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monarch-initiative / phenio

An integrated ontology for Phenomics
https://monarch-initiative.github.io/phenio/
BSD 3-Clause "New" or "Revised" License
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How to deal with CHEBI dependencies of Monarch KG? #99

Open matentzn opened 1 day ago

matentzn commented 1 day ago

Problem: CTD ingest uses Chebi IDs, but Chebi is only a secondary, support ingest in PHENIO (so only those terms are imported relevant to any of the component ontologies.

How do we deal with it?

  1. Import all of chebi? (NO)
  2. Publish a seed for all chemical ingests and extract these from Chebi (increasing runtime and memory requirements a bit in PHENIO but doable, also, PHENIO is always going to reflect the CTD ingest of the last public data release to avoid dependency hell).
  3. Import all of Chebi OBO slim (some 8K or so Chebi classes relevant to OBO ontologies)? This will be a lot more coverage, but it will still be incomplete.

Any other ideas?

caufieldjh commented 15 hours ago

https://github.com/cmungall/chemessence ?

caufieldjh commented 15 hours ago

I'm curious about how incomplete option 3 may be, because that seems like the most immediate solution