Unsatisfiable class in Mondo

[matentzn]

When refreshing the OMIM gene relations (#8108) we noticed the following unsat.

This will be fun to crack! QC fail: https://github.com/monarch-initiative/mondo/actions/runs/11962410332/job/33350758622

osteopetrosis, autosomal dominant 3 SubClassOf Nothing

• osteopetrosis, autosomal dominant 3 SubClassOf osteopetrosis
  • osteopetrosis SubClassOf osteosclerosis
    • osteosclerosis SubClassOf bone remodeling disease
    • bone remodeling disease EquivalentTo bone disorder and (disease disrupts some bone remodeling)
      • bone disorder EquivalentTo disease and (disease has location some bone tissue)
• osteopetrosis, autosomal dominant 3 SubClassOf has characteristic some Autosomal dominant inheritance
• osteopetrosis, autosomal dominant 3 SubClassOf has material basis in germline mutation in some PLEKHM1
• autosomal recessive osteopetrosis 6 SubClassOf has characteristic some Autosomal recessive inheritance
• autosomal recessive osteopetrosis 6 EquivalentTo osteopetrosis and (has material basis in germline mutation in some PLEKHM1)
• autosomal dominant disease EquivalentTo disease and (has characteristic some Autosomal dominant inheritance)
• autosomal recessive disease EquivalentTo disease and (has characteristic some Autosomal recessive inheritance)
• autosomal dominant disease DisjointWith autosomal recessive disease

paroxysmal nocturnal hemoglobinuria 1 SubClassOf Nothing

• paroxysmal nocturnal hemoglobinuria 1 SubClassOf paroxysmal nocturnal hemoglobinuria
  • paroxysmal nocturnal hemoglobinuria SubClassOf acquired aplastic anemia
    • acquired aplastic anemia EquivalentTo aplastic anemia and (has characteristic some acquired)
• paroxysmal nocturnal hemoglobinuria 1 SubClassOf has material basis in germline mutation in some PIGA
  • PIGA SubClassOf gene
• has characteristic some acquired DisjointWith has characteristic some inherited
• has material basis in germline mutation in some gene SubClassOf has characteristic some inherited

Ontologies used:

• axioms.owl (http://purl.obolibrary.org/obo/mondo/imports/axioms.owl)
• mondo.owl (http://purl.obolibrary.org/obo/mondo.owl)
• merged_import.owl (http://purl.obolibrary.org/obo/mondo/imports/merged_import.owl)

[twhetzel]

Only MONDO:0020848 remains as an issue. Due to a bug in the omim ingest pipeline and/or lack information in an omim file, a gene association was added to MONDO:0010438 saying it was germline, when it already had somatic.

[twhetzel]

Related to the QC check error (Unsatisfiable) for MONDO_0020848, Nico pointed this out:

• autosomal recessive osteopetrosis 6 EquivalentTo osteopetrosis and (has material basis in germline mutation in some PLEKHM1)
• osteopetrosis, autosomal dominant 3 SubClassOf has material basis in germline mutation in some PLEKHM1

Based on https://omim.org/entry/611497, MONDO:0012679 'autosomal recessive osteopetrosis 6' has a gene association with evidence from medgen that does not meet our criteria for disease defining gene associations (the phenotype label displayed in omim is prefixed with a special character, e.g. ?) we add from omim. However, other sources like ClinGen include both of these diseases caused by this gene.

@sabrinatoro can you advise how to resolve this issue?

[twhetzel]

I removed the gene association from MONDO:0012679 'autosomal recessive osteopetrosis 6' since this does not meet our rules for adding gene associations based on OMIM data and for now we need to move forward on the Tech side based on discussions with @matentzn. If this is not the right decision from a curation perspective, that needs to be addressed later.

[matentzn]

FWIW I agree with the change for now, here it is for reference:

https://github.com/monarch-initiative/mondo/commit/da20096d18ad980b78c65398ac60867fc3d506d3#diff-889e0a9ba62d62cc6ee7c5c9bead0075444d506253590ef0dcf4786904ac6768L288824