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laminlabs / bionty

Registries for biological entities, coupled to public ontologies.
Apache License 2.0
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Add new Disease source: `ordo` #128

Open sunnyosun opened 1 month ago

sunnyosun commented 1 month ago

https://www.ebi.ac.uk/ols4/ontologies/ordo

Zethson commented 1 month ago

According to https://mondo.monarchinitiative.org/ a part of mondo.

matentzn commented 1 month ago

Sorry I am lurking on your project to see how it is developing :)

Mondo nearly fully covers ORDO, OMIM and Disease Ontology as well as a few other identifiers schemes (such as MedGen and UMLS, but also some more partial onces like SNOMED). However, I would prefer to use the term "covers" then "part of". ORDO is not part of Mondo, but Mondo covers ORDO in the sense that, if there is a disease in ORDO, it will exist somewhere in Mondo. There are a handful of disputed correspondences between ORDO and Mondo, but these are being resolved with between Orphanet (ORDO developers) and Monarch (Mondo developers) as we speak.

Zethson commented 1 month ago

@matentzn thank you for the details and clarification. It's great to hear that you are resolving these disputes. Thank you for your awesome work with mondo and all of the other ontology related projects that you're contributing to!

matentzn commented 1 month ago

You are very welcome! And thank you for your kind words!

sunnyosun commented 3 weeks ago

@Zethson We are filtering with the prefix MONDO: that's why the ordo terms aren't included: https://github.com/laminlabs/bionty/blob/main/bionty/base/entities/_disease.py#L59, we can add the prefix Orphanet: and update the underlying parquet.