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monarch-initiative / omim

Data ingest pipeline for OMIM.
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Use (a) Exomiser (b) Medgen for validating/testing output? #71

Open joeflack4 opened 1 year ago

joeflack4 commented 1 year ago

Overview

Chris Mungall mentioned during the Mondo technical call today that Exomiser has parsed many/all the OMIM files before (e.g. morbidmap.txt). It's a flagship tool that is used in clinical settings, so it would be good to check the output of that against OMIM if we want a way to know if the omim.ttl we generate here is correct. The output format of Exomiser for this is an H2 database.

Note to self: Jules works on Exomiser and can help with questions. I've saved contact info in Workflowy.

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joeflack4 commented 1 year ago

Adding @kanems suggestion (https://github.com/monarch-initiative/mondo/issues/5507#issuecomment-1280755047) that we could use Medgen for an additional source of validation. My initial guess is that Exomiser may be fully sufficient, as Chris M says it is a 'clinical flagship product', but I think it's good to capture all possible means of validation in this issue.

matentzn commented 1 year ago

If you need help coordinating this comparison, feel free to ping me during a call. I have biweekly meetings with Jules and we can make a plan for how best to compare.