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MartinBoleSlo authored Aug 14, 2024
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##   Minimal biological/environmental metadata for human microbiome


| | **metadata** | **definition** | **reference of definition\[\]** | **expected unit of measurement** | **example** | **sources( where this or similar matadata field is mentioned)** |
|-------------------------------------------------------|-----------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| **Site metadata** | Collection date/time | The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated. Restricted text field, [ISO8601](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | [MIXS:0000011](https://w3id.org/mixs/0000011) | YYYY-MM-DD | 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: MimsHumanAssociated”](https://genomicsstandardsconsortium.github.io/mixs/0010007_0016003/), [“GSC MIxS: MimsHostAssociated”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016002/), [“GSC MIxS: MimsHumanGut”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016004/), [“GSC MIxS: MimsHumanOral”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016005/), [“GSC MIxS: MimsHumanSkin”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016006/), [“GSC MIxS: MimsHumanVaginal”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016007/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) |
| **Site metadata** | collection_date | The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated. Restricted text field, [ISO8601](https://www.iso.org/iso-8601-date-and-time-format.html) compliant | [MIXS:0000011](https://w3id.org/mixs/0000011) | YYYY-MM-DD | 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: MimsHumanAssociated”](https://genomicsstandardsconsortium.github.io/mixs/0010007_0016003/), [“GSC MIxS: MimsHostAssociated”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016002/), [“GSC MIxS: MimsHumanGut”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016004/), [“GSC MIxS: MimsHumanOral”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016005/), [“GSC MIxS: MimsHumanSkin”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016006/), [“GSC MIxS: MimsHumanVaginal”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016007/), [“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) | [MIXS:0000010](https://w3id.org/mixs/0000010) | | 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: MimsHumanAssociated”](https://genomicsstandardsconsortium.github.io/mixs/0010007_0016003/), [“GSC MIxS: MimsHostAssociated”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016002/), [“GSC MIxS: MimsHumanGut”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016004/), [“GSC MIxS: MimsHumanOral”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016005/), [“GSC MIxS: MimsHumanSkin”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016006/), [“GSC MIxS: MimsHumanVaginal”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016007/), [“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. | [MIXS:0000009](https://w3id.org/mixs/0000009) | | 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: MimsHumanAssociated”](https://genomicsstandardsconsortium.github.io/mixs/0010007_0016003/), [“GSC MIxS: MimsHostAssociated”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016002/), [“GSC MIxS: MimsHumanGut”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016004/), [“GSC MIxS: MimsHumanOral”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016005/), [“GSC MIxS: MimsHumanSkin”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016006/), [“GSC MIxS: MimsHumanVaginal”]( https://genomicsstandardsconsortium.github.io/mixs/0010007_0016007/), [“GSC MIxS Human Associated; ENA Checklist: ERC000014”](https://www.ebi.ac.uk/ena/browser/view/ERC000014) |
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