Create / redistribute OmicsProcessing & slots

microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

https://microbiomedata.github.io/nmdc-schema/

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Create / redistribute OmicsProcessing & slots #1525

Closed mslarae13 closed 2 months ago

mslarae13 commented 7 months ago

[x] deprecate chimera_check
[x] #1535
[x] #1540
[x] #1541
[x] #1543
[ ] ~remove principal_investigator from OmicsProcessing (DataGeneration)~
[x] deprecate samp_vol_we_dna_ext & confirm the input_mass exisiting slot satisfies
[x] move seq_meth to Class:NucleotideSequecingClass
[x] Remove seq_meth from OmicsProcessing (DataGeneration)
[x] move seq_quality_check to
[x] remove classes that were added to LibraryPreparation from Biosample
[x] remove classes that were added to LibraryPreparation from DataGeneration

mslarae13 commented 7 months ago

https://github.com/microbiomedata/berkeley-schema-fy24/tree/1525-add-slots-to-MaterialProcessing-classes-that-were-on-OmicsProcessing

mslarae13 commented 7 months ago

https://github.com/microbiomedata/berkeley-schema-fy24/pull/42

mslarae13 commented 7 months ago

@aclum to follow up on PI, merging the rest of the changes now.

aclum commented 7 months ago

@mslarae13 I did confirm that JGI provides PI at the sequencing project level in the GOLD projects API endpoint so the best mapping to NMDC classes is to leave this on DataGeneration. An alternative would be to put this on Biosample but would require more graph traversal. The use case for JGI having this slot and for NMDC to keep it is studies will multiple PIs like GROW where more granular resolution is needed.