Modify OrphaGeneToDiseaseParser to avoid associating genes with grouping diseases

[cmungall]

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

[pnrobinson]

@ielis @iimpulse I will take this on if nobody is working on this?