OMIM ingests: Monarch vs Mondo: compare, update, (merge?) - Githubissues

monarch-initiative / omim

Data ingest pipeline for OMIM.

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OMIM ingests: Monarch vs Mondo: compare, update, (merge?) #80

Open joeflack4 opened 2 years ago

joeflack4 commented 2 years ago

Overview

We have been discussing this recently. There seems to be some duplication of efforts between the OMIM ingests used by mondo-ingest and used by monarch-ingest.

Sub-task list

[ ] 1. Compare the ingests
- [ ] 1.1 Compare gene::disease associations
[ ] 2. (a) update the ingest(s) if any offending flaws/differences in either, or (b) merge into a single ingest?

Sub-tasks

1.1 Compare gene::disease associations

Compare counts

Monarch/Koza ingest: As of 2022/11/14, Kevin has found 7,446 omim_gene_to_disease_edges.tsv.zip
Mondo ingest: TODO @joeflack4

Related

76

joeflack4 commented 2 years ago

@cmungall @matentzn @kevinschaper I believe this is something we are trying to do? Feel free to edit my title/OP.

matentzn commented 2 years ago

Yes, we should. Indeed, we should probably strive to:

Have Mondo-OMIM supersede Monarch-OMIM entirely
Have Exomiser-OMIM and Mondo-OMIM be algorithmically identical (probably it will be hard to convince Exomiser to abandon their OMIM parser, but if we can demonstrate we cover all they do, they might in the future)