Refactor lexmatch source configuration

[joeflack4]

Overview

I think probably branching logic inside of lexmatch-sssom-compare.py is not the best location for this kind of configuration. Thinking maybe moving to:

• a. Some existing configuration file
  • a.a. metadata/ONTOLOGY.yml: My initial thought is add a component_filename field to metadata/ONTOLOGY.yml. And then we would have lexmatch simply check that, and then pull the base_prefix_map. Then we would pull subject_prefixes from there, although to do that, we'd have to go with my suggestion of moving subject_prefixes from mondo.config.sssom.yml.
• b. a new lexmatch_config (.py, .json, or .yml)

Additional details

• Original discussion thread

What the configuration currently looks like:

ont2 = ont.upper()
if ont == "omim":
    ont2 = "|".join((["OMIM", "OMIMPS"]))
elif ont == "ordo":
    ont2 = "|".join((["ORDO", "Orphanet"]))
elif ont == "icd11foundation":
    ont2 = 'icd11.foundation'

[joeflack4]

Oh, also @hrshdhgd I don't know if this will happen again in the future, but I have been keeping docs/developer/add-new-source.md updated. Basically when we add a new source, any necessary configuration should go in here. So if you happen to add any new source configuration or change any existing source configuration, please make an update to that file.

[matentzn]

I think probably branching logic inside of lexmatch-sssom-compare.py is not the best location for this kind of configuration.

@joeflack4 I agree with your proposals and prefer a.a at first glance