Food and Production

Any result of a bacterial culture experiment reported as a binary assessment such as positive/negative, active/inactive.

Taxonomic information about the cultured organism(s).

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.

Measurements of biologically distinct samples that show biological variation.

Repeated measurements of the same sample that show independent measures of the noise associated with the equipment and the protocols.

The reason that the sample was collected.

Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)

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.

To what is the entity pathogenic, for instance plant, fungi, bacteria

Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments

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.

Temperature at which sample was transported, e.g. -20 or 4 degree Celsius.

Container in which the sample was stored during transport. Indicate the location name.

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.

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).

The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.

temperature at which sample was stored, e.g. -80

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.

Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name.

Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample

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

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.

reference or method used in determining soil series name or other lower-level classification

reference or method used in determining soil texture

pH measurement of the soil; e.g. 6.2

Description of the material covering the sampled soil. This field accepts terms under ENVO:00010483, environmental material.

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.

Porosity of soil or deposited sediment is volume of voids divided by the total volume of sample.

Conductivity of soil at time of sampling.

Establishment details about the type of facility where the sample was taken. This is independent of the specific product(s) within the facility.

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).

The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.

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.

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.

Name of the project within which the sequencing was organized

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.

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.

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.

The number of times farm equipment is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.

Source of water used on the farm for irrigation of crops or watering of livestock.

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.

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.

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.

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.

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.

Descriptors of the food production system such as wild caught, free-range, organic, free-range, industrial, dairy, beef.

The number of food animals of the same species that are maintained together as a unit, i.e. a herd or flock.

Date of administration of soil amendment or fertilizer. Multiple terms may apply and can be separated by pipes, listing in reverse chronological order.

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.

Amount of crop produced per unit or area of land.

Number of water delivery events within a given period of time.

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).

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.

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

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.

Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).

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.

Targeted gene or locus name for marker gene studies

Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA

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

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

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.

A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL

Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL

Can a 16S gene be recovered from the submitted bin, SAG or MAG?

Tools used for 16S rRNA gene extraction. Add names and versions of software(s), parameters used

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.

Tools used for completion estimate, i.e. checkm, anvi'o, busco. Mandatory for all samples directly linked with SAGs or MAGs.

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

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.

Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community

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.

The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.

The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system

The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system

The geographical origin of the sample as defined by the specific region name followed by the locality name.

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.

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.

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).

The elevation of the sampling site as measured by the vertical distance from mean sea level.

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.

For time-course research studies involving samples of the food commodity, indicate the total duration of the time-course study.

The number of samples collected during the current sampling event.

surface materials at the point of sampling

ventilation rate of the system in the sampled premises

type of indoor surface

The intentional movement of air from outside a building to the inside through forced or natural movement of air

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.

The floor of the building, where the sampling room is located

Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.

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.

Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).

The relative humidity of the fermented food fermentation process.

The length, width and height of sampling room

The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.

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)

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.

characteristic shape, appearance or growth form of a plant species

Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format.

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.

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).

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

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

NCBI taxon id of the host, e.g. 9606

the height of subject

the length of subject

total mass of the host at collection, the unit depends on host

phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO

Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.

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.

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.

amount of water vapour in the air, at the time of sampling

electrical conductivity of water

the amount of solar energy that arrives at a specific area of a surface during a specific time interval

wind direction is the direction from which a wind originates

speed of wind measured at the time of sampling

temperature of the sample at time of sampling

turbidity measurement

pH measurement

reference or method used in determining pH

The type of vessel used for containment of the fermentation.

The amount of headspace oxygen in a fermentation vessel.

The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.

Reference or method used in determining total organic carbon

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

Reference or method used in determining the total nitrogen

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

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.

total carbon content

Definition for soil: total organic C content of the soil units of g C/kg soil. Definition otherwise: total organic carbon content

Total nitrogen content of the sample

pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid.

The pH of the fermented food fermentation process.

Number of bacteria in sample, as defined by bacteria density (http://purl.obolibrary.org/obo/GENEPIO_0000043).

reference or method used in determining salinity

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/

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).

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).

previous land use and dates

whether or not crop is rotated, and if yes, rotation schedule

note method(s) used for tilling

Average humidity of the region throughout the growing season.

Mean seasonal temperature

The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.

Date of unusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order.

Unusual weather events that may have affected microbial populations. Multiple terms can be separated by pipes, listed in reverse chronological order.

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).

observed genotype

The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier.

measurement of dry mass

Tool or approach used for host prediction

For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature

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.

Any chemicals that are added to the fermentation process to achieve the desired final product.

The amount of chemical added to the fermentation process.

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.

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.

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).

The temperature of the fermented food fermentation process.

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.

The amount of starter culture used to inoculate a new batch.

The source from which the microbial starter culture was sourced. If commercially supplied, list supplier.

Information about the protocol or method used to prepare the starter inoculum.

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.

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).

The time duration of the fermented food fermentation process.

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).

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.

Sample incubation temperature if unpublished or unvalidated method is used.

type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types

Sample incubation duration if unpublished or unvalidated method is used. Indicate the timepoint written in ISO 8601 format.

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.

The substance or equipment used as a negative control in an investigation

The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.

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]

Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage

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.

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.

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)

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)

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).

relevant rooting conditions, such as field plot size, sowing density, container dimensions, number of plants per container

measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L)

measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L)

source of organic carbon in the culture rooting medium; e.g. sucrose

pH measurement of the culture rooting medium; e.g. 5.5

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.

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.

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.

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.

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.

For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter

Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.

The location the sequencing run was performed. Indicate the name of the lab or core facility where samples were sequenced.

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.

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.

The name of the extraction kit used to recover the nucleic acid fraction of an input material is performed.

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.

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.

Method used to free DNA from interior of the cell(s) or particle(s)

Name of the kit or standard protocol used for cell(s) or particle(s) lysis

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). ]

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.

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'.

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

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

Total number of clones in the library prepared for the project

Total number of clones sequenced from the library

Cloning vector type(s) used in construction of libraries

Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences

Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'

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

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

Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters

The name(s) (generic or brand) of the antimicrobial(s) given to the food animal within the last 30 days.

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.

Other users sharing access to the same water source. Multiple terms can be separated by one or more pipes.

Type of plant or animal from which the food product or its major ingredient is derived or a chemical food source [FDA CFSAN 1995].

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.

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.

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).

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."

The process of cleaning food to separate other environmental materials from the food source. Multiple terms can be separated by pipes.

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.

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).

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).

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).

The route by which the antimicrobial is administered into the body of the food animal.

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).

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.

The sex and reproductive status of the food animal.

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.

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).

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).

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).

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).

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.

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.

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.

Other names by which the food product is known by (e.g., regional or non-English names).

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.

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.

The duration of time (days) that the antimicrobial was administered to the food animal.

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).

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).

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.

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).

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.

Plant reproductive part used in the field during planting to start the crop.

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.

The frequency per day that the antimicrobial was administered to the food animal.

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.

The quantity of food purchased by consumer.

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).

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.

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.

The prescribed intended use of or the condition treated by the antimicrobial given to the food animal by any route of administration.

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.

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).

The date a food product was purchased by consumer.

Temperature at which food commodity was stored by the consumer, prior to onset of illness or sample collection.

The maximum number of product units within a package

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.

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).

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.

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 ";"

Location of sampled soil to other parts of the farm e.g. under crop plant, near irrigation ditch, from the dirt road.

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.

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.

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

information about treatment involving use of biotic factors, such as bacteria, viruses or fungi

information about any mechanical damage exerted on the plant; can include multiple damages and sites

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