We would skip g2d if there are multiple causal genes for that disease.
We could explore other approaches - e.g. using the Mondo mappings which tell us when an ordo class is subsuming OMIMs, but the g2d cardinality approach is simple and standalone and will leave us in a much better place than we are now
From @pnrobinson on email
In the Exomiser, HPO website, Monarch Web app, we find the same medical error.
Orphanet associated some diseases with tons of genes
ORPHA:91387Familial thoracic aortic aneurysm and aortic dissection
MFAP5 [8076 ] FOXE3 [2301 ] LOX [4015 ] MYH11 [4629 ] PRKG1 [5592 ] TGFB2 [7042 ] MAT2A [4144 ] TGFB3 [7043 ] ACTA2 [59 ] SMAD3 [4088 ] TGFBR2 [7048 ] TGFBR1 [7046 ] HEY2 [23493 ] SMAD4 [4089 ] SMAD2 [4087 ] THSD4 [79875 ] ELN [2006 ] MYLK [4638 ] FBN1 [2200 ]
@cmungall's comments:
Yes, monarch-kg gets these association from phenol via http://purl.obolibrary.org/obo/hp/hpoa/genes_to_disease.txt
I suggest we modify this code as per Peter's suggestion:
https://github.com/monarch-initiative/phenol/blob/master/phenol-annotations/src/main/java/org/monarchinitiative/phenol/annotations/assoc/OrphaGeneToDiseaseParser.java
We would skip g2d if there are multiple causal genes for that disease.
We could explore other approaches - e.g. using the Mondo mappings which tell us when an ordo class is subsuming OMIMs, but the g2d cardinality approach is simple and standalone and will leave us in a much better place than we are now