Update OMIM gene references in Mondo (#8108)

* Adding draft pipeline for updating OMIM genes relations

* Update OMIM gene references in mondo

* Return Mondo edit back to master state

* Update all OMIM links and logical definitions

* Add pipeline for updating logical definitions

* Add comment about mondo genes being too aggresively removed

* remove has_material_basis_in_germline_mutation_in only where OMIM is the source

* Update OMIM refresh pipeline

* Run OMIM pipeline on Mondo edit

* remove incorrectly added germline mutation relationship, error in omim.owl

* remove ?provisional gene association based on https://omim.org/entry/611497

* revert change, clingen shows this gene association

* remove gene association based on omim gene association rules

* fix qc errors from qc/general/qc-single-child.sparql

* fix errors from qc/general/qc-deprecated-class-reference.sparql

* fix errors from qc/mondo/qc-omim-subsumption.sparql

* updated gene association

I made some chances based on the "questionable entries" reported in the spreadsheet

* Exclude QC - multiple gene associations

---------

Co-authored-by: Trish Whetzel <[email protected]>
Co-authored-by: Sabrina Toro <[email protected]>

Author: 3 people