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Human microbiome biological/environmental metadata

  Minimal biological/environmental metadata for human microbiome

metadata definition reference of definition[] expected unit of measurement example sources( where this or similar matadata field is mentioned)
Site metadata collection_date The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated. Restricted text field, ISO8601 compliant MIXS:0000011 YYYY-MM-DD e.g. 2013-03-25T12:42:31+01:00 “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”
Collected by Name of person or institute that collected the sample “ENA Marine Microalgae Checklist; Checklist: ERC000043”
Geographic location The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list, or the GAZ ontology MIXS:0000010 e.g. USA: Maryland, Bethesda; Atlantic Ocean region OR [GAZ:00051071] “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”)
Latitude The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system. MIXS:0000009 e.g. -41.373744 “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”
Longitude The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system. MIXS:0000009 e.g. 146.266145 “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”
Elevation Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m MIXS:0000093 Preferred_unit: meter e.g. 100 m “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”)
Altitude Altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit MIXS:0000094 Preferred_unit: meter e.g. 100 m “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”
env_broad_scale Report the major environmental system the sample or specimen came from. Systems(s) identifiers should provide a coarse, general environmental context of where the sampling was done. Terms, such as anatomical sites, from OBO Library ontologies which interoperate with EnvO (e.g. [UBERON]) are accepted in this field. If more than one term applies to the field, | should be used to separate them. MIXS:0000012 e.g. gut wall [UBERON:0000328] “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”,  “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”
env_local_scale 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. Entry should be of a smaller environmental context than env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. [UBERON]) are accepted in this field. If more than one term applies to the field, | should be used to separate them. MIXS:0000013 e.g. if gut wall [UBERON:0000328] was used to describe the env_broad_scale one of the following subclasses should be used to describe further env_local_scale: wall of esophagus [UBERON:0001096]| wall of intestine [UBERON:0001262]| wall of stomach [UBERON:0001167]; note that further subclasses are available if applicable and better describe the sample “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”,  “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”
env_medium Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. 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). If more than one term applies to the field, | should be used to separate them. MIXS:0000014 e.g. feces [UBERON:0001988]| excreted gas [UBERON:0034945] “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”
Sample size/mass The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected MIXS:0000001 e.g. H x W x L, vol., mass 2000 ml water, 1000 g soil “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”
Site conditions Environmental temp, relative humidity (RH), salinity, pH e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 MSI-ECWSG (Morrison et al. (2007))
Material conditions Sample material temp, RH, salinity, pH e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, MSI-ECWSG (Morrison et al. (2007)), “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”
Microbial ID Taxonomy and/or culture source, if available. Expected_value: [NCBI taxonomy ID] Expected_value: NCBI:txid#### from [NCBI taxonomy ID] e.g. E. coli [NCBI:txid562] “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”
Microbial isolate microbial isolate cultured?: Y/N
Culture medium Composition of processed material providing the needed nourishment for microorganisms or cells to grow in vitro. This field accepts terms listed under culture medium [OBI:0000079]. If the proper descriptor is not listed please use text to describe the culture medium MIXS:0001216 e.g. minimal defined medium [MCO:0000881] “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, MSI-ECWSG (Morrison et al. (2007))
chem_administration List of chemical compounds administered to host where sampling occurred. Can include multiple compounds separated by |. For compunds consult chemical entities of biological interest ontology (chebi) (v 163) MIXS:0000751 e.g. tetracycline [CHEBI:27902];2023-12-11T19:41+01:00|ampicilin[CHEBI:28971];2023-12-11T19:41+01:00 “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”
Host metadata Host name OR host_taxid Scientific name [NCBI taxonomy ID] MIXS:0000250 Expected_value: NCBI:txid#### from [NCBI taxonomy ID] e.g. Canis lupus familiaris [NCBI:txid9615], Homo sapiens [NCBI:txid9606] MSI-ECWSG (Morrison et al. (2007))
host_common_name Common name of the host MIXS:0000248 free text string e.g. human, dog, cattle “GSC MIxS: Host-associatedMIMS”
host_height Height of host or length of host MIXS:0000264 Preferred_unit: centimeter, millimeter, meter e.g. 177 cm “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS”
host_tot_mass Total mass of the host at collection, the unit depends on host MIXS:0000263 Preferred_unit: kilogram, gram e.g. 77 kg OR 3568 g “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS”
host_body_site Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc…). Recomended use of FMA or UBERON ontologies MIXS:0000867 ontologies, separated by “|” if two or more apply e.g. gut [FMA:45615] OR gut wall [UBERON:0000328] “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”
host_body_product Bodily substance where the sample was obtained from. Recomended use of FMA or UBERON ontologies. Multiple ontologies can apply, use | to separate them MIXS:0000888 Expected value : ontology used e.g. feces [FMA:64183]|urine[FMA:12274] “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”
host_age 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 MIXS:0000255 Preferred_unit: year, day, hour e.g. 28 y, 30 d, 30 h, 12 s “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS”
Sex Assigned at Birth NCIT:C205472 The male or female designation that doctors ascribe to a newborn infant, usually based on the appearance of the child's external genitalia, and that is marked on their birth records. NCIT:C205472 ontology e.g. Assigned Male at Birth, Assigned Female at Birth, Intersex “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”
Gender NCITC17357 The male or female designation that doctors ascribe to a newborn infant, usually based on the appearance of the child's external genitalia, and that is marked on their birth records. NCIT:C205472 ontology e.g. Assigned Male at Birth, Assigned Female at Birth, Intersex “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”
host_diet Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types MIXS:0000869 free text string E.g. omnivore [ecocore:00000082], substrate, medium; note here, that multiple possible subclasses exist in organism [OBI:0100026], such as autotroph [ECOCORE:00000023]|heterotroph [ECOCORE:00000010] “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS”
host_subject_id A unique identifier by which each subject can be referred to, de-identified [MIXS:0000861] free text string e.g. s9s8 “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHostAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”
host_disease_stat Diagnosed diseases of host; can hold multiple values, separated by |. Non-human host diseases should be deposited as free text MIXS:0000031 Expected_value: free text disease name or Disease Ontology term e.g. rabies, avian influenza, heartworm disease “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”
ethnicity 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. MIXS:0000895 Expected value: free text string e.g. Slovene OR Turkic “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “U.s. Office of Management and Budget (OMB): About the Topic of Race”, “GSC MIxS: MimsHumanAssociated”, “GSC MIxS: MimsHumanGut”, “GSC MIxS: MimsHumanOral”, “GSC MIxS: MimsHumanSkin”, “GSC MIxS: MimsHumanVaginal”
smoker Specification of smoking status MIXS:0000262 Expected value: free string text e.g. yes “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: MimsHumanAssociated”
disorder_history Terms from DOID ontologies should be used to describe disorder. Host history of pulmonary [DOID:850], nose-throat [DOID:974], blood [DOID:74], kidney [DOID:557] and urogenital tract disorders [DOID:18] . If multiple disorders apply, separate them by | MIXS:0000031 ontologies, separated by “|” if two or more apply e.g. lung abscess [DOID:0060317]|tonsillitis [DOID:10456]|hypochromic anemia [DOID:11759]|etc. “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “U.s. Office of Management and Budget (OMB): About the Topic of Race”

References

“ENA Marine Microalgae Checklist; Checklist: ERC000043.” https://www.ebi.ac.uk/ena/browser/view/ERC000043.

“GOLD Ecosystem Classification Paths.” https://gold.jgi.doe.gov/ecosystem_classification.

“GSC MIxS Human Associated; ENA Checklist: ERC000014.” https://www.ebi.ac.uk/ena/browser/view/ERC000014.

“GSC MIxS: Host-associatedMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/.

“GSC MIxS: Human-associatedMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/.

“GSC MIxS: Human-gutMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Human-gutMIMS/.

“GSC MIxS: Human-oralMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Human-oralMIMS/.

“GSC MIxS: Human-skinMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Human-skinMIMS/.

“GSC MIxS: Human-vaginalMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Human-vaginalMIMS/.

“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package.” https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/.

Morrison, Norman, Daniel Bearden, Jacob G. Bundy, Timothy Collette, Fraser Currie, Matthew Davey, Migdalia Dominguez, et al. 2007. “Standard Reporting Requirements for Biological Samples in Metabolomics Experiments: Environmental Context.” Metabolomics 3 (2): 203–10. https://doi.org/10.1007/s11306-007-0067-1.

“U.s. Office of Management and Budget (OMB): About the Topic of Race.” https://www.census.gov/topics/population/race/about.html.