Refine MassSpectrometry Class

brynnz22 commented 4 months ago

@SamuelPurvine @corilo @kheal @brynnz22 need to continue to work on refining the MassSpectrometry as we work to map DMS MassSpec metadata back to its corresponding metadata in NMDC.

brynnz22 commented 4 months ago

Potential schema changes to be discussed:

[x] @kheal makes a good point of abstracting out the configurations for ChromatographicSeparationProcess and DirectInfusiongProcess so data is not repeated. But keep inputs/outputs has_calibration on process class.
- So create a Configuration class and connect to ChromatographicSeparationProcess class through a slot called has_configuration. This would be connected by id (not inlined to avoid duplicate data), while ChromatographicSeparationProcess would be inlined in MassSpectrometry through the eluent_introduction slot (since metadata would process instance specific).
[x] @SamuelPurvine and @kheal pointed out that mass_spectrum_collection_mode may need to provide more info like allowing multiple scan types and the counts. In this case, it sounds like we may want to abstract out the collection mode as a class? Let me know if I understood this correctly
[x] Need to discuss how to accomadate MS1 and MS2, etc. Is it captured in the same MassSpectrometry instance? Or is it multiple instances connected somehow via parthood or some other method.

brynnz22 commented 3 months ago

See discussions here: https://github.com/microbiomedata/issues/issues/601

brynnz22 commented 3 months ago

I am going to close this, since this is all being addressed as part of the metabolomics squad. See schema update meta issue here: https://github.com/microbiomedata/nmdc-schema/issues/1905

microbiomedata / nmdc-schema

Refine MassSpectrometry Class #1831