GOLD 'ecosystem' slots at study level

[mslarae13]

Why are the 5 GOLD ecosystem terms captured under study class? https://microbiomedata.github.io/nmdc-schema/Study/
Biosample makes sense. https://microbiomedata.github.io/nmdc-schema/Biosample/
But with study is confusing to me.

Should these be deprecated?

• this might be a quick to close issue if I'm just misunderstanding something

@turbomam
@emileyfadrosh
@cmungall

[turbomam]

Hi, @mslarae13

Yes, it could be confusing. Even worse, nothing's in place to make sure that the biosample GOLD ecosystem paths are compatible with the study GOLD ecosystem paths

There's some good discussion of this in #10

[aclum]

@mslarae13 GOLD specifies these terms at the study level
see
https://gold.jgi.doe.gov/study?id=Gs0161344

[mslarae13]

@aclum so the term that is identified at the study level gets applied to all the biosamples?
Is that true for the lower levels?

Or can biosamples in a study differ from the study?

@turbomam thanks, I don't think I saw that discussion... still seems weird to me. You can have a pretty wide variation among biosamples depending on your research questions within your study. If the study is assigned, and biosamples.. then that kinda makes sense to me. TO assign at only the study level seems weird.

[aclum]

BIosamples classification can be more specific that study. For example

for Gs0161344 we have

Ecosystem	Environmental
Ecosystem Category	Terrestrial
Ecosystem Type	Soil
Ecosystem Subtype	Unclassified
Specific Ecosystem	Unclassified
Ecosystem Path ID	4212

The biosamples w/in the study have Ecosystem Subtype specified
ex Gb0356235

Ecosystem	Environmental
Ecosystem Category	Terrestrial
Ecosystem Type	Soil
Ecosystem Subtype	Tundra
Specific Ecosystem	Unclassified
Ecosystem Path Id	5950

[mslarae13]

Ok. in that case, I think this is fine then. Since we pull it from GOLD and it's at both biosample and study level