Minimum information to standardise metadata of binned metagenome samples. Ensures binned and MAG metagenome assembly metadata is compatible.
A Study is a container for a sequencing investigation that may comprise multiple experiments. The Study has an overall goal, but is otherwise minimally defined in the SRA. A Study is composed of a descriptor, zero or more experiments, and zero or more analyses. The submitter may decorate the Study with web links and properties.
Field name | Cardinality | Description | Controlled vocabulary |
---|---|---|---|
alias | mandatory | Unique identificator for a study. this is used to link experiments to the study. | |
title | mandatory | Title of the study as would be used in a publication. | |
study_type | mandatory | The study_type presents a controlled vocabulary for expressing the overall purpose of the study. | Whole Genome Sequencing, Metagenomics, Transcriptome Analysis, Resequencing, Epigenetics, Synthetic Genomics, Forensic or Paleo-genomics, Gene Regulation Study, Cancer Genomics, Population Genomics, RNASeq, Exome Sequencing, Pooled Clone Sequencing, Transcriptome Sequencing, Other |
new_study_type | optional | Optional if 'study_type' is not 'other'. to propose a new term, select other and enter a new study type. | |
study_abstract | optional | Briefly describes the goals, purpose, and scope of the study. this need not be listed if it can be inherited from a referenced publication. |
An experiment object serves as a metadata record encapsulating essential details about a sequencing experiment, including the experimental design, sequencing type, and relevant parameters. This information enhances the interpretation and contextual understanding of nucleotide sequences submitted to the archive.
Field name | Cardinality | Description | Controlled vocabulary |
---|---|---|---|
alias | mandatory | Unique identificator for each experiment. this is used to link runs to experiments. | |
title | mandatory | Short text that can be used to call out experiment records in searches or in displays. this element is technically optional but should be used for all new records. | |
study_alias | mandatory | Identifies the parent study. (from study metadata) | |
sample_alias | mandatory | (from sample metadata) | |
design_description | mandatory | Goal and setup of the individual library including library was constructed. | |
library_name | optional | The submitter's name for this library. | |
library_strategy | mandatory | Sequencing technique intended for this library. | WGS, WGA, WXS, RNA-Seq, ssRNA-seq, snRNA-seq, miRNA-Seq, ncRNA-Seq, FL-cDNA, EST, Hi-C, ATAC-seq, WCS, RAD-Seq, CLONE, POOLCLONE, AMPLICON, CLONEEND, FINISHING, ChIP-Seq, MNase-Seq, DNase-Hypersensitivity, Bisulfite-Seq, CTS, MRE-Seq, MeDIP-Seq, MBD-Seq, Tn-Seq, VALIDATION, FAIRE-seq, SELEX, RIP-Seq, ChIA-PET, Synthetic-Long-Read, Targeted-Capture, Tethered Chromatin Conformation Capture, NOMe-Seq, ChM-Seq, GBS, Ribo-Seq, OTHER |
library_source | mandatory | The library_source specifies the type of source material that is being sequenced. | GENOMIC, GENOMIC SINGLE CELL, TRANSCRIPTOMIC, TRANSCRIPTOMIC SINGLE CELL, METAGENOMIC, METATRANSCRIPTOMIC, SYNTHETIC, VIRAL RNA, OTHER |
library_selection | mandatory | Method used to enrich the target in the sequence library preparation | RANDOM, PCR, RANDOM PCR, RT-PCR, HMPR, MF, repeat fractionation, size fractionation, MSLL, cDNA, cDNA_randomPriming, cDNA_oligo_dT, PolyA, Oligo-dT, Inverse rRNA, Inverse rRNA selection, ChIP, ChIP-Seq, MNase, DNase, Hybrid Selection, Reduced Representation, Restriction Digest, 5-methylcytidine antibody, MBD2 protein methyl-CpG binding domain, CAGE, RACE, MDA, padlock probes capture method, other, unspecified |
library_layout | mandatory | Library_layout specifies whether to expect single, paired, or other configuration of reads. in the case of paired reads, information about the relative distance and orientation is specified. | |
insert_size | optional | Insert size for paired reads | |
library_construction_protocol | optional | Free form text describing the protocol by which the sequencing library was constructed. | |
platform | mandatory | The platform record selects which sequencing platform and platform-specific runtime parameters. this will be determined by the center. optional if 'instrument_model' is provided. | LS454, ILLUMINA, HELICOS, ABI_SOLID, COMPLETE_GENOMICS, BGISEQ, OXFORD_NANOPORE, PACBIO_SMRT, ION_TORRENT, CAPILLARY, DNBSEQ, ELEMENT, ULTIMA, VELA_DIAGNOSTICS, GENAPSYS, GENEMIND, TAPESTRI |
instrument_model | mandatory | Model of the sequencing instrument. | 454 GS, 454 GS 20, 454 GS FLX, 454 GS FLX Titanium, 454 GS FLX+, 454 GS Junior, AB 310 Genetic Analyzer, AB 3130 Genetic Analyzer, AB 3130xL Genetic Analyzer, AB 3500 Genetic Analyzer, AB 3500xL Genetic Analyzer, AB 3730 Genetic Analyzer, AB 3730xL Genetic Analyzer, AB 5500 Genetic Analyzer, AB 5500xl Genetic Analyzer, AB 5500xl-W Genetic Analysis System, AB SOLiD 3 Plus System, AB SOLiD 4 System, AB SOLiD 4hq System, AB SOLiD PI System, AB SOLiD System, AB SOLiD System 2.0, AB SOLiD System 3.0, BGISEQ-50, BGISEQ-500, Complete Genomics, DNBSEQ-G400, DNBSEQ-G400 FAST, DNBSEQ-G50, DNBSEQ-T7, Element AVITI, FASTASeq 300, GENIUS, GS111, Genapsys Sequencer, GenoCare 1600, GenoLab M, GridION, Helicos HeliScope, HiSeq X Five, HiSeq X Ten, Illumina Genome Analyzer, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiScanSQ, Illumina HiSeq 1000, Illumina HiSeq 1500, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 3000, Illumina HiSeq 4000, Illumina HiSeq X, Illumina MiSeq, Illumina MiniSeq, Illumina NovaSeq 6000, Illumina NovaSeq X, Illumina iSeq 100, Ion GeneStudio S5, Ion GeneStudio S5 Plus, Ion GeneStudio S5 Prime, Ion Torrent Genexus, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, Ion Torrent S5 XL, MGISEQ-2000RS, MinION, NextSeq 1000, NextSeq 2000, NextSeq 500, NextSeq 550, Onso, PacBio RS, PacBio RS II, PromethION, Revio, Sentosa SQ301, Sequel, Sequel II, Sequel IIe, Tapestri, UG 100, unspecified |
A run contains a group of reads generated for a particular experiment.
Field name | Cardinality | Description | Controlled vocabulary |
---|---|---|---|
alias | mandatory | Unique identificator for each run. | |
experiment_alias | mandatory | From_experiment_metadata | |
file_name | mandatory | The name or relative pathname of a run data file. | |
file_format | mandatory | The run data file model. | sra, srf, sff, fastq, fasta, tab, 454_native, 454_native_seq, 454_native_qual, Helicos_native, Illumina_native, Illumina_native_seq, Illumina_native_prb, Illumina_native_int, Illumina_native_qseq, Illumina_native_scarf, SOLiD_native, SOLiD_native_csfasta, SOLiD_native_qual, PacBio_HDF5, bam, cram, CompleteGenomics_native, OxfordNanopore_native |
A Sample defines an isolate of sequenceable material upon which sequencing experiments can be based. The Sample object may be a surrogate for taxonomy accession or an anonymized individual identifier. Or, it may fully specify provenance and isolation method of the starting material.
Field name | Cardinality | Description | Controlled vocabulary |
---|---|---|---|
alias | mandatory | Unique identificator for each sample. | |
title | mandatory | Short text that can be used to call out sample records in search results or in displays. | |
taxon_id | mandatory | Ncbi taxonomy identifier. this is appropriate for individual organisms and some environmental samples. | |
sample_description | optional | Free-form text describing the sample, its origin, and its method of isolation. | |
relationship to oxygen | optional | Is this organism an aerobe, anaerobe? please note that aerobic and anaerobic are valid descriptors for microbial environments | aerobe, anaerobe, facultative, microaerophilic, microanaerobe, obligate aerobe, obligate anaerobe |
sample collection method | optional | The method employed for collecting the sample. can be provided in the form of a pmid, doi, url or text. | |
metagenomic source | mandatory | 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 | |
sample derived from | mandatory | 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 | |
project name | mandatory | Name of the project within which the sequencing was organized | |
multiplex identifiers | optional | 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 | |
relevant electronic resources | optional | A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a pmid, doi or url | |
relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | |
number of standard tRNAs extracted | optional | The total number of trnas identified from the bin, sag or mag | |
16s recovered | optional | Can a 16s gene be recovered from the submitted bin, sag or mag? | No, Yes |
16S recovery software | optional | Tools used for 16s rrna gene extraction. add names and versions of software(s), parameters used | |
tRNA extraction software | optional | Tools used for trna identification. add names and versions of software(s), parameters used | |
completeness score | recommended | 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. (Units: %) | |
completeness software | recommended | Tools used for completion estimate, i.e. checkm, anvi'o, busco. mandatory for all samples directly linked with sags or mags. | |
completeness approach | optional | 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 | |
contamination score | recommended | 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. (Units: %) | |
contamination screening input | optional | The type of sequence data used as input | contigs, reads |
contamination screening parameters | optional | 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 | |
decontamination software | optional | Tool(s) used in contamination screening | |
binning software | mandatory | 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) | |
reassembly post binning | optional | Has an assembly been performed on a genome bin extracted from a metagenomic assembly? (Units: Yes) | No, Yes |
MAG coverage software | optional | 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 | |
assembly quality | recommended | 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. | Many fragments with little to no review of assembly other than reporting of standard assembly statistics, Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs, Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better |
investigation type | optional | Nucleic acid sequence report is the root element of all mixs compliant reports as standardised by genomic standards consortium | bacteria_archaea, eukaryote, metagenome, metagenome-assembled genome, metatranscriptome, mimarks-specimen, mimarks-survey, organelle, plasmid, single amplified genome, uncultivated viral genomes, virus |
binning parameters | mandatory | The parameters that have been applied during the extraction of genomes from metagenomic datasets e.g. coverage and kmer | |
taxonomic identity marker | recommended | 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. | |
isolation_source | mandatory | Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived | |
collection date | mandatory | 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. | |
altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | |
geographic location (country and/or sea) | mandatory | 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). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access |
geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | |
geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | |
broad-scale environmental context | mandatory | 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. | |
local environmental context | mandatory | 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. | |
environmental medium | mandatory | 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). | |
elevation | optional | The elevation of the sampling site as measured by the vertical distance from mean sea level. (Units: m) | |
amount or size of sample collected | optional | The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. (Units: m3) | |
size fraction selected | optional | Filtering pore size used in sample preparation e.g. 0-0.22 micrometer | |
source material identifiers | optional | 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). | |
experimental factor | optional | 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] | |
taxonomic classification | optional | 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) | |
reference for biomaterial | optional | Primary publication if isolated before genome publication; otherwise, primary genome report. mandatory for migs of bacteria and archaea. | |
sample material processing | optional | 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. | |
nucleic acid extraction | optional | 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 | |
nucleic acid amplification | optional | 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 | |
library size | optional | Total number of clones in the library prepared for the project | |
library reads sequenced | optional | Total number of clones sequenced from the library | |
library vector | optional | Cloning vector type(s) used in construction of libraries | |
library screening strategy | optional | Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences | |
assembly software | mandatory | 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 | |
adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | |
depth | optional | 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. (Units: mm) |