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Terrestrial(Constructed) microbiome biological/environmental metadata

  Minimal biological/environmental metadata for terrestrial(constructed) microbiome

metadata definition/examples source
Site metadata Collection date/time Restricted text “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: WastewaterSludgeMIMS”
Collected by Name/institute “ENA Marine Microalgae Checklist; Checklist: ERC000043”
Geographic location INSDC list location “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: WastewaterSludgeMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”
Latitude Origin latitude in DD “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: WastewaterSludgeMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”
Longitude Origin longitude in DD “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: WastewaterSludgeMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”
Elevation Origin elevation in m “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: WastewaterSludgeMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”
Altitude/geographic depth E.g. water/soil/cavern depth, or height “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: WastewaterSludgeMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”
Sample site/feature E.g. marine, abdomen “GSC MIxS: Plant-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS”
Sample sub-site/feature E.g. sea surface, appendix “GSC MIxS: Plant-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS”
Sample material E.g. blood, water, soil, particulate “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: WastewaterSludgeMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”
Sample size/mass H x W x L, vol., mass (e.g. 2 L water, 1 kg soil) “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: WastewaterSludgeMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”
Site conditions Environmental temp, RH, salinity, pH “GSC MIxS: BuiltEnvironmentMIMS”, “GSC MIxS: Plant-associatedMIMS”, MSI-ECWSG (Morrison et al. (2007))
Material conditions Sample material temp, RH, salinity, pH “GSC MIxS: SoilMIMS”, “GSC MIxS: WastewaterSludgeMIMS”, MSI-ECWSG (Morrison et al. (2007))
Microbial ID Taxonomy and/or culture source, if available “GSC MIxS: WastewaterSludgeMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”
Microbial isolate Microbial isolate cultured?: Y/N
Culture substrate Microbial culture medium/substrate MSI-ECWSG (Morrison et al. (2007))
Chemical exposure E.g. medications, pollutants, treatments “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”, “GSC MIxS: WastewaterSludgeMIMS”, “GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS”
Host metadata Host name Scientific name “GSC MIxS: Plant-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS”, MSI-ECWSG (Morrison et al. (2007))
Host dim./weight E.g. 30 cm diameter tree, 500 g ascidian “GSC MIxS: Plant-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS”
Host specific sample depth E.g. Skin tissue 3 mm subsurface
Age Age of subject/host “GSC MIxS: Plant-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS”
Gender/Sex Gender and/or sex of subject/host “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS”
Host diet/substrate E.g. omnivore/veg/etc., substrate, medium “GSC MIxS: Plant-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-associatedMIMS”
Additional potential terrestrial(constructed) bio/env considerations Ecosystem Category Category list JGI GOLD (“GOLD Ecosystem Classification Paths”)
Ecosystem Type Type list JGI GOLD (“GOLD Ecosystem Classification Paths”)
Ecosystem Subtype Subtype list JGI GOLD (“GOLD Ecosystem Classification Paths”)
Specific Ecosystem Specific ecosystem list JGI GOLD (“GOLD Ecosystem Classification Paths”)
Habitat Free text JGI GOLD (“GOLD Ecosystem Classification Paths”)
Growth container Type and supplier of bioreactor/shake flask/plate MSI-ECWSG (Morrison et al. (2007))

#References

“ENA Marine Microalgae Checklist; Checklist: ERC000043.” https://www.ebi.ac.uk/ena/browser/view/ERC000043.

“GOLD Ecosystem Classification Paths.” https://gold.jgi.doe.gov/ecosystem_classification.

“GSC MIxS: BuiltEnvironmentMIMS.” https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/.

“GSC MIxS: Host-associatedMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/.

“GSC MIxS: Human-associatedMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/.

“GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS.” https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/.

“GSC MIxS: Plant-associatedMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/.

“GSC MIxS: SoilMIMS.” https://genomicsstandardsconsortium.github.io/mixs/SoilMIMS/.

“GSC MIxS: WastewaterSludgeMIMS.” https://genomicsstandardsconsortium.github.io/mixs/WastewaterSludgeMIMS/.

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.