Annotate the merged table

[berntpopp]

Either add functionality to annotate different data sources (OMIM P, inheritance type, GeneCC, HPO based kidney groups, ClinVar variants) to the merged table in the merge script "MergeAnalysesSources.R" or write a separate script.

The kidney disease groups could be defined into the "Expert Panels" groups from the "Kidney Disease CDWG": https://clinicalgenome.org/working-groups/clinical-domain/clingen-kidney-disease-clinical-domain-working-group/

I would further add a cancer category and maybe the respective ClinGen expert panel.

1. Complement-Mediated Kidney Diseases Gene Curation Expert Panel
2. Congenital Anomalies of the Kidney and Urinary Tract Gene Curation Expert Panel
3. Glomerulopathy Gene Curation Expert Panel
4. Kidney Cystic and Ciliopathy Disorders Gene Curation Expert Panel
5. Tubulopathy Gene Curation Expert Panel
6. [Hereditary Cancer Gene Curation Expert Panel]https://clinicalgenome.org/affiliation/40023/

We need to define HPO terms for automated assignment to the groups and agree on a scoring logic (majority voting).

TODOs:

• [x] annotate all OMIM P numbers for a gene
• [x] annotate inheritance type from OMIM (HPO based)
• [x] annotate GeneCC presence and curated strength
• [ ] define HPO terms for kidney disease groups
• [x] annotate Kidney disease groups by HPO search
• [x] annotate number of ClinVar variants

[berntpopp]

Also annotate the first publication from OMIM. This will allow us to make a time plot of genes associated over time.

[berntpopp]

Further possible annotations:

• Ensemble Gene ID
• Ensemble Protein ID
• NCBI Gene ID
• Mouse Entrez ID
• MGI ID

[berntpopp]

Output the HPO terms for kidney disease groups to files with their names and weights and make the table available in documentation.