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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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increase specificity of has_input relationship on omics_processing #28

Open dehays opened 3 years ago

dehays commented 3 years ago

The need here is driven from metabolomics and metaproteomics where @corilo would like to be able to specify the input as one of:

sample blank QC

ssarrafan commented 2 years ago

@corilo @cmungall I'm removing David and Bill from this issue. Let me know if this is something we should put in the backlog, break down into smaller chunks, or re-assign. I'm so glad you're still here.

turbomam commented 11 months ago

It looks to me like the range of OmicsProcessing.has_input is as wide open as possible right now: NamedThing.

See https://microbiomedata.github.io/nmdc-schema/OmicsProcessing/#induced

I would actually like to constrain this more now.

We have a Biosample class, but no classes for modelling blanks or QC samples. That doesn't sound totally unreasonable to me, but I do wonder if we would want to store the results of blank or QC runs in MongoDB.

aclum commented 10 months ago

@anastasiyaprymolenna @corilo is this going to be addressed in the metabolomics squad?

kheal commented 3 months ago

@anastasiyaprymolenna . My understanding is that we have decided that dealing with blanks is beyond the scope at this time (beyond adding the CalibrationInformation class, which we have completed in the Berkeley fork). If you agree, can you close this issue?