| metadata | definition | reference of definition[<url_to_definition>] | expected unit of measurement | example | sources( where this or similar matadata field is mentioned) | ||
|---|---|---|---|---|---|---|---|
| Site metadata | Collection date/time | Restricted text, 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. ISO8601 compliant | e.g. 2013-03-25T12:42:31+01:00 | “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”, “GSC MIxS: SedimentMIMS”, “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS” | |||
| 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 | e.g. USA: Maryland, Bethesda; Atlantic Ocean region OR [GAZ:00051071] | “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”, “GSC MIxS: SedimentMIMS”, “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS” | ||||
| Latitude | The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system. | e.g. 48.737219 | “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”, “GSC MIxS: SedimentMIMS”, “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS” | ||||
| Longitude | The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system. | e.g. -121.376561 | “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”, “GSC MIxS: SedimentMIMS”, “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS” | ||||
| Elevation | Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m | e.g. 100 m | “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”, “GSC MIxS: SedimentMIMS”, “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS” | ||||
| Altitude | Altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit | e.g. 100 m | “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”, “GSC MIxS: SedimentMIMS”, “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS” | ||||
| 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. Recommended use of EnvO s biome class: [ENVO_00000428]. If more than one term applies to the field, | should be used to separate them.; note here, that subclasses of terrestrial biome [ENVO:00000446] should be used here. | e.g. terrestrial biome [ENVO:00000446] | “GSC MIxS: Plant-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS” | ||||
| 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. | e.g. if terrestrial biome [ENVO:00000446] was used in env_broad_scale, env_local_scale should be one of the following subclasses : anthropogenic terrestrial [ENVO:01000219]|mangrove biome [ENVO:01000181]| shrubland biome [ENVO:01000176]| terrestrial environmental zone [ENVO:01001199] | tundra biome [ENVO:01000180] | woodland biome [ENVO:01000175]; note here, that some ontologies listed here have further subclasses that can be used, if they better describe the local environment of the sample. | “GSC MIxS: Plant-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS” | ||||
| env_medium | Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. Recommended use of EnvO’s subclasses of environmental material [ENVO:00010483]. 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. | e.g. arable soil [ENVO:00005742]|bare soil [ENVO:01001616]|bulk soil [ENVO:00005802] OR arterial blood [UBERON:0013755]|venous blood [UBERON:0013756]|blood plasma [UBERON:0001969] | “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”, “GSC MIxS: SedimentMIMS”, “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS” | ||||
| Sample size/mass | The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected | e.g. H x W x L, vol., mass 2000 ml water, 1000 g soil | “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”, “GSC MIxS: SedimentMIMS”, “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS” | ||||
| Site conditions | Environmental temp, RH, salinity, pH | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: Plant-associatedMIMS”, 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 | “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS”, MSI-ECWSG (Morrison et al. (2007)) | ||||
| Microbial ID | Taxonomy and/or culture source, if available. Expected_value: [NCBI taxonomy ID] | e.g. E. coli [NCBI:txid562] | “GSC MIxS: SedimentMIMS”, “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS” | ||||
| Microbial isolate | Microbial isolate cultured?: Y/N | ||||||
| Culture substrate | 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 | e.g. minimal defined medium [MCO:0000881] | MSI-ECWSG (Morrison et al. (2007)) | ||||
| chem_administration | List of chemical compounds administered to host or on site where sampling occurred. Can include multiple compounds separated by |. For compounds consult chemical entities of biological interest ontology (chebi) (v 163) | e.g. agar [CHEBI:2509];2018-05-11T20:00Z|castor oil [CHEBI:140618];2023-12-07T17:00+02:00 | “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”, “GSC MIxS: SedimentMIMS”, “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS” | ||||
| Host metadata | Host name | Scientific name [NCBI taxonomy ID] | e.g. Canis lupus familiaris [NCBI:txid9615], Homo sapiens [NCBI:txid9606] | “GSC MIxS: Plant-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS”, MSI-ECWSG (Morrison et al. (2007)) | |||
| host_common_name | Common name of the host | e.g. human, dog, cattle | “GSC MIxS: Host-associatedMIMS” | ||||
| host_height OR host_length | Height of host or length of host | e.g. 177 cm | “GSC MIxS: Plant-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS” | ||||
| host_tot_mass | Total mass of host | 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 | e.g. gut [FMA:45615] OR gut wall [UBERON:0000328] | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package” | ||||
| 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 | e.g. year, day, hour | “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_sex | Gender and/or physical sex of subject/host | “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_diet | Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types | 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” | ||||
| Additional potential terrestrial bio/env considerations | Ecosystem Category | Category list | JGI GOLD (“GOLD Ecosystem Classification Paths”) | ||||
| Ecosystem Type | Type list | JGI GOLD (“GOLD Ecosystem Classification Paths”) | |||||
| Ecosystem Subtype | Subtype list | JGI GOLD (“GOLD Ecosystem Classification Paths”) | |||||
| Specific Ecosystem | Specific ecosystem list | JGI GOLD (“GOLD Ecosystem Classification Paths”) | |||||
| Habitat | Free text | JGI GOLD (“GOLD Ecosystem Classification Paths”) |
“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: BuiltEnvironmentMIMS.” https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/.
“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/.
“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS.” https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/.
“GSC MIxS: Plant-associatedMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/.
“GSC MIxS: SedimentMIMS.” https://genomicsstandardsconsortium.github.io/mixs/SedimentMIMS/.
“GSC MIxS: SoilMIMS.” https://genomicsstandardsconsortium.github.io/mixs/SoilMIMS/.
“GSC MIxS: WastewaterSludgeMIMS.” https://genomicsstandardsconsortium.github.io/mixs/WastewaterSludgeMIMS/.
“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.