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microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model
https://microbiomedata.github.io/nmdc-schema/
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categorical tags for biosamples #465

Open turbomam opened 1 year ago

turbomam commented 1 year ago

@emileyfadrosh has requested tags that would make it easier to find biosamples with shared methods, funding, etc. in the Data Portal. Other NMDC team members have been supportive.

I will implement this as a new slot on the Biosmaple class, whose range will be an enumeration

@emileyfadrosh and others will be responsible for

  1. adding descriptions, meanings and see_also links for the permissible values
  2. annotating a dump of the MongoDB bisoample_set collection with the appropriate permissible values
    • @dwinston said that may have a good way to make a spreadsheet out of the bisoample_set collection. But can't we just do a CSV export from Compass?

Proposed permissible values:

cc @sujaypatil96 @cmungall

dwinston commented 1 year ago

@turbomam my contribution to enabling a csv export of biosamples for annotation would be this nmdc-runtime code that demos flattening JSON hierarchy and folding in other pertinent info to a biosample row if desired. In this case, it was including all omics types associated with omics_processing_set documents that has_input that biosample.

turbomam commented 1 year ago

See also https://github.com/microbiomedata/nmdc-schema/issues/467

mslarae13 commented 1 month ago

@turbomam We have #467 and there's a merged PR for this issue. Can we close this one if favor of the new issue?