ERC000029

ERC000029: ENA Global Microbial Identifier reporting standard checklist GMI_MDM:1.1

Minimum Data for Matching (MDM). A checklist for reporting metadata of pathogen samples for the Global Microbial Identifier (GMI) reporting system. More about GMI can be found here http://www.g-m-i.org/

Study

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.

Experiment

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	optional	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	optional	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

Run

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

Sample

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 run.
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.
sample storage conditions	optional	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).
subject exposure	optional	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
travel-relation	optional	Designates the relation of the main diagnosis to the patient's travel.	not ascertainable, not travel-related, travel-related
clinical setting	optional	The timing of the clinic visit in relation to travel.	after travel, during travel
country of travel	optional	The name of the country of patient's travel.	Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burma, 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, Cyprus, Czech Republic, Czechoslovakia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands, Faroe Islands, Federal Republic of Germany, Fiji, Finland, Former Yugoslav Republic of Macedonia, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, GDR, 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, 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, Kingman Reef, Kiribati, Korea, 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, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Namibia, Nauru, Navassa Island, Nepal, Netherlands, Netherlands Antilles, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, Northern Mariana Islands, Norway, Oman, 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, Russia, Rwanda, Saint Barthelemy, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Martin, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Serbia and Montenegro, Seychelles, Sierra Leone, Singapore, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, South Sudan, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Thailand, Timor-Leste, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, USSR, 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
collected_by	mandatory	Name of persons or institute who collected the specimen
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)
geographic location (region and locality)	optional	The geographical origin of the sample as defined by the specific region name followed by the locality name.
identified_by	optional	Name of the expert who identified the specimen taxonomically
subject exposure duration	optional	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: year)
amount or size of sample collected	optional	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. (Units: m3)
environmental_sample	mandatory	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	No, Yes
mating_type	optional	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
pathotype	optional	Name or code for pathotype of organism
host disease status	optional	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
host disease outcome	optional	Disease outcome in the host.	dead, recovered, recovered with sequelae
host subject id	optional	A unique identifier by which each subject can be referred to, de-identified, e.g. #131
host age	optional	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 (Units: years)
host taxid	optional	Ncbi taxon id of the host, e.g. 9606
host life stage	optional	Description of life stage of host
host health state	mandatory	Health status of the host at the time of sample collection.	diseased, healthy, 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
host sex	optional	Gender or sex of the host.	female, hermaphrodite, male, 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, neuter, not applicable, not collected, not provided, other, restricted access
lab_host	optional	Scientific name of the laboratory host used to propagate the source organism from which the sample was obtained
host scientific name	mandatory	Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.
passage_history	optional	Details of passage of culture between time of isolation and sequencing
Is the sequenced pathogen host associated?	mandatory	Is the sequenced pathogen host associated? ('yes' or 'no')	No, Yes
bio_material	optional	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/
culture_collection	optional	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/
specimen_voucher	optional	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/
isolate	mandatory	Individual isolate from which the sample was obtained
sub_species	optional	Name of sub-species of organism from which sample was obtained
sub_strain	optional	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
sub_group	optional	Name of sub-group of organism from which sample was obtained
sub_type	optional	Name of sub-type of organism from which sample was obtained
serovar	recommended	Serological variety of a species (usually a prokaryote) characterized by its antigenic properties
strain	recommended	Name of the strain from which the sample was obtained.
host disease stage	optional	Disease stage of host
isolation source host-associated	recommended	Name of host tissue or organ sampled for analysis. example: tracheal tissue
host description	optional	Other descriptive information relating to the host.
genotype	optional	Name or code for genotype of organism
isolation source non-host-associated	recommended	Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. example: soil
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)