diff --git a/Biological_Environmental/AnimalAssoc_BioEnv_Metadata.md b/Biological_Environmental/AnimalAssoc_BioEnv_Metadata.md index ff89380..b681934 100644 --- a/Biological_Environmental/AnimalAssoc_BioEnv_Metadata.md +++ b/Biological_Environmental/AnimalAssoc_BioEnv_Metadata.md @@ -2,41 +2,41 @@ ##   Minimal biological/environmental metadata for animal-associated microbiome -| | **metadata** | **definition** | **reference of definition\[\]** | **expected unit of measurement** | **example** | **sources( where this or similar matadata field is mentioned)** | | +| | **metadata** | **definition** | **reference of 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](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | e.g. 2013-03-25T12:42:31+01:00 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | -| | Collected by | | | Name of person or institute that collected the sample | | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/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](https://www.insdc.org/submitting-standards/country-qualifier-vocabulary/), or the [GAZ ontology](http://purl.bioontology.org/ontology/GAZ) | e.g. USA: Maryland, Bethesda; Atlantic Ocean region **OR** [\[GAZ:00051071\]](http://purl.obolibrary.org/obo/GAZ_00051071) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | -| | 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. 33.361547 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | -| | 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. -116.403519 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | -| | Elevation | | | Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m | e.g. 100 m | [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | -| | Depth | | | The vertical distance below local surface. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples | e.g. 100 m | [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/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. Recommended use of EnvO s biome class: [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en). If more than one term applies to the field, \| should be used to separate them. | E.g. aquatic biome [\[ENVO:00002030\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00002030?lang=en)\|terrestrial biome [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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](https://obofoundry.org/) ontologies which interoperate with EnvO (e.g. [UBERON](https://www.ebi.ac.uk/ols4/ontologies/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 [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) was used in env_broad_scale, env_local_scale should be one of the following subclasses : anthropogenic terrestrial [\[ENVO:01000219\]](http://purl.obolibrary.org/obo/ENVO_01000219)\|mangrove biome [\[ENVO:01000181\]](http://purl.obolibrary.org/obo/ENVO_01000181)\| shrubland biome [\[ENVO:01000176\]](http://purl.obolibrary.org/obo/ENVO_01000176)\| terrestrial environmental zone [\[ENVO:01001199\]](http://purl.obolibrary.org/obo/ENVO_01001199) \| tundra biome [\[ENVO:01000180\]](http://purl.obolibrary.org/obo/ENVO_01000180) \| woodland biome [\[ENVO:01000175\]](http://purl.obolibrary.org/obo/ENVO_01000175) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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 [\[ENVO:00010483\]](http://purl.obolibrary.org/obo/ENVO_00010483). Terms from other [OBO ontologies](https://obofoundry.org/) 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. glacial ice [\[ENVO:03000004\]](http://purl.obolibrary.org/obo/ENVO_03000004) **OR** arable soil [\[ENVO:00005742\]](http://purl.obolibrary.org/obo/ENVO_00005742)\|bare soil [\[ENVO:01001616\]](http://purl.obolibrary.org/obo/ENVO_01001616)\|bulk soil [\[ENVO:00005802\]](http://purl.obolibrary.org/obo/ENVO_00005802) **OR** arterial blood [\[UBERON:0013755\]](http://purl.obolibrary.org/obo/UBERON_0013755)\|venous blood [\[UBERON:0013756\]](http://purl.obolibrary.org/obo/UBERON_0013756)\|blood plasma [\[UBERON:0001969\]](http://purl.obolibrary.org/obo/UBERON_0001969) | [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | Site conditions | | Environmental temp, RH, salinity, pH | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | | -| | 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”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | Microbial ID | | | Taxonomy and/or culture source, if available. Expected_value: [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | e.g. *E. coli* [\[NCBI:txid562\]](https://www.ncbi.xyz/Taxonomy/Browser/wwwtax.cgi?id=562) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | -| | Microbial isolate | Microbial isolate cultured?: Y/N | | | | | | -| | Culture substrate | | | This field accepts terms listed under culture medium [\[OBI:0000079\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_0000079?lang=en). If the proper descriptor is not listed please use text to describe the culture medium | e.g. minimal defined medium [\[MCO:0000881\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMCO_0000881?lang=en) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | -| | 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)](http://purl.bioontology.org/ontology/chebi) | E.g. agar [\[CHEBI:2509\]](https://www.ebi.ac.uk/ols4/ontologies/micro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_2509);2018-05-11T20:00Z\|castor oil [\[CHEBI:140618\]](https://www.ebi.ac.uk/ols4/ontologies/chebi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_140618?lang=en);2023-12-07T17:00+02:00 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| **Host metadata** | Host name **OR** host_taxid | Scientific name [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | e.g. *Canis lupus familiaris* [\[NCBI:txid9615\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9615), *Homo sapiens* [\[NCBI:txid9606\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&lin=f&keep=1&srchmode=1&unlock) | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | | | -| | host_common_name | | | Common name of the host | e.g. human, dog, cattle | [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | -| | host_height **OR** host_length | | | Height of host or length of host | e.g. 177 cm | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | host_tot_mass | Total mass of host | | | e.g. 77 kg **OR** 3568 g | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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](https://www.ebi.ac.uk/ols4/ontologies/fma) or [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon) ontologies | e.g. gut [\[FMA:45615\]](http://purl.obolibrary.org/obo/FMA_45615) **OR** gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/UBERON_0000328) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | -| | 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”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | host_sex | | | Gender and/or physical sex of subject/host | | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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 [\[ecocore:00000082\]](http://purl.obolibrary.org/obo/ecocore_00000082), substrate, medium; note here, that multiple possible subclasses exist in organism [\[OBI:0100026\]](http://purl.obolibrary.org/obo/OBI_0100026), such as autotroph [\[ECOCORE:00000023\]](http://purl.obolibrary.org/obo/ECOCORE_00000023)\|heterotroph [\[ECOCORE:00000010\]](http://purl.obolibrary.org/obo/ECOCORE_00000010) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | host_disease_stat | | | Diagnosed diseases of host; can hold multiple values, separated by \|. Non-human host diseases should be deposited as free text | e.g. rabies, avian influenza, heartworm disease | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | -| **Additional potential animal-associated bio/env considerations** | *Ecosystem Category* | *Category list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | | -| | *Ecosystem Type* | | | *Type list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Ecosystem Subtype* | | | *Subtype list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Specific Ecosystem* | | | *Specific ecosystem list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Habitat* | *Free text* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Means of capture* | | | *How was the animal captured/trapped/sampled(e.g. net, stunned, anaesthetized, etc.)* | | *MSI-ECWSG* ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| **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](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | | | e.g. 2013-03-25T12:42:31+01:00 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | +| | Collected by | Name of person or institute that collected the sample | | | | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/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](https://www.insdc.org/submitting-standards/country-qualifier-vocabulary/), or the [GAZ ontology](http://purl.bioontology.org/ontology/GAZ) | | | e.g. USA: Maryland, Bethesda; Atlantic Ocean region **OR** [\[GAZ:00051071\]](http://purl.obolibrary.org/obo/GAZ_00051071) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | +| | 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. 33.361547 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | +| | 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. -116.403519 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | +| | Elevation | Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m | | | e.g. 100 m | [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | +| | Depth | The vertical distance below local surface. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples | | | e.g. 100 m | [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/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. Recommended use of EnvO s biome class: [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en). If more than one term applies to the field, \| should be used to separate them. | | | E.g. aquatic biome [\[ENVO:00002030\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00002030?lang=en)\|terrestrial biome [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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](https://obofoundry.org/) ontologies which interoperate with EnvO (e.g. [UBERON](https://www.ebi.ac.uk/ols4/ontologies/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 [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) was used in env_broad_scale, env_local_scale should be one of the following subclasses : anthropogenic terrestrial [\[ENVO:01000219\]](http://purl.obolibrary.org/obo/ENVO_01000219)\|mangrove biome [\[ENVO:01000181\]](http://purl.obolibrary.org/obo/ENVO_01000181)\| shrubland biome [\[ENVO:01000176\]](http://purl.obolibrary.org/obo/ENVO_01000176)\| terrestrial environmental zone [\[ENVO:01001199\]](http://purl.obolibrary.org/obo/ENVO_01001199) \| tundra biome [\[ENVO:01000180\]](http://purl.obolibrary.org/obo/ENVO_01000180) \| woodland biome [\[ENVO:01000175\]](http://purl.obolibrary.org/obo/ENVO_01000175) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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 [\[ENVO:00010483\]](http://purl.obolibrary.org/obo/ENVO_00010483). Terms from other [OBO ontologies](https://obofoundry.org/) 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. glacial ice [\[ENVO:03000004\]](http://purl.obolibrary.org/obo/ENVO_03000004) **OR** arable soil [\[ENVO:00005742\]](http://purl.obolibrary.org/obo/ENVO_00005742)\|bare soil [\[ENVO:01001616\]](http://purl.obolibrary.org/obo/ENVO_01001616)\|bulk soil [\[ENVO:00005802\]](http://purl.obolibrary.org/obo/ENVO_00005802) **OR** arterial blood [\[UBERON:0013755\]](http://purl.obolibrary.org/obo/UBERON_0013755)\|venous blood [\[UBERON:0013756\]](http://purl.obolibrary.org/obo/UBERON_0013756)\|blood plasma [\[UBERON:0001969\]](http://purl.obolibrary.org/obo/UBERON_0001969) | [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | Site conditions | | Environmental temp, RH, salinity, pH | | | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | +| | 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”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | | | +| | Microbial ID | Taxonomy and/or culture source, if available. Expected_value: [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | | | e.g. *E. coli* [\[NCBI:txid562\]](https://www.ncbi.xyz/Taxonomy/Browser/wwwtax.cgi?id=562) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | +| | Microbial isolate | Microbial isolate cultured?: Y/N | | | | | | +| | Culture substrate | This field accepts terms listed under culture medium [\[OBI:0000079\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_0000079?lang=en). If the proper descriptor is not listed please use text to describe the culture medium | | | e.g. minimal defined medium [\[MCO:0000881\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMCO_0000881?lang=en) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | 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)](http://purl.bioontology.org/ontology/chebi) | | | E.g. agar [\[CHEBI:2509\]](https://www.ebi.ac.uk/ols4/ontologies/micro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_2509);2018-05-11T20:00Z\|castor oil [\[CHEBI:140618\]](https://www.ebi.ac.uk/ols4/ontologies/chebi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_140618?lang=en);2023-12-07T17:00+02:00 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| **Host metadata** | Host name **OR** host_taxid | Scientific name [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | | | e.g. *Canis lupus familiaris* [\[NCBI:txid9615\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9615), *Homo sapiens* [\[NCBI:txid9606\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&lin=f&keep=1&srchmode=1&unlock) | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | host_common_name | Common name of the host | | | e.g. human, dog, cattle | [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | +| | host_height **OR** host_length | Height of host or length of host | | | e.g. 177 cm | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | host_tot_mass | Total mass of host | | | e.g. 77 kg **OR** 3568 g | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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](https://www.ebi.ac.uk/ols4/ontologies/fma) or [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon) ontologies | | | e.g. gut [\[FMA:45615\]](http://purl.obolibrary.org/obo/FMA_45615) **OR** gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/UBERON_0000328) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | +| | 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”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | host_sex | Gender and/or physical sex of subject/host | | | | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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 [\[ecocore:00000082\]](http://purl.obolibrary.org/obo/ecocore_00000082), substrate, medium; note here, that multiple possible subclasses exist in organism [\[OBI:0100026\]](http://purl.obolibrary.org/obo/OBI_0100026), such as autotroph [\[ECOCORE:00000023\]](http://purl.obolibrary.org/obo/ECOCORE_00000023)\|heterotroph [\[ECOCORE:00000010\]](http://purl.obolibrary.org/obo/ECOCORE_00000010) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | host_disease_stat | Diagnosed diseases of host; can hold multiple values, separated by \|. Non-human host diseases should be deposited as free text | | | e.g. rabies, avian influenza, heartworm disease | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | +| **Additional potential animal-associated bio/env considerations** | *Ecosystem Category* | *Category list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | | +| | *Ecosystem Type* | *Type list* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Ecosystem Subtype* | *Subtype list* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Specific Ecosystem* | *Specific ecosystem list* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Habitat* | *Free text* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Means of capture* | *How was the animal captured/trapped/sampled(e.g. net, stunned, anaesthetized, etc.)* | | | | *MSI-ECWSG* ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | For readers of this repository, confused by the use of EnvO s ontologies, we recommend they read the EnvO s use documentation here: diff --git a/Biological_Environmental/Human_BioEnv_Metadata.md b/Biological_Environmental/Human_BioEnv_Metadata.md index 101dbd6..5294517 100644 --- a/Biological_Environmental/Human_BioEnv_Metadata.md +++ b/Biological_Environmental/Human_BioEnv_Metadata.md @@ -2,46 +2,45 @@ ##   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)** | | +| | **metadata** | **definition** | **reference of 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](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | e.g. 2013-03-25T12:42:31+01:00 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | -| | Collected by | | | Name of person or institute that collected the sample | | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/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](https://www.insdc.org/submitting-standards/country-qualifier-vocabulary/), or the [GAZ ontology](http://purl.bioontology.org/ontology/GAZ) | e.g. USA: Maryland, Bethesda; Atlantic Ocean region **OR** [\[GAZ:00051071\]](http://purl.obolibrary.org/obo/GAZ_00051071) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | -| | 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. -41.373744 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | -| | 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. 146.266145 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | -| | Elevation | | | Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m | e.g. 100 m | [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/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](https://obofoundry.org/) ontologies which interoperate with EnvO (e.g. [\[UBERON\]](https://www.ebi.ac.uk/ols4/ontologies/uberon)) are accepted in this field. If more than one term applies to the field, \| should be used to separate them. | e.g. gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/UBERON_0000328) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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](https://obofoundry.org/) ontologies which interoperate with EnvO (e.g. [\[UBERON\]](https://www.ebi.ac.uk/ols4/ontologies/uberon)) are accepted in this field. If more than one term applies to the field, \| should be used to separate them. | e.g. if gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/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 [\[UBERON:0001096\]](http://purl.obolibrary.org/obo/UBERON_0001096)\| wall of intestine [\[UBERON:0001262\]](http://purl.obolibrary.org/obo/UBERON_0001262)\| wall of stomach [\[UBERON:0001167\]](http://purl.obolibrary.org/obo/UBERON_0001167); note that further subclasses are available if applicable and better describe the sample | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | env_medium | | | Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. Terms from other [OBO ontologies](https://obofoundry.org/) 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. feces [\[UBERON:0001988\]](http://purl.obolibrary.org/obo/UBERON_0001988)\| excreted gas [\[UBERON:0034945\]](http://purl.obolibrary.org/obo/UBERON_0034945) | [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | Sample size/mass | | | 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 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | -| | Site conditions | | | Environmental temp, RH, salinity, pH | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | -| | 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”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | Microbial ID | | | Taxonomy and/or culture source, if available. Expected_value: [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | e.g. *E. coli* [\[NCBI:txid562\]](https://www.ncbi.xyz/Taxonomy/Browser/wwwtax.cgi?id=562) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | -| | Microbial isolate | | | icrobial isolate cultured?: Y/N | | | | -| | Culture substrate | | | This field accepts terms listed under culture medium [\[OBI:0000079\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_0000079?lang=en). If the proper descriptor is not listed please use text to describe the culture medium | e.g. minimal defined medium [\[MCO:0000881\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMCO_0000881?lang=en) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | -| | 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)](http://purl.bioontology.org/ontology/chebi) | E.g. tetracycline [\[CHEBI:27902\]](http://purl.obolibrary.org/obo/CHEBI_27902);2023-12-11T19:41+01:00\|ampicilin[\[CHEBI:28971\]](http://purl.obolibrary.org/obo/CHEBI_28971);2023-12-11T19:41+01:00 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| **Host metadata** | host_name | Scientific name [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | e.g. *Homo sapiens* [\[NCBI:txid9606\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&lin=f&keep=1&srchmode=1&unlock) | [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | | | -| | host_common_name | | | Common name of the host | e.g. human, dog, cattle | [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | -| | host_height | | | Height of host | e.g. 177 cm | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | host_tot_mass | | | Total mass of host | e.g. 77 kg **OR** 3568 g | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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](https://www.ebi.ac.uk/ols4/ontologies/fma) or [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon) ontologies. Multiple ontologies can apply, use \| to separate them. Ontologies should be specific enough to discern body site and goal. | e.g. gut [\[FMA:45615\]](http://purl.obolibrary.org/obo/FMA_45615) **OR** gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/UBERON_0000328) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | -| | host_body_product | | | Bodily substance where the sample was obtained from. Recomended use of [FMA](https://www.ebi.ac.uk/ols4/ontologies/fma) or [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon) ontologies. Multiple ontologies can apply, use \| to separate them | e.g. feces [\[FMA:64183\]](http://purl.obolibrary.org/obo/FMA_64183)\|urine[\[FMA:12274\]](http://purl.obolibrary.org/obo/FMA_12274) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | host_age | | | Age of host at the time of sampling; relevant scale depends on study | e.g. year, day, hour | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | host_sex | | | Gender and/or physical sex of subject/host | | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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. Recommended use diet [\[OMIT:0005302\]](http://purl.obolibrary.org/obo/OMIT_0005302) subclasses | e.g. diet, high-fat [\[OMIT:0027565\]](http://purl.obolibrary.org/obo/OMIT_0027565) **OR** diet, mediterranean [\[OMIT:0022848\]](http://purl.obolibrary.org/obo/ECOCORE_00000019) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | host_subject_id | | | A unique identifier by which each subject can be referred to, de-identified | e.g. s9s8 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | host_disease_stat | | | Diagnosed diseases of host; can hold multiple values, separated by \|. Recommended use of [DOID ontoligies](https://www.ebi.ac.uk/ols4/ontologies/doid) | e.g. inflammatory bowel disease 1 [\[DOID:0110892\]](http://purl.obolibrary.org/obo/DOID_0110892)\|avian influenza [\[DOID:4492\]](http://purl.obolibrary.org/obo/DOID_4492) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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. | e.g. Slovene **OR** Turkic | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“U.s. Office of Management and Budget (OMB): About the Topic of Race”](https://www.census.gov/topics/population/race/about.html) | | -| | smoker | | | Specification of smoking status | e.g. yes | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“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/) | | -| | disorder_history | | | Terms from [DOID ontoligies](https://www.ebi.ac.uk/ols4/ontologies/doid) should be used to describe disorder. Host history of pulmonary [\[DOID:850\]](http://purl.obolibrary.org/obo/DOID_850), nose-throat [\[DOID:974\]](http://purl.obolibrary.org/obo/DOID_974), blood [\[DOID:74\]](http://purl.obolibrary.org/obo/DOID_74), kidney [\[DOID:557\]](http://purl.obolibrary.org/obo/DOID_557) and urogenital tract disorders [\[DOID:18\]](http://purl.obolibrary.org/obo/DOID_18) . If multiple disorders apply, separate them by \| | e.g. lung abscess [\[DOID:0060317\]](http://purl.obolibrary.org/obo/DOID_0060317)\|tonsillitis [\[DOID:10456\]](http://purl.obolibrary.org/obo/DOID_10456)\|hypochromic anemia [\[DOID:11759\]](http://purl.obolibrary.org/obo/DOID_11759)\|etc. | | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“U.s. Office of Management and Budget (OMB): About the Topic of Race”](https://www.census.gov/topics/population/race/about.html) | -| | smoker | | | Specification of smoking status | e.g. yes | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“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/) | | -| **Additional potential human bio/env considerations** | *Ecosystem Category* | *Category list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | | -| | *Ecosystem Type* | | | *Type list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Ecosystem Subtype* | | | *Subtype list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Specific Ecosystem* | | | *Specific ecosystem list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Habitat* | | | *Free text* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Medical Record Number* | | | *Record number (list)* | | | | +| **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](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | | | e.g. 2013-03-25T12:42:31+01:00 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | +| | Collected by | Name of person or institute that collected the sample | | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/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](https://www.insdc.org/submitting-standards/country-qualifier-vocabulary/), or the [GAZ ontology](http://purl.bioontology.org/ontology/GAZ) | | | e.g. USA: Maryland, Bethesda; Atlantic Ocean region **OR** [\[GAZ:00051071\]](http://purl.obolibrary.org/obo/GAZ_00051071) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | +| | 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. -41.373744 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | +| | 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. 146.266145 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) | | +| | Elevation | Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m | | | e.g. 100 m | [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/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](https://obofoundry.org/) ontologies which interoperate with EnvO (e.g. [\[UBERON\]](https://www.ebi.ac.uk/ols4/ontologies/uberon)) are accepted in this field. If more than one term applies to the field, \| should be used to separate them. | | | e.g. gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/UBERON_0000328) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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](https://obofoundry.org/) ontologies which interoperate with EnvO (e.g. [\[UBERON\]](https://www.ebi.ac.uk/ols4/ontologies/uberon)) are accepted in this field. If more than one term applies to the field, \| should be used to separate them. | | | e.g. if gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/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 [\[UBERON:0001096\]](http://purl.obolibrary.org/obo/UBERON_0001096)\| wall of intestine [\[UBERON:0001262\]](http://purl.obolibrary.org/obo/UBERON_0001262)\| wall of stomach [\[UBERON:0001167\]](http://purl.obolibrary.org/obo/UBERON_0001167); note that further subclasses are available if applicable and better describe the sample | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | env_medium | Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. Terms from other [OBO ontologies](https://obofoundry.org/) 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. feces [\[UBERON:0001988\]](http://purl.obolibrary.org/obo/UBERON_0001988)\| excreted gas [\[UBERON:0034945\]](http://purl.obolibrary.org/obo/UBERON_0034945) | [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | Sample size/mass | 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 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | +| | Site conditions | Environmental temp, RH, salinity, pH | | | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | 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”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | Microbial ID | Taxonomy and/or culture source, if available. Expected_value: [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | | | e.g. *E. coli* [\[NCBI:txid562\]](https://www.ncbi.xyz/Taxonomy/Browser/wwwtax.cgi?id=562) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | +| | Microbial isolate | icrobial isolate cultured?: Y/N | | | | | | +| | Culture substrate | This field accepts terms listed under culture medium [\[OBI:0000079\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_0000079?lang=en). If the proper descriptor is not listed please use text to describe the culture medium | | | e.g. minimal defined medium [\[MCO:0000881\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMCO_0000881?lang=en) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | 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)](http://purl.bioontology.org/ontology/chebi) | | | e.g. tetracycline [\[CHEBI:27902\]](http://purl.obolibrary.org/obo/CHEBI_27902);2023-12-11T19:41+01:00\|ampicilin[\[CHEBI:28971\]](http://purl.obolibrary.org/obo/CHEBI_28971);2023-12-11T19:41+01:00 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| **Host metadata** | host_name | Scientific name [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | e.g. *Homo sapiens* [\[NCBI:txid9606\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&lin=f&keep=1&srchmode=1&unlock) | [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | | | +| | host_common_name | Common name of the host | | | e.g. human, dog, cattle | [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | +| | host_height | Height of host | | | e.g. 177 cm | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | host_tot_mass | Total mass of host | | | e.g. 77 kg **OR** 3568 g | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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](https://www.ebi.ac.uk/ols4/ontologies/fma) or [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon) ontologies. Multiple ontologies can apply, use \| to separate them. Ontologies should be specific enough to discern body site and goal. | | | e.g. gut [\[FMA:45615\]](http://purl.obolibrary.org/obo/FMA_45615) **OR** gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/UBERON_0000328) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | +| | host_body_product | Bodily substance where the sample was obtained from. Recomended use of [FMA](https://www.ebi.ac.uk/ols4/ontologies/fma) or [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon) ontologies. Multiple ontologies can apply, use \| to separate them | | | e.g. feces [\[FMA:64183\]](http://purl.obolibrary.org/obo/FMA_64183)\|urine[\[FMA:12274\]](http://purl.obolibrary.org/obo/FMA_12274) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | host_age | Age of host at the time of sampling; relevant scale depends on study | | | e.g. year, day, hour | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | host_sex | Gender and/or physical sex of subject/host | | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | | | +| | 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. Recommended use diet [\[OMIT:0005302\]](http://purl.obolibrary.org/obo/OMIT_0005302) subclasses | | | e.g. diet, high-fat [\[OMIT:0027565\]](http://purl.obolibrary.org/obo/OMIT_0027565) **OR** diet, mediterranean [\[OMIT:0022848\]](http://purl.obolibrary.org/obo/ECOCORE_00000019) | +| | host_subject_id | A unique identifier by which each subject can be referred to, de-identified | | | e.g. s9s8 | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | host_disease_stat | Diagnosed diseases of host; can hold multiple values, separated by \|. Recommended use of [DOID ontoligies](https://www.ebi.ac.uk/ols4/ontologies/doid) | | | e.g. inflammatory bowel disease 1 [\[DOID:0110892\]](http://purl.obolibrary.org/obo/DOID_0110892)\|avian influenza [\[DOID:4492\]](http://purl.obolibrary.org/obo/DOID_4492) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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. | | | e.g. Slovene **OR** Turkic | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“U.s. Office of Management and Budget (OMB): About the Topic of Race”](https://www.census.gov/topics/population/race/about.html) | | +| | smoker | Specification of smoking status | e.g. yes | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“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/) | | | | +| | disorder_history | Terms from [DOID ontoligies](https://www.ebi.ac.uk/ols4/ontologies/doid) should be used to describe disorder. Host history of pulmonary [\[DOID:850\]](http://purl.obolibrary.org/obo/DOID_850), nose-throat [\[DOID:974\]](http://purl.obolibrary.org/obo/DOID_974), blood [\[DOID:74\]](http://purl.obolibrary.org/obo/DOID_74), kidney [\[DOID:557\]](http://purl.obolibrary.org/obo/DOID_557) and urogenital tract disorders [\[DOID:18\]](http://purl.obolibrary.org/obo/DOID_18) . If multiple disorders apply, separate them by \| | | e.g. lung abscess [\[DOID:0060317\]](http://purl.obolibrary.org/obo/DOID_0060317)\|tonsillitis [\[DOID:10456\]](http://purl.obolibrary.org/obo/DOID_10456)\|hypochromic anemia [\[DOID:11759\]](http://purl.obolibrary.org/obo/DOID_11759)\|etc. | | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“U.s. Office of Management and Budget (OMB): About the Topic of Race”](https://www.census.gov/topics/population/race/about.html) | | +| **Additional potential human bio/env considerations** | *Ecosystem Category* | *Category list* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Ecosystem Type* | *Type list* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Ecosystem Subtype* | *Subtype list* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Specific Ecosystem* | *Specific ecosystem list* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Habitat* | *Free text* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Medical Record Number* | | | *Record number (list)* | | | | # References diff --git a/Biological_Environmental/Marine_BioEnv_Metadata.md b/Biological_Environmental/Marine_BioEnv_Metadata.md index dd98fd0..bf20feb 100644 --- a/Biological_Environmental/Marine_BioEnv_Metadata.md +++ b/Biological_Environmental/Marine_BioEnv_Metadata.md @@ -2,39 +2,39 @@ ##   Minimal biological/environmental metadata for marine microbiome -| | **metadata** | **definition** | **reference of definition\[\]** | **expected unit of measurement** | **example** | **sources( where this or similar matadata field is mentioned)** | | +| | **metadata** | **definition** | **reference of 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](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | e.g. 2013-03-25T12:42:31+01:00 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | Collected by | Name of person or institute that collected the sample | | | | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/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](https://www.insdc.org/submitting-standards/country-qualifier-vocabulary/), or the [GAZ ontology](http://purl.bioontology.org/ontology/GAZ) | e.g. USA: Maryland, Bethesda; Atlantic Ocean region **OR** Mediterranean Sea, Eastern Basin [\[GAZ:00002536\]](http://purl.obolibrary.org/obo/GAZ_00002536) | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | 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. -50.605389 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | 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. 165.967333 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | Elevation | | | Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m | e.g. 100 m | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | 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: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | Depth | | | The vertical distance below local (sea) surface. Depth can be reported as an interval for subsurface samples | e.g. 100 m | [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/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. Recommended use of EnvO s biome class: [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en). If more than one term applies to the field, \| should be used to separate them. | e.g. aquatic biome [\[ENVO:00002030\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00002030?lang=en)\|marine biome [\[ENVO:00000447\]](http://purl.obolibrary.org/obo/ENVO_00000447); Note here, that marine biome is a subclass of aquatic biome. Considering overlaping biomes can also apply e.g. polar biome [\[ENVO:01000339\]](http://purl.obolibrary.org/obo/ENVO_01000339)\|marine biome [\[ENVO:00000447\]](http://purl.obolibrary.org/obo/ENVO_00000447) | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | 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](https://obofoundry.org/) ontologies which interoperate with EnvO (e.g. [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon)) are accepted in this field. If more than one term applies to the field, \| should be used to separate them. | e.g. if marine biome [\[ENVO:00000447\]](http://purl.obolibrary.org/obo/ENVO_00000447) was used in env_broad_scale, env_local_scale should be one of the (corresponding) subclasses : estuarine biome [\[ENVO:01000020\]](http://purl.obolibrary.org/obo/ENVO_01000020)\|ocean bioime [\[ENVO:01000048\]](http://purl.obolibrary.org/obo/ENVO_01000048)\|marine pelagic bioime[\[ENVO:01000048\]](http://purl.obolibrary.org/obo/ENVO_01000048)\| etc.; Note here, that further subclasses exist if they are applicable and better describe the environment in direct vicinity of sampling | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | 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 [\[ENVO:00010483\]](http://purl.obolibrary.org/obo/ENVO_00010483). Terms from other [OBO ontologies](https://obofoundry.org/) 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. glacial ice [\[ENVO:03000004\]](http://purl.obolibrary.org/obo/ENVO_03000004) **OR** coastal sea water [\[ENVO:00002150\]](http://purl.obolibrary.org/obo/ENVO_00002150)\|estuarine water [\[ENVO:01000301\]](http://purl.obolibrary.org/obo/ENVO_01000301) **OR** arterial blood [\[UBERON:0013755\]](http://purl.obolibrary.org/obo/UBERON_0013755)\|venous blood [\[UBERON:0013756\]](http://purl.obolibrary.org/obo/UBERON_0013756)\|blood plasma [\[UBERON:0001969\]](http://purl.obolibrary.org/obo/UBERON_0001969) **OR** algal material [\[ENVO:01001189\]](http://purl.obolibrary.org/obo/ENVO_01001189)\| planktonic material [\[ENVO:01000063\]](http://purl.obolibrary.org/obo/ENVO_01000063) | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | 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: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | -| | Site conditions | Environmental temp, RH, salinity, pH | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | | | -| | Material conditions | | | Sample material temp, RH, salinity, pH | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030) | | -| | Microbial ID | | | Taxonomy and/or culture source, if available. Expected_value: [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | e.g. *Prochlorococcus marinus* biovar HNLC1 [\[NCBI:txid1041938\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1041938&lvl=3&lin=f&keep=1&srchmode=1&unlock) | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043) | | -| | Microbial isolate | | | Microbial isolate cultured?: Y/N | | | | -| | Culture substrate | | | This field accepts terms listed under microbiological culture medium [\[MICRO:0000067\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMICRO_0000067). If the proper descriptor is not listed please use text to describe the culture medium | e.g. rich medium [\[MCO:0000882\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMCO_0000882?lang=en) | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | -| | 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)](http://purl.bioontology.org/ontology/chebi) | e.g. polystyrene polymer [\[CHEBI:61642\]](http://purl.obolibrary.org/obo/CHEBI_61642);2023-12-12T16:00+02:00\|poly(vinyl chloride) [\[CHEBI:53243\]](http://purl.obolibrary.org/obo/CHEBI_53243);2023-12-12T16:02+02:00\|polycyclic arene [\[CHEBI:33848\]](http://purl.obolibrary.org/obo/CHEBI_33848);2023-12-12T16:08+02:00 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| **Host metadata** | Host name | Scientific name [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | e.g. *Pocillopora inflata* [\[NCBI:txid490833\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=490833&lvl=3&lin=f&keep=1&srchmode=1&unlock) | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | | | -| | host_common_name | | | Common name of the host | e.g. human, dog, cattle | [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | -| | host_height **OR** host_length | | | Height of host or length of host | e.g. 177 cm | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | host_tot_mass | Total mass of host | e.g. 77 kg **OR** 3568 g | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | | | -| | host_body_site | | | Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc…). Recommended use of [FMA](https://www.ebi.ac.uk/ols4/ontologies/fma) or [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon) ontologies | e.g. gut [\[FMA:45615\]](http://purl.obolibrary.org/obo/FMA_45615) **OR** gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/UBERON_0000328) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | -| | 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 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | host_sex | | | Gender and/or physical sex of subject/host | | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | host_diet | | | Type of diet depending on the host, for animals omnivore, herbivore etc.; can include multiple diet types | e.g. omnivore [\[ecocore:00000082\]](http://purl.obolibrary.org/obo/ecocore_00000082) **OR** herbivore [\[ECOCORE:00000019\]](http://purl.obolibrary.org/obo/ECOCORE_00000019); note here, that multiple possible subclasses exist in organism [\[OBI:0100026\]](http://purl.obolibrary.org/obo/OBI_0100026), such as autotroph [\[ECOCORE:00000023\]](http://purl.obolibrary.org/obo/ECOCORE_00000023)\|heterotroph [\[ECOCORE:00000010\]](http://purl.obolibrary.org/obo/ECOCORE_00000010) | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| **Additional potential marine bio/env considerations** | *Ecosystem Category* | *Category list* | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | | | -| | *Ecosystem Type* | | | *Type list* | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | -| | *Ecosystem Subtype* | | | *Subtype list* | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | -| | *Specific Ecosystem* | | | *Specific ecosystem list* | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | -| | *Habitat* | | | *Free text* | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | +| **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](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | | | e.g. 2013-03-25T12:42:31+01:00 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | Collected by | Name of person or institute that collected the sample | | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/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](https://www.insdc.org/submitting-standards/country-qualifier-vocabulary/), or the [GAZ ontology](http://purl.bioontology.org/ontology/GAZ) | | | e.g. USA: Maryland, Bethesda; Atlantic Ocean region **OR** Mediterranean Sea, Eastern Basin [\[GAZ:00002536\]](http://purl.obolibrary.org/obo/GAZ_00002536) | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | 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. -50.605389 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | 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. 165.967333 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | Elevation | Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m | | | e.g. 100 m | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | 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: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | Depth | The vertical distance below local (sea) surface. Depth can be reported as an interval for subsurface samples | | | e.g. 100 m | [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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 Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/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. Recommended use of EnvO s biome class: [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en). If more than one term applies to the field, \| should be used to separate them. | | | e.g. aquatic biome [\[ENVO:00002030\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00002030?lang=en)\|marine biome [\[ENVO:00000447\]](http://purl.obolibrary.org/obo/ENVO_00000447); Note here, that marine biome is a subclass of aquatic biome. Considering overlaping biomes can also apply e.g. polar biome [\[ENVO:01000339\]](http://purl.obolibrary.org/obo/ENVO_01000339)\|marine biome [\[ENVO:00000447\]](http://purl.obolibrary.org/obo/ENVO_00000447) | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | 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](https://obofoundry.org/) ontologies which interoperate with EnvO (e.g. [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon)) are accepted in this field. If more than one term applies to the field, \| should be used to separate them. | | | e.g. if marine biome [\[ENVO:00000447\]](http://purl.obolibrary.org/obo/ENVO_00000447) was used in env_broad_scale, env_local_scale should be one of the (corresponding) subclasses : estuarine biome [\[ENVO:01000020\]](http://purl.obolibrary.org/obo/ENVO_01000020)\|ocean bioime [\[ENVO:01000048\]](http://purl.obolibrary.org/obo/ENVO_01000048)\|marine pelagic bioime[\[ENVO:01000048\]](http://purl.obolibrary.org/obo/ENVO_01000048)\| etc.; Note here, that further subclasses exist if they are applicable and better describe the environment in direct vicinity of sampling | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | 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 [\[ENVO:00010483\]](http://purl.obolibrary.org/obo/ENVO_00010483). Terms from other [OBO ontologies](https://obofoundry.org/) 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. glacial ice [\[ENVO:03000004\]](http://purl.obolibrary.org/obo/ENVO_03000004) **OR** coastal sea water [\[ENVO:00002150\]](http://purl.obolibrary.org/obo/ENVO_00002150)\|estuarine water [\[ENVO:01000301\]](http://purl.obolibrary.org/obo/ENVO_01000301) **OR** arterial blood [\[UBERON:0013755\]](http://purl.obolibrary.org/obo/UBERON_0013755)\|venous blood [\[UBERON:0013756\]](http://purl.obolibrary.org/obo/UBERON_0013756)\|blood plasma [\[UBERON:0001969\]](http://purl.obolibrary.org/obo/UBERON_0001969) **OR** algal material [\[ENVO:01001189\]](http://purl.obolibrary.org/obo/ENVO_01001189)\| planktonic material [\[ENVO:01000063\]](http://purl.obolibrary.org/obo/ENVO_01000063) | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | 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: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | +| | Site conditions | Environmental temp, RH, salinity, pH | | | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | Material conditions | Sample material temp, RH, salinity, pH | | | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030) | | +| | Microbial ID | Taxonomy and/or culture source, if available. Expected_value: [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | | | e.g. *Prochlorococcus marinus* biovar HNLC1 [\[NCBI:txid1041938\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1041938&lvl=3&lin=f&keep=1&srchmode=1&unlock) | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043) | | +| | Microbial isolate | Microbial isolate cultured?: Y/N | | | | | | +| | Culture substrate | This field accepts terms listed under microbiological culture medium [\[MICRO:0000067\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMICRO_0000067). If the proper descriptor is not listed please use text to describe the culture medium | | | e.g. rich medium [\[MCO:0000882\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMCO_0000882?lang=en) | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | 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)](http://purl.bioontology.org/ontology/chebi) | | | e.g. polystyrene polymer [\[CHEBI:61642\]](http://purl.obolibrary.org/obo/CHEBI_61642);2023-12-12T16:00+02:00\|poly(vinyl chloride) [\[CHEBI:53243\]](http://purl.obolibrary.org/obo/CHEBI_53243);2023-12-12T16:02+02:00\|polycyclic arene [\[CHEBI:33848\]](http://purl.obolibrary.org/obo/CHEBI_33848);2023-12-12T16:08+02:00 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| **Host metadata** | Host name | Scientific name [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | | | e.g. *Pocillopora inflata* [\[NCBI:txid490833\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=490833&lvl=3&lin=f&keep=1&srchmode=1&unlock) | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | host_common_name | Common name of the host | | | e.g. human, dog, cattle | [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | +| | host_height **OR** host_length | Height of host or length of host | | | e.g. 177 cm | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | host_tot_mass | Total mass of host | | | e.g. 77 kg **OR** 3568 g | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | host_body_site | Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc…). Recommended use of [FMA](https://www.ebi.ac.uk/ols4/ontologies/fma) or [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon) ontologies | | | e.g. gut [\[FMA:45615\]](http://purl.obolibrary.org/obo/FMA_45615) **OR** gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/UBERON_0000328) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | +| | 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 | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | host_sex | Gender and/or physical sex of subject/host | | | | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | host_diet | Type of diet depending on the host, for animals omnivore, herbivore etc.; can include multiple diet types | | | e.g. omnivore [\[ecocore:00000082\]](http://purl.obolibrary.org/obo/ecocore_00000082) **OR** herbivore [\[ECOCORE:00000019\]](http://purl.obolibrary.org/obo/ECOCORE_00000019); note here, that multiple possible subclasses exist in organism [\[OBI:0100026\]](http://purl.obolibrary.org/obo/OBI_0100026), such as autotroph [\[ECOCORE:00000023\]](http://purl.obolibrary.org/obo/ECOCORE_00000023)\|heterotroph [\[ECOCORE:00000010\]](http://purl.obolibrary.org/obo/ECOCORE_00000010) | [“GSC MIxS: WaterMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| **Additional potential marine bio/env considerations** | *Ecosystem Category* | *Category list* | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | | | +| | *Ecosystem Type* | *Type list* | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | +| | *Ecosystem Subtype* | *Subtype list* | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | +| | *Specific Ecosystem* | *Specific ecosystem list* | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | +| | *Habitat* | *Free text* | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | # References diff --git a/Biological_Environmental/PlantAssoc_BioEnv_Metadata.md b/Biological_Environmental/PlantAssoc_BioEnv_Metadata.md index cfec17a..1229882 100644 --- a/Biological_Environmental/PlantAssoc_BioEnv_Metadata.md +++ b/Biological_Environmental/PlantAssoc_BioEnv_Metadata.md @@ -2,39 +2,39 @@ ##   Minimal biological/environmental metadata for plant-associated microbiome -| | **metadata** | **definition** | **reference of definition\[\]** | **expected unit of measurement** | **example** | **sources( where this or similar matadata field is mentioned)** | | +| | **metadata** | **definition** | **reference of 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](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | e.g. 2013-03-25T12:42:31+01:00 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | Collected by | | | Name of person or institute that collected the sample | | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/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](https://www.insdc.org/submitting-standards/country-qualifier-vocabulary/), or the [GAZ ontology](http://purl.bioontology.org/ontology/GAZ) | e.g. USA: Maryland, Bethesda; Atlantic Ocean region **OR** [\[GAZ:00051071\]](http://purl.obolibrary.org/obo/GAZ_00051071) | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | 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. 54.400939 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | 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. -1.340951 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | Elevation | | | Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m | e.g. 100 m | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | -| | 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: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | -| | 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: [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en). If more than one term applies to the field, \| should be used to separate them.; note here, that multiple subclasses of biome [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en) can apply here. | E.g. terrestrial biome [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) **OR** subtropical biome [\[ENVO:01001832\]](http://purl.obolibrary.org/obo/ENVO_01001832) **OR** tropical biome [\[ENVO:01001830\]](http://purl.obolibrary.org/obo/ENVO_01001830) **OR** etc. ; note here, that most of ontology classes found under biome have further subclasses that may apply, if they can better describe the broad environmental context of the sample, use \| to separate them | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-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. If more than one term applies to the field, \| should be used to separate them. | e.g. if tropical biome [\[ENVO:01001830\]](http://purl.obolibrary.org/obo/ENVO_01001830) was used in env_broad_scale, env_local_scale should be one of the following subclasses : tropical savanna biome [\[ENVO:01000188\]](http://purl.obolibrary.org/obo/ENVO_01000188)\|tropical shrubland biome [\[ENVO:01000214\]](http://purl.obolibrary.org/obo/ENVO_01000214)\|tropical woodland biome [\[ENVO:01000220\]](http://purl.obolibrary.org/obo/ENVO_01000220); note here, that some ontologies listed here under other subclasses of biome [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en), have further subclasses that can be used, if they better describe the local environment of the sample. | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-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 [\[ENVO:00010483\]](http://purl.obolibrary.org/obo/ENVO_00010483). Terms from other [OBO ontologies](https://obofoundry.org/) 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 [\[ENVO:00005742\]](http://purl.obolibrary.org/obo/ENVO_00005742)\|bare soil [\[ENVO:01001616\]](http://purl.obolibrary.org/obo/ENVO_01001616)\|bulk soil [\[ENVO:00005802\]](http://purl.obolibrary.org/obo/ENVO_00005802); note here, that these are only examples, there is a variety of different ontology classes that can apply here | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | -| | 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: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | -| | Site conditions | | | Environmental temp, RH, salinity, pH | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | -| | Material conditions | | | Sample material temp, RH, salinity, pH | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030) | | -| | Microbial ID | | | Taxonomy and/or culture source, if available. Expected_value: [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | e.g. *E. coli* [\[NCBI:txid562\]](https://www.ncbi.xyz/Taxonomy/Browser/wwwtax.cgi?id=562) | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043) | | -| | Microbial isolate | | | Microbial isolate cultured?: Y/N | | | | -| | Culture substrate | | | This field accepts terms listed under culture medium [\[OBI:0000079\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_0000079?lang=en). If the proper descriptor is not listed please use text to describe the culture medium | e.g. minimal defined medium [\[MCO:0000881\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMCO_0000881?lang=en) | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | -| | 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)](http://purl.bioontology.org/ontology/chebi) | E.g. agar [\[CHEBI:2509\]](https://www.ebi.ac.uk/ols4/ontologies/micro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_2509);2018-05-11T20:00Z\|castor oil [\[CHEBI:140618\]](https://www.ebi.ac.uk/ols4/ontologies/chebi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_140618?lang=en);2023-12-07T17:00+02:00 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | -| **Host metadata** | Host name **OR** host_taxid | | | Scientific name [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | e.g. *Arabidopsis thaliana * [\[NCBI:txid3702\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name=Arabidopsis+thaliana) | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | -| | host_common_name | | | Common name of the host | e.g. thale cress | [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | -| | host_height **OR** host_length | | | Height of host or length of host | e.g. 177 cm | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | -| | host_tot_mass | | | Total mass of host | e.g. 77 kg **OR** 3568 g | [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | -| | plant_struc | | | Name of plant structure the sample was obtained from, such as a specific organ or tissue (epidermis, etc…). Recommended use of plant anatomical entity [\[PO:0025131\]](http://purl.obolibrary.org/obo/PO_0025131) subclasses | e.g. root system ground meristem [\[PO:0025596\]](http://purl.obolibrary.org/obo/PO_0025596); note here that multiple ontology classes and subclasses may apply here, use \| to separate them | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | -| | 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 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | -| | plant_sex | | | Sex of the reproductive parts on the whole plant | e.g. pistillate, staminate, monoecieous, hermaphrodite | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | -| | host_disease_stat | | | Diagnosed diseases of host; can hold multiple values, separated by \|. Non-human host diseases should be deposited as free text | e.g. powdery mildew, late blight, citrus canker etc. | [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | -| | host_symbiont | | | Name the organism found living in a symbiotic, commensalistic, mutualistic relationship with the host. Expected values: Scientific or common name of species | e.g. *Rhizobium tropici* | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | -| **Additional potential plant-associated bio/env considerations** | | | *Ecosystem Category* | *Category list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Ecosystem Type* | | | *Type list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Ecosystem Subtype* | | | *Subtype list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Specific Ecosystem* | | | *Specific ecosystem list* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | -| | *Habitat* | | | *Free text* | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| **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](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | | | e.g. 2013-03-25T12:42:31+01:00 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | Collected by | Name of person or institute that collected the sample | | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/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](https://www.insdc.org/submitting-standards/country-qualifier-vocabulary/), or the [GAZ ontology](http://purl.bioontology.org/ontology/GAZ) | | | e.g. USA: Maryland, Bethesda; Atlantic Ocean region **OR** [\[GAZ:00051071\]](http://purl.obolibrary.org/obo/GAZ_00051071) | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | 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. 54.400939 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | 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. -1.340951 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | Elevation | Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m | | | e.g. 100 m | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | +| | 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: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030), [“GSC MIxS Water; ENA Checklist: ERC000024”](https://www.ebi.ac.uk/ena/browser/view/ERC000024) | | +| | 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: [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en). If more than one term applies to the field, \| should be used to separate them.; note here, that multiple subclasses of biome [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en) can apply here. | E.g. terrestrial biome [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) **OR** subtropical biome [\[ENVO:01001832\]](http://purl.obolibrary.org/obo/ENVO_01001832) **OR** tropical biome [\[ENVO:01001830\]](http://purl.obolibrary.org/obo/ENVO_01001830) **OR** etc. ; note here, that most of ontology classes found under biome have further subclasses that may apply, if they can better describe the broad environmental context of the sample, use \| to separate them | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-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. If more than one term applies to the field, \| should be used to separate them. | | | e.g. if tropical biome [\[ENVO:01001830\]](http://purl.obolibrary.org/obo/ENVO_01001830) was used in env_broad_scale, env_local_scale should be one of the following subclasses : tropical savanna biome [\[ENVO:01000188\]](http://purl.obolibrary.org/obo/ENVO_01000188)\|tropical shrubland biome [\[ENVO:01000214\]](http://purl.obolibrary.org/obo/ENVO_01000214)\|tropical woodland biome [\[ENVO:01000220\]](http://purl.obolibrary.org/obo/ENVO_01000220); note here, that some ontologies listed here under other subclasses of biome [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en), have further subclasses that can be used, if they better describe the local environment of the sample. | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-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 [\[ENVO:00010483\]](http://purl.obolibrary.org/obo/ENVO_00010483). Terms from other [OBO ontologies](https://obofoundry.org/) 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 [\[ENVO:00005742\]](http://purl.obolibrary.org/obo/ENVO_00005742)\|bare soil [\[ENVO:01001616\]](http://purl.obolibrary.org/obo/ENVO_01001616)\|bulk soil [\[ENVO:00005802\]](http://purl.obolibrary.org/obo/ENVO_00005802); note here, that these are only examples, there is a variety of different ontology classes that can apply here | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | +| | 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: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | +| | Site conditions | Environmental temp, RH, salinity, pH | | | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | Material conditions | Sample material temp, RH, salinity, pH | | | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)), [“ENA Tara Oceans; Checklist: ERC000030”](https://www.ebi.ac.uk/ena/browser/view/ERC000030) | | +| | Microbial ID | Taxonomy and/or culture source, if available. Expected_value: [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | | | e.g. *E. coli* [\[NCBI:txid562\]](https://www.ncbi.xyz/Taxonomy/Browser/wwwtax.cgi?id=562) | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/ERC000043) | | +| | Microbial isolate | Microbial isolate cultured?: Y/N | | | | | | +| | Culture substrate | This field accepts terms listed under culture medium [\[OBI:0000079\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_0000079?lang=en). If the proper descriptor is not listed please use text to describe the culture medium | | | e.g. minimal defined medium [\[MCO:0000881\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMCO_0000881?lang=en) | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | 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)](http://purl.bioontology.org/ontology/chebi) | E.g. agar [\[CHEBI:2509\]](https://www.ebi.ac.uk/ols4/ontologies/micro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_2509);2018-05-11T20:00Z\|castor oil [\[CHEBI:140618\]](https://www.ebi.ac.uk/ols4/ontologies/chebi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_140618?lang=en);2023-12-07T17:00+02:00 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | | | +| **Host metadata** | Host name **OR** host_taxid | Scientific name [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | | | e.g. *Arabidopsis thaliana * [\[NCBI:txid3702\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name=Arabidopsis+thaliana) | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | host_common_name | Common name of the host | | | e.g. thale cress | [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | +| | host_height **OR** host_length | Height of host or length of host | | | e.g. 177 cm | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | +| | host_tot_mass | Total mass of host | | | e.g. 77 kg **OR** 3568 g | [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | +| | plant_struc | Name of plant structure the sample was obtained from, such as a specific organ or tissue (epidermis, etc…). Recommended use of plant anatomical entity [\[PO:0025131\]](http://purl.obolibrary.org/obo/PO_0025131) subclasses | | | e.g. root system ground meristem [\[PO:0025596\]](http://purl.obolibrary.org/obo/PO_0025596); note here that multiple ontology classes and subclasses may apply here, use \| to separate them | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | +| | 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 | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | +| | plant_sex | Sex of the reproductive parts on the whole plant | | | e.g. pistillate, staminate, monoecieous, hermaphrodite | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | +| | host_disease_stat | Diagnosed diseases of host; can hold multiple values, separated by \|. Non-human host diseases should be deposited as free text | | | e.g. powdery mildew, late blight, citrus canker etc. | [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | +| | host_symbiont | Name the organism found living in a symbiotic, commensalistic, mutualistic relationship with the host. Expected values: Scientific or common name of species | | | e.g. *Rhizobium tropici* | [“GSC MIxS: AgricultureMIMS”](https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/), [“GSC MIxS: Symbiont-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/) | | +| **Additional potential plant-associated bio/env considerations** | *Ecosystem Category* | *Category list* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Ecosystem Type* | *Type list* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Ecosystem Subtype* | *Subtype list* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Specific Ecosystem* | *Specific ecosystem list* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | +| | *Habitat* | *Free text* | | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | # References diff --git a/Biological_Environmental/Terrestrial_BioEnv_Metadata.md b/Biological_Environmental/Terrestrial_BioEnv_Metadata.md index d29b511..fdd0ec4 100644 --- a/Biological_Environmental/Terrestrial_BioEnv_Metadata.md +++ b/Biological_Environmental/Terrestrial_BioEnv_Metadata.md @@ -2,38 +2,38 @@ ##   Minimal biological/environmental metadata for terrestrial microbiome -| | **metadata** | **definition** | **reference of definition\[\]** | **expected unit of measurement** | **example** | **sources( where this or similar matadata field is mentioned)** | | +| | **metadata** | **definition** | **reference of 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](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | e.g. 2013-03-25T12:42:31+01:00 | [“GSC MIxS: BuiltEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | -| | Collected by | | | Name of person or institute that collected the sample | | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/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](https://www.insdc.org/submitting-standards/country-qualifier-vocabulary/), or the [GAZ ontology](http://purl.bioontology.org/ontology/GAZ) | e.g. USA: Maryland, Bethesda; Atlantic Ocean region **OR** [\[GAZ:00051071\]](http://purl.obolibrary.org/obo/GAZ_00051071) | [“GSC MIxS: BuiltEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | -| | 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”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | -| | 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”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | -| | 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”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | -| | 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”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | -| | 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: [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en). If more than one term applies to the field, \| should be used to separate them.; note here, that subclasses of terrestrial biome [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) should be used here. | E.g. terrestrial biome [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) | [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/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](https://obofoundry.org/) ontologies which interoperate with EnvO (e.g. [UBERON](https://www.ebi.ac.uk/ols4/ontologies/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 [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) was used in env_broad_scale, env_local_scale should be one of the following subclasses : anthropogenic terrestrial [\[ENVO:01000219\]](http://purl.obolibrary.org/obo/ENVO_01000219)\|mangrove biome [\[ENVO:01000181\]](http://purl.obolibrary.org/obo/ENVO_01000181)\| shrubland biome [\[ENVO:01000176\]](http://purl.obolibrary.org/obo/ENVO_01000176)\| terrestrial environmental zone [\[ENVO:01001199\]](http://purl.obolibrary.org/obo/ENVO_01001199) \| tundra biome [\[ENVO:01000180\]](http://purl.obolibrary.org/obo/ENVO_01000180) \| woodland biome [\[ENVO:01000175\]](http://purl.obolibrary.org/obo/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”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/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 [\[ENVO:00010483\]](http://purl.obolibrary.org/obo/ENVO_00010483). Terms from other [OBO ontologies](https://obofoundry.org/) 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 [\[ENVO:00005742\]](http://purl.obolibrary.org/obo/ENVO_00005742)\|bare soil [\[ENVO:01001616\]](http://purl.obolibrary.org/obo/ENVO_01001616)\|bulk soil [\[ENVO:00005802\]](http://purl.obolibrary.org/obo/ENVO_00005802) **OR** arterial blood [\[UBERON:0013755\]](http://purl.obolibrary.org/obo/UBERON_0013755)\|venous blood [\[UBERON:0013756\]](http://purl.obolibrary.org/obo/UBERON_0013756)\|blood plasma [\[UBERON:0001969\]](http://purl.obolibrary.org/obo/UBERON_0001969) | | [“GSC MIxS: BuiltEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | -| | 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”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | -| | Site conditions | | | Environmental temp, RH, salinity, pH | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | [“GSC MIxS: BuiltEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | -| | Material conditions | | | Sample material temp, RH, salinity, pH | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | [“GSC MIxS: SoilMIMS”](https://genomicsstandardsconsortium.github.io/mixs/SoilMIMS/), [“GSC MIxS: WastewaterSludgeMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WastewaterSludgeMIMS/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | -| | Microbial ID | | | Taxonomy and/or culture source, if available. Expected_value: [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | e.g. *E. coli* [\[NCBI:txid562\]](https://www.ncbi.xyz/Taxonomy/Browser/wwwtax.cgi?id=562) | [“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/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/) | | -| | Microbial isolate | | | Microbial isolate cultured?: Y/N | | | | -| | Culture substrate | | | This field accepts terms listed under culture medium [\[OBI:0000079\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_0000079?lang=en). If the proper descriptor is not listed please use text to describe the culture medium | e.g. minimal defined medium [\[MCO:0000881\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMCO_0000881?lang=en) | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | -| | 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)](http://purl.bioontology.org/ontology/chebi) | E.g. agar [\[CHEBI:2509\]](https://www.ebi.ac.uk/ols4/ontologies/micro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_2509);2018-05-11T20:00Z\|castor oil [\[CHEBI:140618\]](https://www.ebi.ac.uk/ols4/ontologies/chebi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_140618?lang=en);2023-12-07T17:00+02:00 | [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | -| **Host metadata** | Host name | | | Scientific name [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | e.g. *Canis lupus familiaris* [\[NCBI:txid9615\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9615), *Homo sapiens* [\[NCBI:txid9606\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&lin=f&keep=1&srchmode=1&unlock) | [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | -| | host_common_name | | | Common name of the host | e.g. human, dog, cattle | [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | -| | host_height **OR** host_length | | | Height of host or length of host | e.g. 177 cm | [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/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”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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](https://www.ebi.ac.uk/ols4/ontologies/fma) or [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon) ontologies | e.g. gut [\[FMA:45615\]](http://purl.obolibrary.org/obo/FMA_45615) **OR** gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/UBERON_0000328) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | -| | 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”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | host_sex | | | Gender and/or physical sex of subject/host | | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| | 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 [\[ecocore:00000082\]](http://purl.obolibrary.org/obo/ecocore_00000082), substrate, medium; note here, that multiple possible subclasses exist in organism [\[OBI:0100026\]](http://purl.obolibrary.org/obo/OBI_0100026), such as autotroph [\[ECOCORE:00000023\]](http://purl.obolibrary.org/obo/ECOCORE_00000023)\|heterotroph [\[ECOCORE:00000010\]](http://purl.obolibrary.org/obo/ECOCORE_00000010) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | -| **Additional potential terrestrial bio/env considerations** | | | *Ecosystem Category* | *Category list* | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | -| | *Ecosystem Type* | | | *Type list* | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | -| | *Ecosystem Subtype* | | | *Subtype list* | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | -| | *Specific Ecosystem* | | | *Specific ecosystem list* | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | -| | *Habitat* | | | *Free text* | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | +| **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](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | | | e.g. 2013-03-25T12:42:31+01:00 | [“GSC MIxS: BuiltEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | +| | Collected by | Name of person or institute that collected the sample | | [“ENA Marine Microalgae Checklist; Checklist: ERC000043”](https://www.ebi.ac.uk/ena/browser/view/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](https://www.insdc.org/submitting-standards/country-qualifier-vocabulary/), or the [GAZ ontology](http://purl.bioontology.org/ontology/GAZ) | | | e.g. USA: Maryland, Bethesda; Atlantic Ocean region **OR** [\[GAZ:00051071\]](http://purl.obolibrary.org/obo/GAZ_00051071) | [“GSC MIxS: BuiltEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | +| | 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”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | +| | 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”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | +| | 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”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | +| | 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”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | +| | 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: [\[ENVO_00000428\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000428?lang=en). If more than one term applies to the field, \| should be used to separate them.; note here, that subclasses of terrestrial biome [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) should be used here. | | | e.g. terrestrial biome [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) | [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/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](https://obofoundry.org/) ontologies which interoperate with EnvO (e.g. [UBERON](https://www.ebi.ac.uk/ols4/ontologies/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 [\[ENVO:00000446\]](https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00000446?lang=en) was used in env_broad_scale, env_local_scale should be one of the following subclasses : anthropogenic terrestrial [\[ENVO:01000219\]](http://purl.obolibrary.org/obo/ENVO_01000219)\|mangrove biome [\[ENVO:01000181\]](http://purl.obolibrary.org/obo/ENVO_01000181)\| shrubland biome [\[ENVO:01000176\]](http://purl.obolibrary.org/obo/ENVO_01000176)\| terrestrial environmental zone [\[ENVO:01001199\]](http://purl.obolibrary.org/obo/ENVO_01001199) \| tundra biome [\[ENVO:01000180\]](http://purl.obolibrary.org/obo/ENVO_01000180) \| woodland biome [\[ENVO:01000175\]](http://purl.obolibrary.org/obo/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”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/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 [\[ENVO:00010483\]](http://purl.obolibrary.org/obo/ENVO_00010483). Terms from other [OBO ontologies](https://obofoundry.org/) 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 [\[ENVO:00005742\]](http://purl.obolibrary.org/obo/ENVO_00005742)\|bare soil [\[ENVO:01001616\]](http://purl.obolibrary.org/obo/ENVO_01001616)\|bulk soil [\[ENVO:00005802\]](http://purl.obolibrary.org/obo/ENVO_00005802) **OR** arterial blood [\[UBERON:0013755\]](http://purl.obolibrary.org/obo/UBERON_0013755)\|venous blood [\[UBERON:0013756\]](http://purl.obolibrary.org/obo/UBERON_0013756)\|blood plasma [\[UBERON:0001969\]](http://purl.obolibrary.org/obo/UBERON_0001969) | | [“GSC MIxS: BuiltEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | +| | 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”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | +| | Site conditions | Environmental temp, RH, salinity, pH | | | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | [“GSC MIxS: BuiltEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/), [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | Material conditions | Sample material temp, RH, salinity, pH | | | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | [“GSC MIxS: SoilMIMS”](https://genomicsstandardsconsortium.github.io/mixs/SoilMIMS/), [“GSC MIxS: WastewaterSludgeMIMS”](https://genomicsstandardsconsortium.github.io/mixs/WastewaterSludgeMIMS/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | Microbial ID | Taxonomy and/or culture source, if available. Expected_value: [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | | | e.g. *E. coli* [\[NCBI:txid562\]](https://www.ncbi.xyz/Taxonomy/Browser/wwwtax.cgi?id=562) | [“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/), [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/) | | +| | Microbial isolate | Microbial isolate cultured?: Y/N | | | | | | +| | Culture substrate | This field accepts terms listed under culture medium [\[OBI:0000079\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_0000079?lang=en). If the proper descriptor is not listed please use text to describe the culture medium | | | e.g. minimal defined medium [\[MCO:0000881\]](https://www.ebi.ac.uk/ols4/ontologies/mco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMCO_0000881?lang=en) | **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | 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)](http://purl.bioontology.org/ontology/chebi) | | | e.g. agar [\[CHEBI:2509\]](https://www.ebi.ac.uk/ols4/ontologies/micro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_2509);2018-05-11T20:00Z\|castor oil [\[CHEBI:140618\]](https://www.ebi.ac.uk/ols4/ontologies/chebi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCHEBI_140618?lang=en);2023-12-07T17:00+02:00 | [“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”](https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/), [“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/) | | +| **Host metadata** | Host name | Scientific name [\[NCBI taxonomy ID\]](https://www.ncbi.nlm.nih.gov/taxonomy) | | | e.g. *Canis lupus familiaris* [\[NCBI:txid9615\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9615), *Homo sapiens* [\[NCBI:txid9606\]](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&lin=f&keep=1&srchmode=1&unlock) | [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), **MSI-ECWSG** ([Morrison et al. (2007)](https://doi.org/10.1007/s11306-007-0067-1)) | | +| | host_common_name | Common name of the host | | | e.g. human, dog, cattle | [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/) | | +| | host_height **OR** host_length | Height of host or length of host | | | e.g. 177 cm | [“GSC MIxS: Plant-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/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”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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](https://www.ebi.ac.uk/ols4/ontologies/fma) or [UBERON](https://www.ebi.ac.uk/ols4/ontologies/uberon) ontologies | | | e.g. gut [\[FMA:45615\]](http://purl.obolibrary.org/obo/FMA_45615) **OR** gut wall [\[UBERON:0000328\]](http://purl.obolibrary.org/obo/UBERON_0000328) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/) | | +| | 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”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | host_sex | Gender and/or physical sex of subject/host | | | | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| | 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 [\[ecocore:00000082\]](http://purl.obolibrary.org/obo/ecocore_00000082), substrate, medium; note here, that multiple possible subclasses exist in organism [\[OBI:0100026\]](http://purl.obolibrary.org/obo/OBI_0100026), such as autotroph [\[ECOCORE:00000023\]](http://purl.obolibrary.org/obo/ECOCORE_00000023)\|heterotroph [\[ECOCORE:00000010\]](http://purl.obolibrary.org/obo/ECOCORE_00000010) | [“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014), [“GSC MIxS: Human-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/), [“GSC MIxS: Host-associatedMIMS”](https://genomicsstandardsconsortium.github.io/mixs/Host-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/) | | +| **Additional potential terrestrial bio/env considerations** | *Ecosystem Category* | *Category list* | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | +| | *Ecosystem Type* | *Type list* | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | +| | *Ecosystem Subtype* | *Subtype list* | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | +| | *Specific Ecosystem* | *Specific ecosystem list* | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | +| | *Habitat* | *Free text* | | | *JGI GOLD* ([“GOLD Ecosystem Classification Paths”](https://gold.jgi.doe.gov/ecosystem_classification)) | | | # References