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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 “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “ENA Marine Microalgae Checklist; Checklist: ERC000043”, “ENA Tara Oceans; Checklist: ERC000030”, “GSC MIxS Water; ENA Checklist: ERC000024”
Collected by Name/institute “ENA Marine Microalgae Checklist; Checklist: ERC000043”
Geographic location INSDC list location “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “ENA Marine Microalgae Checklist; Checklist: ERC000043”, “ENA Tara Oceans; Checklist: ERC000030”, “GSC MIxS Water; ENA Checklist: ERC000024”
Latitude Origin latitude in DD “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “ENA Marine Microalgae Checklist; Checklist: ERC000043”, “ENA Tara Oceans; Checklist: ERC000030”, “GSC MIxS Water; ENA Checklist: ERC000024”
Longitude Origin longitude in DD “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “ENA Marine Microalgae Checklist; Checklist: ERC000043”, “ENA Tara Oceans; Checklist: ERC000030”, “GSC MIxS Water; ENA Checklist: ERC000024”
Elevation Origin elevation in m “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”
Altitude/geographic depth E.g. water/soil/cavern depth, or height “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “ENA Marine Microalgae Checklist; Checklist: ERC000043”, “ENA Tara Oceans; Checklist: ERC000030”, “GSC MIxS Water; ENA Checklist: ERC000024”
Sample site/feature E.g. marine, abdomen “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”
Sample sub-site/feature E.g. sea surface, appendix “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”
Sample material E.g. blood, water, soil, particulate “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”
Sample size/mass H x W x L, vol., mass (e.g. 2 L water, 1 kg soil) “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”
Site conditions Environmental temp, RH, salinity, pH “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”, MSI-ECWSG (Morrison et al. (2007))
Material conditions Sample material temp, RH, salinity, pH MSI-ECWSG (Morrison et al. (2007)), “ENA Tara Oceans; Checklist: ERC000030”
Microbial ID Taxonomy and/or culture source, if available “ENA Marine Microalgae Checklist; Checklist: ERC000043”
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: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”
Host metadata Host name Scientific name “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”, MSI-ECWSG (Morrison et al. (2007))
Host dim./weight E.g. 30 cm diameter tree, 500 g ascidian “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”
Host specific sample depth E.g. Skin tissue 3 mm subsurface
Age Age of subject/host “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”
Gender/Sex Gender and/or sex of subject/host “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”
Host diet/substrate E.g. omnivore/veg/etc., substrate, medium “GSC MIxS: WaterMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS Water; ENA Checklist: ERC000024”
Additional potential marine 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”)

#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 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: WaterMIMS.” https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/.

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.