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monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza
https://monarchinitiative.org
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Mondo derived g2d's should not be presented on the website as "associations" #592

Open matentzn opened 2 weeks ago

matentzn commented 2 weeks ago

During @caufieldjh last presentation, I had the impression that you were actually showing d2g edges in Mondo as "associations" in the KG. I think this is not a good idea, for various reasons.

  1. We should present d2gs from authoritative sources only - Mondo is not an authoritative source for d2gs.
  2. Mondo d2gs are largely redundant with OMIM d2gs... (which alone is an argument to drop)
  3. ...but out of sync. So we may present d2gs in Mondo that have been revised in OMIM. If that revision was a retraction, we may be presenting faulty associations in Monarch KG.

I think (1) is reason enough. Ontologies should generally not be used as sources for associations in my opinion; happy to be challenged on this, just wanted to drop this here while it is still fresh on my mind.