This is related to/partly duplicates #265

Clinical-grade disease-gene associations: 3928 genes in OMIM currently associated to disease, <3500 single-gene, classical Mendelian though

1. work with PanelApp team to get an OMIM disease ID for every curated gene - resurrect what I did before and see if they made progress with OpenTargets
2. do a similar level of curation on the remaining dis-gene associations in OMIM and Orphanet

See Slack commentary in curation channel

@damiansm There is ClinGen and TheGenCC which could fulfill this criteria, assuming we used the 'definitive' associations.

This would require a database change to store the data and some means of enabling this from the user command through to the application only using these annotations.

@julesjacobsen Yes - this recent work makes this task a lot easier. It could be as easy as trimming the disease2gene table we load into Exomiser based on knowledge from GenCC. Looks like MONOD based but original OMIM ID is also stored: https://search.thegencc.org/genes/HGNC:13666

Good to know they have the original OMIM ID in there as that will be really useful. The next question is what classification to use when there are conflicts between submitters. In this case Ambry and TGMI say Definitive, Invitae go for Strong (although they never use definitive (https://search.thegencc.org/submitters/GENCC_000106)) and Orphanet only ever use Supportive, so I guess going with a Strong or Definitive assertion should be safe to do if trying to summarise.

For example:

https://search.thegencc.org/genes/HGNC:17416

The only problem is that ClinGen only curate to MONDO and these don't always align with OMIM (at least in this case it does with Orphanet) so the Orphanet and ClinGen submissions could be merged with Definitive evidence but there is still an issue about if and where to use MONDO identifiers.

The issue is the Orphanet only assert Supporting, ClinGen assert the full range and only use MONDO identifiers. PanelApp (GEL & Aus) use mostly OMIM identifiers for original submissions, but The GenCC map everything to MONDO. OMIM still haven't submitted any assertions.

Our current disease table looks like this:

Altering it to look like this, would be a lot more useful (the OMIM_GENE_ID column is unused in the application):

This would involve some kind or four-way merge of OMIM, HPOA, Orphanet and GenCC annotations 😱

Lets decide what if we are going to use the data for first and for what? If we just want to have a definitive only setting then we can just flag those associations in the disease table. If we want to display the tag for all rows or use it for weighting etc then we need all the data.