GSC MIUVIGS

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

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.

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

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

Name of the project within which the sequencing was organized

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.

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

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

The total number of tRNAs identified from the bin, SAG or MAG

Method used to predict UViGs features such as ORFs, integration site, etc. Add names and versions of software(s), parameters used

Tool used to compare ORFs with database, along with version and cutoffs used. Add names and versions of software(s), parameters used

Tools used for tRNA identification. 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

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)

Has an assembly been performed on a genome bin extracted from a metagenomic assembly?

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

The parameters that have been applied during the extraction of genomes from metagenomic datasets e.g. coverage and kmer

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.

Type of dataset from which the UViG was obtained

Type of genome predicted for the UViG

Expected structure of the viral genome

Type of UViG detection

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

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

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

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

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.

describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived

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.

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

Filtering pore size used in sample preparation e.g. 0-0.22 micrometer

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).

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

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).

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

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]

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)

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.

List of database(s) used for ORF annotation, along with version number and reference to website or publication

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

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.

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

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

Method used to amplify genomic DNA in preparation for sequencing

Kit used to amplify genomic DNA in preparation for sequencing

Method used to sort/isolate cells or particles of interest

List of approaches used to enrich the sample for viruses, if any

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

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.