Listing all 'rare X' disease terms in EFO where an 'x' term also exists

[paolaroncaglia]

@cmungall summarized the MONDO strategy re obsoletion of 'rare' terms: "We obsoleted the ones for which there was a clear replacement, Rare X --> X, i.e. where we trivially shadow an existing class with a rare subclass. So ones like "rare disease with dentinogenesis imperfecta" remain, because we have no "disease with dentinogenesis imperfecta" (such a disease would already be rare I imagine). I think we need to discuss these kinds of grouping classes (e.g. X with Y) separately. I think many could be obsoleted but this would be done in a very conservative way, in contrast to the Rare X --> X case."

@simonjupp asked: "Paola, can we compile a list of all the Rare X -> X that would be candidates for removal from EFO? We should check internally if any of these have been used for direct annotation and ensure there's a migration path for the downstream consumers."

[zoependlington]

A list of all "rare" terms in EFO: https://docs.google.com/spreadsheets/d/1Sb7SGwNdBzU3wMrsjsHtpJlwUYrel2a042zsu0SR3mY/edit?usp=sharing

[paolaroncaglia]

@zoependlington Thank you very much for providing the spreadsheet of 'rare' terms in EFO.

I split the list into ORDO vs MONDO terms. Based on what Chris wrote above, I'll assume that the MONDO terms that are still labeled as 'rare' do not have a simple replacement, and that those terms are for MONDO to look into. So I'll focus on the ORDO terms (tab "Paola's notes - ORDO terms"). Note, "Leave as is" means that there isn't an existing term fit to replace the 'rare x' one, in either EFO or MONDO; a new term would need to be created altogether.

• [ ] To be continued.

[paolaroncaglia]

Making a note here that this ticket should be linked to https://github.com/EBISPOT/efo/issues/463 (now closed as duplicate of https://github.com/EBISPOT/efo/issues/493). EFO:0000508 'genetic disorder' is in the 'therapeutic area' subset of terms that Open Targets needs. It is also parent or ancestor of all ORDO terms in the spreadsheet above. So,

• [ ] Before merging a 'rare x' ORDO term with its 'x' replacement, all children of 'rare x' should be given the (additional) parent 'genetic disorder'. However, if the resolution from #463 (actually, https://github.com/EBISPOT/efo/issues/493) is to keep MONDO:0003847 'inherited genetic disease' instead of EFO:0000508 'genetic disorder', the MONDO term should be added as parent instead.
• [ ] We may also want to run the obsolete/merge proposal for 'rare x' terms with Open Targets before implementing it.