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ERC000014

ERC000014: GSC MIxS human associated

Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms.

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 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

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 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.
trophic level optional Trophic levels are the feeding position in a food chain. microbes can be a range of producers (e.g. chemolithotroph) autotroph, carboxydotroph, chemoautotroph, chemoheterotroph, chemolithoautotroph, chemolithotroph, chemoorganoheterotroph, chemoorganotroph, chemosynthetic, chemotroph, copiotroph, diazotroph, facultative autotroph, heterotroph, lithoautotroph, lithoheterotroph, lithotroph, methanotroph, methylotroph, mixotroph, obligate chemoautolithotroph, oligotroph, organoheterotroph, organotroph, photoautotroph, photoheterotroph, photolithoautotroph, photolithotroph, photosynthetic, phototroph
observed biotic relationship optional 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. commensal, free living, mutualism, parasite, symbiont
known pathogenicity optional To what is the entity pathogenic, for instance plant, fungi, bacteria
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
propagation optional 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.
observed host symbionts optional The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.
sample collection device optional 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).
sample collection method optional The method employed for collecting the sample. can be provided in the form of a pmid, doi, url or text.
urine/collection method optional Specification of urine collection method catheter, clean catch
sample storage temperature optional Temperature at which sample was stored, e.g. -80 (Units: °C)
sample storage location optional Location at which sample was stored, usually name of a specific freezer/room. indicate the location name.
oxygenation status of sample optional Oxygenation status of sample aerobic, anaerobic
medical history performed optional Whether full medical history was collected No, Yes
study completion status optional Specification of study completion status, if no the reason should be specified No - adverse event, No - lost to follow up, No - non-compliance, No - other, Yes
project name mandatory Name of the project within which the sequencing was organized
ploidy optional 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
number of replicons optional 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.
extrachromosomal elements optional Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). megaplasmids? other plasmids (borrelia has 15+ plasmids).
estimated size optional 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.
target gene optional Targeted gene or locus name for marker gene studies
target subfragment optional Name of subfragment of a gene or locus. important to e.g. identify special regions on marker genes like v6 on 16s rrna
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
sequence quality check optional 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 manual, none, software
chimera check software optional 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.
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
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.
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)
organism count optional 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)
sample storage duration optional Duration for which the sample was stored. indicate the duration for which the sample was stored written in iso 8601 format.
nose/mouth/teeth/throat disorder optional History of nose/mouth/teeth/throat disorders; can include multiple disorders. the terms should be chosen from the do (human disease ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=doid:2825), mouth disease (https://disease-ontology.org/?id=doid:403), tooth disease (https://disease-ontology.org/?id=doid:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=doid:974).
host HIV status optional Hiv status of subject, if yes haart initiation status should also be indicated as [yes or no] No, Yes
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
lung/pulmonary disorder optional History of pulmonary disorders; can include multiple disorders. the terms should be chosen from the do (human disease ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=doid:850).
lung/nose-throat disorder optional History of nose-throat disorders; can include multiple disorders, the terms should be chosen from the do (human disease ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=doid:850), upper respiratory tract disease (https://disease-ontology.org/?id=doid:974).
blood/blood disorder optional History of blood disorders; can include multiple disorders. the terms should be chosen from the do (human disease ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=doid:74).
urine/kidney disorder optional History of kidney disorders; can include multiple disorders. the terms should be chosen from the do (human disease ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=doid:557).
urine/urogenital tract disorder optional History of urogenital tract disorders; can include multiple disorders. the terms should be chosen from the do (human disease ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=doid:18).
host subject id optional A unique identifier by which each subject can be referred to, de-identified, e.g. #131
IHMC medication code optional Can include multiple medication codes 01=1=Analgesics/NSAIDS, 02=2=Anesthetics, 03=3=Antacids/H2 antagonists, 04=4=Anti-acne, 05=5=Anti-asthma/bronchodilators, 06=6=Anti-cholesterol/Anti-hyperlipidemic, 07=7=Anti-coagulants, 08=8=Antibiotics/(anti)-infectives, parasitics, microbials, 09=9=Antidepressants/mood-altering drugs, 10=10=Antihistamines/ Decongestants, 11=11=Antihypertensives, 12=12=Cardiovascular, other than hyperlipidemic/HTN, 13=13=Contraceptives (oral, implant, injectable), 14=14=Emergency/support medications, 15=15=Endocrine/Metabolic agents, 16=16=GI meds (anti-diarrheal, emetic, spasmodics), 17=17=Herbal/homeopathic products, 18=18=Hormones/steroids, 19=19=OTC cold & flu, 20=20=Vaccine prophylaxis, 21=21=Vitamins, minerals, food supplements, 99=99=Other
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 body site optional Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). for foundational model of anatomy ontology (fma) (v 3.1) terms, please see http://purl.bioontology.org/ontology/fma
drug usage optional Any drug used by subject and the frequency of usage; can include multiple drugs used
host height optional The height of subject (Units: mm)
host body-mass index optional Body mass index, calculated as weight/(height)squared (Units: kg/m2)
ethnicity optional A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/list_of_contemporary_ethnic_groups
host occupation optional Most frequent job performed by subject 01=01 Accounting/Finance, 02=02 Advertising/Public Relations, 03=03 Arts/Entertainment/Publishing, 04=04 Automotive, 05=05 Banking/ Mortgage, 06=06 Biotech, 07=07 Broadcast/Journalism, 08=08 Business Development, 09=09 Clerical/Administrative, 10=10 Construction/Trades, 11=11 Consultant, 12=12 Customer Services, 13=13 Design, 14=14 Education, 15=15 Engineering, 16=16 Entry Level, 17=17 Executive, 18=18 Food Service, 19=19 Government, 20=20 Grocery, 21=21 Healthcare, 22=22 Hospitality, 23=23 Human Resources, 24=24 Information Technology, 25=25 Insurance, 26=26 Law/Legal, 27=27 Management, 28=28 Manufacturing, 29=29 Marketing, 30=30 Pharmaceutical, 31=31 Professional Services, 32=32 Purchasing, 33=33 Quality Assurance (QA), 34=34 Research, 35=35 Restaurant, 36=36 Retail, 37=37 Sales, 38=38 Science, 39=39 Security/Law Enforcement, 40=40 Shipping/Distribution, 41=41 Strategy, 42=42 Student, 43=43 Telecommunications, 44=44 Training, 45=45 Transportation, 46=46 Warehouse, 47=47 Other, 99=99 Unknown/Refused
host total mass optional Total mass of the host at collection, the unit depends on host (Units: kg)
host phenotype optional Phenotype of host. for phenotypic quality ontology (pato) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/pato
host body temperature optional Core body temperature of the host when sample was collected (Units: ºC)
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
host scientific name optional Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.
presence of pets, animals, or insects optional The type and number of animals or insects present in the sampling space.
temperature optional Temperature of the sample at time of sampling (Units: ºC)
salinity optional 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. (Units: psu)
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).
smoker optional Specification of smoking status ex-smoker, non-smoker, smoker
major diet change in last six months optional Specification of major diet changes in the last six months, if yes the change should be specified
weight loss in last three months optional Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss (Units: kg)
travel outside the country in last six months optional Specification of the countries travelled in the last six months; can include multiple travels
host diet optional Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, mediterranean etc.; can include multiple diet types
twin sibling presence optional Specification of twin sibling presence
host last meal optional Content of last meal and time since feeding; can include multiple values
amniotic fluid/gestation state optional Specification of the gestation state
host family relationship optional Familial relationships to other hosts in the same study; can include multiple relationships
amniotic fluid/maternal health status optional Specification of the maternal health status
host genotype optional Observed genotype
amniotic fluid/foetal health status optional Specification of foetal health status, should also include abortion
host pulse optional Resting pulse, measured as beats per minute (Units: bpm)
amniotic fluid/color optional Specification of the color of the amniotic fluid sample
host body product optional Substance produced by the body, e.g. stool, mucus, where the sample was obtained from. for foundational model of anatomy ontology (fma) (v 3.1) terms, please see http://purl.bioontology.org/ontology/fma
perturbation optional Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types
negative control type optional The substance or equipment used as a negative control in an investigation
positive control type optional The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.
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]
encoded traits optional Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage
subspecific genetic lineage optional 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.
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)
isolation and growth condition optional 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.
annotation source optional For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
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.
sample volume or weight for DNA extraction optional 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'. (Units: ng)
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 construction method optional Library construction method used for clone libraries
library vector optional Cloning vector type(s) used in construction of libraries