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Update depth Terrestrial_BioEnv_Metadata.md
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Closes issue #30
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MartinBoleSlo authored Apr 1, 2024
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| | 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/) |
| | 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.; 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) | |
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