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microbiomedata / metadata-template-transformation

ETL between NMDC submission portal study records and user facility templates
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Will 'Biosafety Material Category' ever change? #16

Open mslarae13 opened 1 year ago

mslarae13 commented 1 year ago

Currently, NMDC does not capture the JGI column "Biosafety Material Category". Rather it's assumed to be "Metagenome (Environmental)".

Do we expect to need to add this slot so users can select "Metagenome (Environmental) or Metagenome (Host-associated)"?

What is host-associated as it pertains to JGI? NMDC does have a host-associated package. Are these the same?

@emileyfadrosh @aclum @ssarrafan : Hoping you can provide some information here to determine the path forward.

To decide

ssarrafan commented 1 year ago

@mslarae13 I've added this to the decision log.

aclum commented 1 year ago

I do find records for a few hundred JGI metagenome and metatranscriptomes since 2021 that a biosafety material category of 'Metagenome (Host-associated)'. These are typically gut or plant associated. Ex https://gold.jgi.doe.gov/biosample?id=Gb0258889 or https://gold.jgi.doe.gov/biosample?id=Gb0157741

mslarae13 commented 1 year ago

So, with @aclum 's response, it sounds like we need to add this slot. This is a JGI specific slot. Does this need to be an NMDC schema & submission schema change? @pkalita-lbl , @turbomam

pkalita-lbl commented 1 year ago

If it's going to be collected through the submission portal then, yes, it does.

mslarae13 commented 1 month ago

For now, I can continue to complete this field in the JGI sheet. Eventually, when we can provide fields in the submission portal that don't come from the schema, we should add this Biosafety Material Category term for JGI. Backlog, post berk, and post sorting out submission terms vs NMDC schema terms