label":"tissue_type","name":"tissue_type","required":false,"visible":true,"helpText":"tissue type from which the sample was obtained","group":"Part and developmental stage of organism"},{"type":"text","label":"isolation_source","name":"isolation_source","required":false,"visible":true,"helpText":"describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived","group":"Collection event information"},{"type":"text","label":"lat_lon","name":"lat_lon","required":false,"visible":true,"helpText":"geographical coordinates of the location where the specimen was collected","group":"Collection event information"},{"type":"text","label":"collected_by","name":"collected_by","required":false,"visible":true,"helpText":"name of persons or institute who collected the specimen","group":"Collection event information"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","group":"Collection event information","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)"}},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_and_or_sea","required":true,"visible":true,"helpText":"The location the sample was collected from with the intention of sequencing, as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","group":"Collection event information","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d&apos;Ivoire","label":"Cote d&apos;Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czech Republic","label":"Czech Republic"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"East Timor","label":"East Timor"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Macedonia","label":"Macedonia"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia","label":"Micronesia"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Swaziland","label":"Swaziland"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wake Island","label":"Wake Island"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}]},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"identified_by","name":"identified_by","required":false,"visible":true,"helpText":"name of the expert who identified the specimen taxonomically","group":"Collection event information"},{"type":"select","label":"environmental_sample","name":"environmental_sample","required":false,"visible":true,"helpText":"identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism","group":"sample collection","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}]},{"type":"text","label":"mating_type","name":"mating_type","required":false,"visible":true,"helpText":"mating type of the organism from which the sequence was obtained; mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes","group":"Organism characteristics"},{"type":"text","label":"sex","name":"sex","required":false,"visible":true,"helpText":"sex of the organism from which the sample was obtained","group":"Organism characteristics"},{"type":"text","label":"lab_host","name":"lab_host","required":false,"visible":true,"helpText":"scientific name of the laboratory host used to propagate the source organism from which the sample was obtained","group":"host description"},{"type":"text","label":"host scientific name","name":"host_scientific_name","required":false,"visible":true,"helpText":"Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.","group":"host description"},{"type":"text","label":"bio_material","name":"bio_material","required":false,"visible":true,"helpText":"Unique identifier that references the biological material from which the sample was obtained and that ideally exists in a curated collection (e.g. stock centres, seed banks, DNA banks). The ID should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). Please note institution codes and collection codes are taken from a controlled vocabulary maintained by the INSDC: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/","group":"Pointer to physical material"},{"type":"text","label":"culture_collection","name":"culture_collection","required":false,"visible":true,"helpText":"Unique identifier that references the culture (e.g. live microbial and viral cultures and cell lines) from which the sample has been obtained and that have been deposited in curated culture collections. The ID needs to provide an institution code and the culture id, with optional collection code, in the following structure: (-institution_code:(collection_code):voucher_id. Please note institution codes (and optional collection codes) are taken from a controlled vocabulary maintained by the INSDC: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/","group":"Pointer to physical material"},{"type":"text","label":"specimen_voucher","name":"specimen_voucher","required":false,"visible":true,"helpText":"Unique identifier that references the physical specimen that remains after the sequence has been obtained and that ideally exists in a curated collection. The ID should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). Please note institution codes and collection codes are taken from a controlled vocabulary maintained by the INSDC: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/","group":"Pointer to physical material"},{"type":"text","label":"cultivar","name":"cultivar","required":false,"visible":true,"helpText":"cultivar (cultivated variety) of plant from which sample was obtained","group":"Infraspecies information"},{"type":"text","label":"ecotype","name":"ecotype","required":false,"visible":true,"helpText":"a population within a given species displaying genetically based, phenotypic traits that reflect adaptation to a local habitat.","group":"Infraspecies information"},{"type":"text","label":"isolate","name":"isolate","required":false,"visible":true,"helpText":"individual isolate from which the sample was obtained","group":"Infraspecies information"},{"type":"text","label":"sub_species","name":"sub_species","required":false,"visible":true,"helpText":"name of sub-species of organism from which sample was obtained","group":"Infraspecies information"},{"type":"text","label":"variety","name":"variety","required":false,"visible":true,"helpText":"variety (= varietas, a formal Linnaean rank) of organism from which sample was derived.","group":"Infraspecies information"},{"type":"text","label":"sub_strain","name":"sub_strain","required":false,"visible":true,"helpText":"name or identifier of a genetically or otherwise modified strain from which sample was obtained, derived from a parental strain (which should be annotated in the strain field; sub_strain from which sample was obtained","group":"Infraspecies information"},{"type":"text","label":"cell_line","name":"cell_line","required":false,"visible":true,"helpText":"cell line from which the sample was obtained","group":"Infraspecies information"},{"type":"text","label":"serotype","name":"serotype","required":false,"visible":true,"helpText":"serological variety of a species characterized by its antigenic properties","group":"Infraspecies information"},{"type":"text","label":"serovar","name":"serovar","required":false,"visible":true,"helpText":"serological variety of a species (usually a prokaryote) characterized by its antigenic properties","group":"Infraspecies information"},{"type":"text","label":"strain","name":"strain","required":false,"visible":true,"helpText":"Name of the strain from which the sample was obtained.","group":"Infraspecies information"}]},{"name":"ENA binned metagenome","description":"Minimum information to standardise metadata of binned metagenome samples. Ensures binned and MAG metagenome assembly metadata is compatible.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000050","category":"mixs","accession":"ERC000050","fields":[{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","group":"Organism characteristics: ecosystem","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}]},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"metagenomic source","name":"metagenomic_source","required":true,"visible":true,"helpText":"The metagenomic source of the sample. This value should contain “metagenome” and be in the taxonomy database e.g. wastewater metagenome or human gut metagenome. Please note “metagenome” alone will not be accepted. Check here for more details on metagenome taxonomy: https://ena-docs.readthedocs.io/en/latest/faq_taxonomy.html#environmental-taxonomic-classifications","group":"sample collection: core sample properties"},{"type":"text","label":"sample derived from","name":"sample_derived_from","required":true,"visible":true,"helpText":"Reference to parental sample(s) or original run(s) that the assembly is derived from. The referenced samples or runs should already be registered in INSDC. This should be formatted as one of the following. A single sample/run e.g. ERSxxxxxx OR a comma separated list e.g. ERSxxxxxx,ERSxxxxxx OR a range e.g. ERSxxxxxx-ERSxxxxxx","group":"sample collection: core sample properties","simpleValidation":{"pattern":"(^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)","patternMessage":"Must match pattern: (^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)"}},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"number of standard tRNAs extracted","name":"number_of_standard_trnas_extracted","required":false,"visible":true,"helpText":"The total number of tRNAs identified from the bin, SAG or MAG","group":"non-sample terms","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"}},{"type":"select","label":"16s recovered","name":"16s_recovered","required":false,"visible":true,"helpText":"Can a 16S gene be recovered from the submitted bin, SAG or MAG?","group":"non-sample terms","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}]},{"type":"text","label":"16S recovery software","name":"16s_recovery_software","required":false,"visible":true,"helpText":"Tools used for 16S rRNA gene extraction. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"tRNA extraction software","name":"trna_extraction_software","required":false,"visible":true,"helpText":"Tools used for tRNA identification. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"completeness score","name":"completeness_score","required":false,"visible":true,"helpText":"Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. Completeness score is one of 3 attributes which in combination reflect the standard quality of a MAG, see here for more information: https://ena-docs.readthedocs.io/en/latest/faq_metagenomes.html. Mandatory for all samples directly linked with SAGs or MAGs.","group":"non-sample terms","simpleValidation":{"pattern":"^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$","patternMessage":"Must match pattern: ^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$"},"units":[{"value":"%","label":"%"}]},{"type":"text","label":"completeness software","name":"completeness_software","required":false,"visible":true,"helpText":"Tools used for completion estimate, i.e. checkm, anvi&apos;o, busco. Mandatory for all samples directly linked with SAGs or MAGs.","group":"non-sample terms"},{"type":"text","label":"completeness approach","name":"completeness_approach","required":false,"visible":true,"helpText":"The approach used to determine the completeness of a given bin, SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome","group":"non-sample terms"},{"type":"text","label":"contamination score","name":"contamination_score","required":false,"visible":true,"helpText":"The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. Contamination score is one of 3 attributes which in combination reflect the standard quality of a MAG, see here for more information: https://ena-docs.readthedocs.io/en/latest/faq_metagenomes.html. If contamination ≥ 10% then please submit as a binned assembly. In SAGs, contamination score is mandatory for prokaryotes and optional for eukaryotes.","group":"non-sample terms","simpleValidation":{"pattern":"^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$","patternMessage":"Must match pattern: ^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$"},"units":[{"value":"%","label":"%"}]},{"type":"select","label":"contamination screening input","name":"contamination_screening_input","required":false,"visible":true,"helpText":"The type of sequence data used as input","group":"non-sample terms","options":[{"value":"contigs","label":"contigs"},{"value":"reads","label":"reads"}]},{"type":"text","label":"contamination screening parameters","name":"contamination_screening_parameters","required":false,"visible":true,"helpText":"Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer","group":"non-sample terms"},{"type":"text","label":"decontamination software","name":"decontamination_software","required":false,"visible":true,"helpText":"Tool(s) used in contamination screening","group":"non-sample terms"},{"type":"text","label":"binning software","name":"binning_software","required":true,"visible":true,"helpText":"Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used. E.g. MetaCluster-TA (RRID:SCR_004599) or MaxBin (biotools:maxbin)","group":"non-sample terms"},{"type":"select","label":"reassembly post binning","name":"reassembly_post_binning","required":false,"visible":true,"helpText":"Has an assembly been performed on a genome bin extracted from a metagenomic assembly?","group":"non-sample terms","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"units":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}]},{"type":"text","label":"MAG coverage software","name":"mag_coverage_software","required":false,"visible":true,"helpText":"Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets e.g. bwa, bbmap, bowtie, other","group":"non-sample terms"},{"type":"select","label":"assembly quality","name":"assembly_quality","required":false,"visible":true,"helpText":"The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling &lt; 90% of the expected genome or replicon sequence, or for which no genome size could be estimated.","group":"non-sample terms","options":[{"value":"Many fragments with little to no review of assembly other than reporting of standard assembly statistics","label":"Many fragments with little to no review of assembly other than reporting of standard assembly statistics"},{"value":"Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs","label":"Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs"},{"value":"Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better","label":"Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better"}]},{"type":"select","label":"investigation type","name":"investigation_type","required":false,"visible":true,"helpText":"Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardised by Genomic Standards Consortium","group":"non-sample terms","options":[{"value":"bacteria_archaea","label":"bacteria_archaea"},{"value":"eukaryote","label":"eukaryote"},{"value":"metagenome","label":"metagenome"},{"value":"metagenome-assembled genome","label":"metagenome-assembled genome"},{"value":"metatranscriptome","label":"metatranscriptome"},{"value":"mimarks-specimen","label":"mimarks-specimen"},{"value":"mimarks-survey","label":"mimarks-survey"},{"value":"organelle","label":"organelle"},{"value":"plasmid","label":"plasmid"},{"value":"single amplified genome","label":"single amplified genome"},{"value":"uncultivated viral genomes","label":"uncultivated viral genomes"},{"value":"virus","label":"virus"}]},{"type":"text","label":"binning parameters","name":"binning_parameters","required":true,"visible":true,"helpText":"The parameters that have been applied during the extraction of genomes from metagenomic datasets e.g. coverage and kmer","group":"non-sample terms"},{"type":"text","label":"taxonomic identity marker","name":"taxonomic_identity_marker","required":false,"visible":true,"helpText":"The phylogenetic marker(s) used to assign an organism name to the bin, SAG or MAG. Examples are 16S gene, multi-marker approach or other e.g. rpoB gene. Mandatory for all samples directly linked with SAGs or MAGs.","group":"non-sample terms"},{"type":"text","label":"isolation_source","name":"isolation_source","required":true,"visible":true,"helpText":"describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived","group":"Collection event information"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","group":"Collection event information","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"}},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth&apos;s surface above Sea Level and the sampled position in the air.","group":"Collection event information","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}]},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","group":"Collection event information","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}]},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","group":"Collection event information","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}]},{"type":"text","label":"broad-scale environmental context","name":"broad_scale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for &quot;broad-scale environmental context&quot;. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of &apos;environmental material&apos; (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","group":"Collection event information","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}]},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","group":"sample collection","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"L","label":"L"},{"value":"g","label":"g"},{"value":"kg","label":"kg"},{"value":"m2","label":"m2"},{"value":"m3","label":"m3"}]},{"type":"text","label":"size fraction selected","name":"size_fraction_selected","required":false,"visible":true,"helpText":"Filtering pore size used in sample preparation e.g. 0-0.22 micrometer","group":"sample collection"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_and_or_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","group":"Organism characteristics","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d&apos;Ivoire","label":"Cote d&apos;Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"East Timor","label":"East Timor"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Macedonia","label":"Macedonia"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia","label":"Micronesia"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Swaziland","label":"Swaziland"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wake Island","label":"Wake Island"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}]},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain &apos;UAM:Herps:14&apos; , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","group":"sample processing","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"}},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","group":"sample processing","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"}},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"assembly software","name":"assembly_software","required":true,"visible":true,"helpText":"Tool(s) used for assembly, including version number and parameters in the format {software};{version};{parameters} e.g. metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","group":"Environmental information","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"},{"value":"mm","label":"mm"}]}]},{"name":"GSC MIMAGS","description":"Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.","version":"1.0.0","source":"https://www.ebi.ac.uk/ena/browser/view/ERC000047","category":"mixs","accession":"ERC000047","fields":[{"type":"select","label":"relationship to oxygen","name":"relationship_to_oxygen","required":false,"visible":true,"helpText":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments","group":"Organism characteristics: ecosystem","options":[{"value":"aerobe","label":"aerobe"},{"value":"anaerobe","label":"anaerobe"},{"value":"facultative","label":"facultative"},{"value":"microaerophilic","label":"microaerophilic"},{"value":"microanaerobe","label":"microanaerobe"},{"value":"obligate aerobe","label":"obligate aerobe"},{"value":"obligate anaerobe","label":"obligate anaerobe"}]},{"type":"text","label":"sample collection device","name":"sample_collection_device","required":false,"visible":true,"helpText":"The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).","group":"sample collection: methods, storage and transport"},{"type":"text","label":"sample collection method","name":"sample_collection_method","required":false,"visible":true,"helpText":"The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.","group":"sample collection: methods, storage and transport"},{"type":"text","label":"metagenomic source","name":"metagenomic_source","required":true,"visible":true,"helpText":"The metagenomic source of the sample. This value should contain “metagenome” and be in the taxonomy database e.g. wastewater metagenome or human gut metagenome. Please note “metagenome” alone will not be accepted. Check here for more details on metagenome taxonomy: https://ena-docs.readthedocs.io/en/latest/faq_taxonomy.html#environmental-taxonomic-classifications","group":"sample collection: core sample properties"},{"type":"text","label":"sample derived from","name":"sample_derived_from","required":true,"visible":true,"helpText":"Reference to parental sample(s) or original run(s) that the assembly is derived from. The referenced samples or runs should already be registered in INSDC. This should be formatted as one of the following. A single sample/run e.g. ERSxxxxxx OR a comma separated list e.g. ERSxxxxxx,ERSxxxxxx OR a range e.g. ERSxxxxxx-ERSxxxxxx","group":"sample collection: core sample properties","simpleValidation":{"pattern":"(^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)","patternMessage":"Must match pattern: (^[ESD]R[SR]\\d{6,}(,[ESD]R[SR]\\d{6,})*$)|(^SAM[END][AG]?\\d+(,SAM[END][AG]?\\d+)*$)|(^EGA[NR]\\d{11}(,EGA[NR]\\d{11})*$)|(^[ESD]R[SR]\\d{6,}-[ESD]R[SR]\\d{6,}$)|(^SAM[END][AG]?\\d+-SAM[END][AG]?\\d+$)|(^EGA[NR]\\d{11}-EGA[NR]\\d{11}$)"}},{"type":"text","label":"project name","name":"project_name","required":true,"visible":true,"helpText":"Name of the project within which the sequencing was organized","group":"non-sample terms: study or project"},{"type":"text","label":"multiplex identifiers","name":"multiplex_identifiers","required":false,"visible":true,"helpText":"Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters","group":"non-sample terms"},{"type":"text","label":"relevant electronic resources","name":"relevant_electronic_resources","required":false,"visible":true,"helpText":"A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"relevant standard operating procedures","name":"relevant_standard_operating_procedures","required":false,"visible":true,"helpText":"Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL","group":"non-sample terms"},{"type":"text","label":"number of standard tRNAs extracted","name":"number_of_standard_trnas_extracted","required":false,"visible":true,"helpText":"The total number of tRNAs identified from the bin, SAG or MAG","group":"non-sample terms","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"}},{"type":"text","label":"feature prediction","name":"feature_prediction","required":false,"visible":true,"helpText":"Method used to predict UViGs features such as ORFs, integration site, etc. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"similarity search method","name":"similarity_search_method","required":false,"visible":true,"helpText":"Tool used to compare ORFs with database, along with version and cutoffs used. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"select","label":"16s recovered","name":"16s_recovered","required":false,"visible":true,"helpText":"Can a 16S gene be recovered from the submitted bin, SAG or MAG?","group":"non-sample terms","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}]},{"type":"text","label":"16S recovery software","name":"16s_recovery_software","required":false,"visible":true,"helpText":"Tools used for 16S rRNA gene extraction. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"tRNA extraction software","name":"trna_extraction_software","required":false,"visible":true,"helpText":"Tools used for tRNA identification. Add names and versions of software(s), parameters used","group":"non-sample terms"},{"type":"text","label":"completeness score","name":"completeness_score","required":true,"visible":true,"helpText":"Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. Completeness score is one of 3 attributes which in combination reflect the standard quality of a MAG, see here for more information: https://ena-docs.readthedocs.io/en/latest/faq_metagenomes.html. Mandatory for all samples directly linked with SAGs or MAGs.","group":"non-sample terms","simpleValidation":{"pattern":"^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$","patternMessage":"Must match pattern: ^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$"},"units":[{"value":"%","label":"%"}]},{"type":"text","label":"completeness software","name":"completeness_software","required":true,"visible":true,"helpText":"Tools used for completion estimate, i.e. checkm, anvi&apos;o, busco. Mandatory for all samples directly linked with SAGs or MAGs.","group":"non-sample terms"},{"type":"text","label":"completeness approach","name":"completeness_approach","required":false,"visible":true,"helpText":"The approach used to determine the completeness of a given bin, SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome","group":"non-sample terms"},{"type":"text","label":"contamination score","name":"contamination_score","required":true,"visible":true,"helpText":"The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. Contamination score is one of 3 attributes which in combination reflect the standard quality of a MAG, see here for more information: https://ena-docs.readthedocs.io/en/latest/faq_metagenomes.html. If contamination ≥ 10% then please submit as a binned assembly. In SAGs, contamination score is mandatory for prokaryotes and optional for eukaryotes.","group":"non-sample terms","simpleValidation":{"pattern":"^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$","patternMessage":"Must match pattern: ^(\\d|[1-9]\\d|\\d\\.\\d{1,2}|[1-9]\\d\\.\\d{1,2}|100)$"},"units":[{"value":"%","label":"%"}]},{"type":"select","label":"contamination screening input","name":"contamination_screening_input","required":false,"visible":true,"helpText":"The type of sequence data used as input","group":"non-sample terms","options":[{"value":"contigs","label":"contigs"},{"value":"reads","label":"reads"}]},{"type":"text","label":"contamination screening parameters","name":"contamination_screening_parameters","required":false,"visible":true,"helpText":"Specific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer","group":"non-sample terms"},{"type":"text","label":"decontamination software","name":"decontamination_software","required":false,"visible":true,"helpText":"Tool(s) used in contamination screening","group":"non-sample terms"},{"type":"text","label":"binning software","name":"binning_software","required":true,"visible":true,"helpText":"Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used. E.g. MetaCluster-TA (RRID:SCR_004599) or MaxBin (biotools:maxbin)","group":"non-sample terms"},{"type":"select","label":"reassembly post binning","name":"reassembly_post_binning","required":false,"visible":true,"helpText":"Has an assembly been performed on a genome bin extracted from a metagenomic assembly?","group":"non-sample terms","options":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}],"units":[{"value":"No","label":"No"},{"value":"Yes","label":"Yes"}]},{"type":"text","label":"MAG coverage software","name":"mag_coverage_software","required":false,"visible":true,"helpText":"Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets e.g. bwa, bbmap, bowtie, other","group":"non-sample terms"},{"type":"select","label":"assembly quality","name":"assembly_quality","required":true,"visible":true,"helpText":"The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling &lt; 90% of the expected genome or replicon sequence, or for which no genome size could be estimated.","group":"non-sample terms","options":[{"value":"Many fragments with little to no review of assembly other than reporting of standard assembly statistics","label":"Many fragments with little to no review of assembly other than reporting of standard assembly statistics"},{"value":"Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs","label":"Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs"},{"value":"Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better","label":"Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better"}]},{"type":"text","label":"binning parameters","name":"binning_parameters","required":true,"visible":true,"helpText":"The parameters that have been applied during the extraction of genomes from metagenomic datasets e.g. coverage and kmer","group":"non-sample terms"},{"type":"text","label":"taxonomic identity marker","name":"taxonomic_identity_marker","required":true,"visible":true,"helpText":"The phylogenetic marker(s) used to assign an organism name to the bin, SAG or MAG. Examples are 16S gene, multi-marker approach or other e.g. rpoB gene. Mandatory for all samples directly linked with SAGs or MAGs.","group":"non-sample terms"},{"type":"text","label":"isolation_source","name":"isolation_source","required":true,"visible":true,"helpText":"describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived","group":"Collection event information"},{"type":"text","label":"collection date","name":"collection_date","required":true,"visible":true,"helpText":"The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.","group":"Collection event information","simpleValidation":{"pattern":"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"}},{"type":"text","label":"altitude","name":"altitude","required":false,"visible":true,"helpText":"The altitude of the sample is the vertical distance between Earth&apos;s surface above Sea Level and the sampled position in the air.","group":"Collection event information","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}]},{"type":"text","label":"geographic location (latitude)","name":"geographic_location_latitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system","group":"Collection event information","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}]},{"type":"text","label":"geographic location (longitude)","name":"geographic_location_longitude","required":true,"visible":true,"helpText":"The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system","group":"Collection event information","simpleValidation":{"pattern":"(^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)","patternMessage":"Must match pattern: (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)"},"units":[{"value":"DD","label":"DD"}]},{"type":"text","label":"geographic location (region and locality)","name":"geographic_location_region_and_locality","required":false,"visible":true,"helpText":"The geographical origin of the sample as defined by the specific region name followed by the locality name.","group":"Collection event information"},{"type":"text","label":"broad-scale environmental context","name":"broad_scale_environmental_context","required":true,"visible":true,"helpText":"Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"local environmental context","name":"local_environmental_context","required":true,"visible":true,"helpText":"Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for &quot;broad-scale environmental context&quot;. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.","group":"Collection event information"},{"type":"text","label":"environmental medium","name":"environmental_medium","required":true,"visible":true,"helpText":"Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of &apos;environmental material&apos; (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).","group":"Collection event information"},{"type":"text","label":"elevation","name":"elevation","required":false,"visible":true,"helpText":"The elevation of the sampling site as measured by the vertical distance from mean sea level.","group":"Collection event information","simpleValidation":{"pattern":"([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ([+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"}]},{"type":"text","label":"amount or size of sample collected","name":"amount_or_size_of_sample_collected","required":false,"visible":true,"helpText":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.","group":"sample collection","simpleValidation":{"pattern":"(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?","patternMessage":"Must match pattern: (0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"},"units":[{"value":"L","label":"L"},{"value":"g","label":"g"},{"value":"kg","label":"kg"},{"value":"m2","label":"m2"},{"value":"m3","label":"m3"}]},{"type":"text","label":"size fraction selected","name":"size_fraction_selected","required":false,"visible":true,"helpText":"Filtering pore size used in sample preparation e.g. 0-0.22 micrometer","group":"sample collection"},{"type":"select","label":"geographic location (country and/or sea)","name":"geographic_location_country_and_or_sea","required":true,"visible":true,"helpText":"The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).","group":"Organism characteristics","options":[{"value":"Afghanistan","label":"Afghanistan"},{"value":"Albania","label":"Albania"},{"value":"Algeria","label":"Algeria"},{"value":"American Samoa","label":"American Samoa"},{"value":"Andorra","label":"Andorra"},{"value":"Angola","label":"Angola"},{"value":"Anguilla","label":"Anguilla"},{"value":"Antarctica","label":"Antarctica"},{"value":"Antigua and Barbuda","label":"Antigua and Barbuda"},{"value":"Arctic Ocean","label":"Arctic Ocean"},{"value":"Argentina","label":"Argentina"},{"value":"Armenia","label":"Armenia"},{"value":"Aruba","label":"Aruba"},{"value":"Ashmore and Cartier Islands","label":"Ashmore and Cartier Islands"},{"value":"Atlantic Ocean","label":"Atlantic Ocean"},{"value":"Australia","label":"Australia"},{"value":"Austria","label":"Austria"},{"value":"Azerbaijan","label":"Azerbaijan"},{"value":"Bahamas","label":"Bahamas"},{"value":"Bahrain","label":"Bahrain"},{"value":"Baker Island","label":"Baker Island"},{"value":"Baltic Sea","label":"Baltic Sea"},{"value":"Bangladesh","label":"Bangladesh"},{"value":"Barbados","label":"Barbados"},{"value":"Bassas da India","label":"Bassas da India"},{"value":"Belarus","label":"Belarus"},{"value":"Belgium","label":"Belgium"},{"value":"Belize","label":"Belize"},{"value":"Benin","label":"Benin"},{"value":"Bermuda","label":"Bermuda"},{"value":"Bhutan","label":"Bhutan"},{"value":"Bolivia","label":"Bolivia"},{"value":"Borneo","label":"Borneo"},{"value":"Bosnia and Herzegovina","label":"Bosnia and Herzegovina"},{"value":"Botswana","label":"Botswana"},{"value":"Bouvet Island","label":"Bouvet Island"},{"value":"Brazil","label":"Brazil"},{"value":"British Virgin Islands","label":"British Virgin Islands"},{"value":"Brunei","label":"Brunei"},{"value":"Bulgaria","label":"Bulgaria"},{"value":"Burkina Faso","label":"Burkina Faso"},{"value":"Burundi","label":"Burundi"},{"value":"Cambodia","label":"Cambodia"},{"value":"Cameroon","label":"Cameroon"},{"value":"Canada","label":"Canada"},{"value":"Cape Verde","label":"Cape Verde"},{"value":"Cayman Islands","label":"Cayman Islands"},{"value":"Central African Republic","label":"Central African Republic"},{"value":"Chad","label":"Chad"},{"value":"Chile","label":"Chile"},{"value":"China","label":"China"},{"value":"Christmas Island","label":"Christmas Island"},{"value":"Clipperton Island","label":"Clipperton Island"},{"value":"Cocos Islands","label":"Cocos Islands"},{"value":"Colombia","label":"Colombia"},{"value":"Comoros","label":"Comoros"},{"value":"Cook Islands","label":"Cook Islands"},{"value":"Coral Sea Islands","label":"Coral Sea Islands"},{"value":"Costa Rica","label":"Costa Rica"},{"value":"Cote d&apos;Ivoire","label":"Cote d&apos;Ivoire"},{"value":"Croatia","label":"Croatia"},{"value":"Cuba","label":"Cuba"},{"value":"Curacao","label":"Curacao"},{"value":"Cyprus","label":"Cyprus"},{"value":"Czechia","label":"Czechia"},{"value":"Democratic Republic of the Congo","label":"Democratic Republic of the Congo"},{"value":"Denmark","label":"Denmark"},{"value":"Djibouti","label":"Djibouti"},{"value":"Dominica","label":"Dominica"},{"value":"Dominican Republic","label":"Dominican Republic"},{"value":"East Timor","label":"East Timor"},{"value":"Ecuador","label":"Ecuador"},{"value":"Egypt","label":"Egypt"},{"value":"El Salvador","label":"El Salvador"},{"value":"Equatorial Guinea","label":"Equatorial Guinea"},{"value":"Eritrea","label":"Eritrea"},{"value":"Estonia","label":"Estonia"},{"value":"Ethiopia","label":"Ethiopia"},{"value":"Europa Island","label":"Europa Island"},{"value":"Falkland Islands (Islas Malvinas)","label":"Falkland Islands (Islas Malvinas)"},{"value":"Faroe Islands","label":"Faroe Islands"},{"value":"Fiji","label":"Fiji"},{"value":"Finland","label":"Finland"},{"value":"France","label":"France"},{"value":"French Guiana","label":"French Guiana"},{"value":"French Polynesia","label":"French Polynesia"},{"value":"French Southern and Antarctic Lands","label":"French Southern and Antarctic Lands"},{"value":"Gabon","label":"Gabon"},{"value":"Gambia","label":"Gambia"},{"value":"Gaza Strip","label":"Gaza Strip"},{"value":"Georgia","label":"Georgia"},{"value":"Germany","label":"Germany"},{"value":"Ghana","label":"Ghana"},{"value":"Gibraltar","label":"Gibraltar"},{"value":"Glorioso Islands","label":"Glorioso Islands"},{"value":"Greece","label":"Greece"},{"value":"Greenland","label":"Greenland"},{"value":"Grenada","label":"Grenada"},{"value":"Guadeloupe","label":"Guadeloupe"},{"value":"Guam","label":"Guam"},{"value":"Guatemala","label":"Guatemala"},{"value":"Guernsey","label":"Guernsey"},{"value":"Guinea","label":"Guinea"},{"value":"Guinea-Bissau","label":"Guinea-Bissau"},{"value":"Guyana","label":"Guyana"},{"value":"Haiti","label":"Haiti"},{"value":"Heard Island and McDonald Islands","label":"Heard Island and McDonald Islands"},{"value":"Honduras","label":"Honduras"},{"value":"Hong Kong","label":"Hong Kong"},{"value":"Howland Island","label":"Howland Island"},{"value":"Hungary","label":"Hungary"},{"value":"Iceland","label":"Iceland"},{"value":"India","label":"India"},{"value":"Indian Ocean","label":"Indian Ocean"},{"value":"Indonesia","label":"Indonesia"},{"value":"Iran","label":"Iran"},{"value":"Iraq","label":"Iraq"},{"value":"Ireland","label":"Ireland"},{"value":"Isle of Man","label":"Isle of Man"},{"value":"Israel","label":"Israel"},{"value":"Italy","label":"Italy"},{"value":"Jamaica","label":"Jamaica"},{"value":"Jan Mayen","label":"Jan Mayen"},{"value":"Japan","label":"Japan"},{"value":"Jarvis Island","label":"Jarvis Island"},{"value":"Jersey","label":"Jersey"},{"value":"Johnston Atoll","label":"Johnston Atoll"},{"value":"Jordan","label":"Jordan"},{"value":"Juan de Nova Island","label":"Juan de Nova Island"},{"value":"Kazakhstan","label":"Kazakhstan"},{"value":"Kenya","label":"Kenya"},{"value":"Kerguelen Archipelago","label":"Kerguelen Archipelago"},{"value":"Kingman Reef","label":"Kingman Reef"},{"value":"Kiribati","label":"Kiribati"},{"value":"Kosovo","label":"Kosovo"},{"value":"Kuwait","label":"Kuwait"},{"value":"Kyrgyzstan","label":"Kyrgyzstan"},{"value":"Laos","label":"Laos"},{"value":"Latvia","label":"Latvia"},{"value":"Lebanon","label":"Lebanon"},{"value":"Lesotho","label":"Lesotho"},{"value":"Liberia","label":"Liberia"},{"value":"Libya","label":"Libya"},{"value":"Liechtenstein","label":"Liechtenstein"},{"value":"Lithuania","label":"Lithuania"},{"value":"Luxembourg","label":"Luxembourg"},{"value":"Macau","label":"Macau"},{"value":"Macedonia","label":"Macedonia"},{"value":"Madagascar","label":"Madagascar"},{"value":"Malawi","label":"Malawi"},{"value":"Malaysia","label":"Malaysia"},{"value":"Maldives","label":"Maldives"},{"value":"Mali","label":"Mali"},{"value":"Malta","label":"Malta"},{"value":"Marshall Islands","label":"Marshall Islands"},{"value":"Martinique","label":"Martinique"},{"value":"Mauritania","label":"Mauritania"},{"value":"Mauritius","label":"Mauritius"},{"value":"Mayotte","label":"Mayotte"},{"value":"Mediterranean Sea","label":"Mediterranean Sea"},{"value":"Mexico","label":"Mexico"},{"value":"Micronesia","label":"Micronesia"},{"value":"Midway Islands","label":"Midway Islands"},{"value":"Moldova","label":"Moldova"},{"value":"Monaco","label":"Monaco"},{"value":"Mongolia","label":"Mongolia"},{"value":"Montenegro","label":"Montenegro"},{"value":"Montserrat","label":"Montserrat"},{"value":"Morocco","label":"Morocco"},{"value":"Mozambique","label":"Mozambique"},{"value":"Myanmar","label":"Myanmar"},{"value":"Namibia","label":"Namibia"},{"value":"Nauru","label":"Nauru"},{"value":"Navassa Island","label":"Navassa Island"},{"value":"Nepal","label":"Nepal"},{"value":"Netherlands","label":"Netherlands"},{"value":"New Caledonia","label":"New Caledonia"},{"value":"New Zealand","label":"New Zealand"},{"value":"Nicaragua","label":"Nicaragua"},{"value":"Niger","label":"Niger"},{"value":"Nigeria","label":"Nigeria"},{"value":"Niue","label":"Niue"},{"value":"Norfolk Island","label":"Norfolk Island"},{"value":"North Korea","label":"North Korea"},{"value":"North Sea","label":"North Sea"},{"value":"Northern Mariana Islands","label":"Northern Mariana Islands"},{"value":"Norway","label":"Norway"},{"value":"Oman","label":"Oman"},{"value":"Pacific Ocean","label":"Pacific Ocean"},{"value":"Pakistan","label":"Pakistan"},{"value":"Palau","label":"Palau"},{"value":"Palmyra Atoll","label":"Palmyra Atoll"},{"value":"Panama","label":"Panama"},{"value":"Papua New Guinea","label":"Papua New Guinea"},{"value":"Paracel Islands","label":"Paracel Islands"},{"value":"Paraguay","label":"Paraguay"},{"value":"Peru","label":"Peru"},{"value":"Philippines","label":"Philippines"},{"value":"Pitcairn Islands","label":"Pitcairn Islands"},{"value":"Poland","label":"Poland"},{"value":"Portugal","label":"Portugal"},{"value":"Puerto Rico","label":"Puerto Rico"},{"value":"Qatar","label":"Qatar"},{"value":"Republic of the Congo","label":"Republic of the Congo"},{"value":"Reunion","label":"Reunion"},{"value":"Romania","label":"Romania"},{"value":"Ross Sea","label":"Ross Sea"},{"value":"Russia","label":"Russia"},{"value":"Rwanda","label":"Rwanda"},{"value":"Saint Helena","label":"Saint Helena"},{"value":"Saint Kitts and Nevis","label":"Saint Kitts and Nevis"},{"value":"Saint Lucia","label":"Saint Lucia"},{"value":"Saint Pierre and Miquelon","label":"Saint Pierre and Miquelon"},{"value":"Saint Vincent and the Grenadines","label":"Saint Vincent and the Grenadines"},{"value":"Samoa","label":"Samoa"},{"value":"San Marino","label":"San Marino"},{"value":"Sao Tome and Principe","label":"Sao Tome and Principe"},{"value":"Saudi Arabia","label":"Saudi Arabia"},{"value":"Senegal","label":"Senegal"},{"value":"Serbia","label":"Serbia"},{"value":"Seychelles","label":"Seychelles"},{"value":"Sierra Leone","label":"Sierra Leone"},{"value":"Singapore","label":"Singapore"},{"value":"Sint Maarten","label":"Sint Maarten"},{"value":"Slovakia","label":"Slovakia"},{"value":"Slovenia","label":"Slovenia"},{"value":"Solomon Islands","label":"Solomon Islands"},{"value":"Somalia","label":"Somalia"},{"value":"South Africa","label":"South Africa"},{"value":"South Georgia and the South Sandwich Islands","label":"South Georgia and the South Sandwich Islands"},{"value":"South Korea","label":"South Korea"},{"value":"Southern Ocean","label":"Southern Ocean"},{"value":"Spain","label":"Spain"},{"value":"Spratly Islands","label":"Spratly Islands"},{"value":"Sri Lanka","label":"Sri Lanka"},{"value":"Sudan","label":"Sudan"},{"value":"Suriname","label":"Suriname"},{"value":"Svalbard","label":"Svalbard"},{"value":"Swaziland","label":"Swaziland"},{"value":"Sweden","label":"Sweden"},{"value":"Switzerland","label":"Switzerland"},{"value":"Syria","label":"Syria"},{"value":"Taiwan","label":"Taiwan"},{"value":"Tajikistan","label":"Tajikistan"},{"value":"Tanzania","label":"Tanzania"},{"value":"Tasman Sea","label":"Tasman Sea"},{"value":"Thailand","label":"Thailand"},{"value":"Togo","label":"Togo"},{"value":"Tokelau","label":"Tokelau"},{"value":"Tonga","label":"Tonga"},{"value":"Trinidad and Tobago","label":"Trinidad and Tobago"},{"value":"Tromelin Island","label":"Tromelin Island"},{"value":"Tunisia","label":"Tunisia"},{"value":"Turkey","label":"Turkey"},{"value":"Turkmenistan","label":"Turkmenistan"},{"value":"Turks and Caicos Islands","label":"Turks and Caicos Islands"},{"value":"Tuvalu","label":"Tuvalu"},{"value":"USA","label":"USA"},{"value":"Uganda","label":"Uganda"},{"value":"Ukraine","label":"Ukraine"},{"value":"United Arab Emirates","label":"United Arab Emirates"},{"value":"United Kingdom","label":"United Kingdom"},{"value":"Uruguay","label":"Uruguay"},{"value":"Uzbekistan","label":"Uzbekistan"},{"value":"Vanuatu","label":"Vanuatu"},{"value":"Venezuela","label":"Venezuela"},{"value":"Viet Nam","label":"Viet Nam"},{"value":"Virgin Islands","label":"Virgin Islands"},{"value":"Wake Island","label":"Wake Island"},{"value":"Wallis and Futuna","label":"Wallis and Futuna"},{"value":"West Bank","label":"West Bank"},{"value":"Western Sahara","label":"Western Sahara"},{"value":"Yemen","label":"Yemen"},{"value":"Zambia","label":"Zambia"},{"value":"Zimbabwe","label":"Zimbabwe"},{"value":"missing","label":"missing"},{"value":"missing: control sample","label":"missing: control sample"},{"value":"missing: data agreement established pre-2023","label":"missing: data agreement established pre-2023"},{"value":"missing: endangered species","label":"missing: endangered species"},{"value":"missing: human-identifiable","label":"missing: human-identifiable"},{"value":"missing: lab stock","label":"missing: lab stock"},{"value":"missing: sample group","label":"missing: sample group"},{"value":"missing: synthetic construct","label":"missing: synthetic construct"},{"value":"missing: third party data","label":"missing: third party data"},{"value":"not applicable","label":"not applicable"},{"value":"not collected","label":"not collected"},{"value":"not provided","label":"not provided"},{"value":"restricted access","label":"restricted access"}]},{"type":"text","label":"source material identifiers","name":"source_material_identifiers","required":false,"visible":true,"helpText":"A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain &apos;UAM:Herps:14&apos; , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).","group":"Pointer to physical material"},{"type":"text","label":"experimental factor","name":"experimental_factor","required":false,"visible":true,"helpText":"Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI. E.g. time series design [EFO:EFO_0001779]","group":"experimental factor and block"},{"type":"text","label":"taxonomic classification","name":"taxonomic_classification","required":false,"visible":true,"helpText":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)","group":"Organism characteristics: genetic"},{"type":"text","label":"annotation source","name":"annotation_source","required":false,"visible":true,"helpText":"For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter","group":"Reference"},{"type":"text","label":"reference for biomaterial","name":"reference_for_biomaterial","required":false,"visible":true,"helpText":"Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.","group":"Reference"},{"type":"text","label":"reference database(s)","name":"reference_database_s","required":false,"visible":true,"helpText":"List of database(s) used for ORF annotation, along with version number and reference to website or publication","group":"Reference"},{"type":"text","label":"sample material processing","name":"sample_material_processing","required":false,"visible":true,"helpText":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.","group":"sample processing"},{"type":"text","label":"nucleic acid extraction","name":"nucleic_acid_extraction","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample","group":"sample processing"},{"type":"text","label":"nucleic acid amplification","name":"nucleic_acid_amplification","required":false,"visible":true,"helpText":"A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids","group":"sample processing"},{"type":"text","label":"library size","name":"library_size","required":false,"visible":true,"helpText":"Total number of clones in the library prepared for the project","group":"sample processing","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"}},{"type":"text","label":"library reads sequenced","name":"library_reads_sequenced","required":false,"visible":true,"helpText":"Total number of clones sequenced from the library","group":"sample processing","simpleValidation":{"pattern":"[+-]?[0-9]+","patternMessage":"Must match pattern: [+-]?[0-9]+"}},{"type":"text","label":"library vector","name":"library_vector","required":false,"visible":true,"helpText":"Cloning vector type(s) used in construction of libraries","group":"sample processing"},{"type":"text","label":"library screening strategy","name":"library_screening_strategy","required":false,"visible":true,"helpText":"Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences","group":"sample processing"},{"type":"text","label":"assembly software","name":"assembly_software","required":false,"visible":true,"helpText":"Tool(s) used for assembly, including version number and parameters in the format {software};{version};{parameters} e.g. metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise","group":"sample processing"},{"type":"text","label":"adapters","name":"adapters","required":false,"visible":true,"helpText":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters","group":"sample processing"},{"type":"text","label":"depth","name":"depth","required":false,"visible":true,"helpText":"The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.","group":"Environmental information","simpleValidation":{"pattern":"((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))","patternMessage":"Must match pattern: ((0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$))"},"units":[{"value":"m","label":"m"},{"value":"mm","label":"mm"}]}]}]}