Add pipeline to update gene links in Mondo

[sabrinatoro]

The following axioms should be created/updated from OMIM: 'has material basis in germline mutation in' some GENE

• gene-to-disease information from OMIM, based on rules discussed HERE (need to be updated, add document with requirements)

• the pipeline should proceed as follow (based on discussions on 2024-06-05 technical call)

  1. remove all OMIM source annotations for axioms'has material basis in germline mutation in' some GENE
  2. based on OMIM EquivalentTo x-ref, add OMIM xref as source to existing 'has material basis in germline mutation in' some GENE axioms
  3. based on OMIM EquivalentTo x-ref, create new 'has material basis in germline mutation in' some GENE axioms, with OMIM x-ref as source when no axioms exist.
  4. FOR THE FIRST PASS: create a report with 'has material basis in germline mutation in' some GENE axiom which
     • do not have a source (curator to review and either remove the axiom or add source)
     • does have a source different from OMIM (curator to review)

QC checks:

• report diseases that have more than one 'has material basis in germline mutation in' some GENE" axiom
• report disease with 'has material basis in germline mutation in' some GENE axiom without a source annotation

[joeflack4]

@matentzn Thanks for handling. I added to your / the board(s) as medium priority.

[joeflack4]

Related issues:

• https://github.com/monarch-initiative/mondo/issues/7229
• https://github.com/monarch-initiative/mondo-ingest/issues/558