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Marine_BioEnv_Metadata.md
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## Marine microbiome biological/environmental metadata
## Minimal biological/environmental metadata for marine microbiome
| | **metadata** | **definition** | **examples** | **source** |
|---|---------------|---------------------|------------------|-----------------|
| **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 | |
| | 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
“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>.
“GOLD Ecosystem Classification Paths.”
<https://gold.jgi.doe.gov/ecosystem_classification>.
“GSC MIxS Human Associated; ENA Checklist: ERC000014.”
<https://www.ebi.ac.uk/ena/browser/view/ERC000014>.
“GSC MIxS Water; ENA Checklist: ERC000024.”
<https://www.ebi.ac.uk/ena/browser/view/ERC000024>.
“GSC MIxS: Host-associatedMIMS.”
<https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/>.
“GSC MIxS: Human-associatedMIMS.”
<https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/>.
“GSC MIxS: Human-gutMIMS.”
<https://genomicsstandardsconsortium.github.io/mixs/Human-gutMIMS/>.
“GSC MIxS: Human-oralMIMS.”
<https://genomicsstandardsconsortium.github.io/mixs/Human-oralMIMS/>.
“GSC MIxS: Human-skinMIMS.”
<https://genomicsstandardsconsortium.github.io/mixs/Human-skinMIMS/>.
“GSC MIxS: Human-vaginalMIMS.”
<https://genomicsstandardsconsortium.github.io/mixs/Human-vaginalMIMS/>.
“GSC MIxS: WaterMIMS.”
<https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/>.
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package.”
<https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/>.
Morrison, Norman, Daniel Bearden, Jacob G. Bundy, Timothy Collette,
Fraser Currie, Matthew Davey, Migdalia Dominguez, et al. 2007. “Standard
Reporting Requirements for Biological Samples in Metabolomics
Experiments: Environmental Context.” *Metabolomics* 3 (2): 203–10.
<https://doi.org/10.1007/s11306-007-0067-1>.