paolaroncaglia
commented
5 years ago Following discussion with MONDO, where it’s uncertain if they’d want to keep grouping classes such as 'pregnancy disorder' and 'puerperal disorder', while EFO needs to have them for our main collaborators, I’ll write down a few ideas for EFO.
Currently, ‘pregnancy disorder’ is a subclass of ‘female reproductive system disease’. I suggest to
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[ ] Change this to ‘pregnancy disorder’ subclass of ‘disease’;
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[ ] Add an axiom to link ‘pregnancy disorder’ and PATO:0000383 ‘female’. Consult with colleagues about the best axiom to use; at present, in EFO ‘female’ and ‘male’ are only used in axioms about cell lines, e.g. HeLa SubClassOf has_quality some female; we could say that ‘pregnancy disorder’ occurs_in some female? Or would we want to use is_about, or another axiom?
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[ ] Add an axiom to link ‘pregnancy disorder’ and EFO:0002950 ‘pregnancy’. (This was suggested by @cmungall too, see https://github.com/monarch-initiative/mondo/issues/652#issuecomment-477827877: “Maybe define pregnancy disorder more generally, to include during or having a causal link to?”) Consult with colleagues about the best axiom to use.
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[ ] As for children of ‘pregnancy disorder’: they should keep that parent as it’s a useful grouping class and needed for our mappings to ICD10; however, currently, children of ‘pregnancy disorder’ inherit from their parent the link to ‘female reproductive system disease’, which is incorrect in some cases. This link needs to be revised depending on the fate of ‘pregnancy disorder’, and more appropriate link may need to be added. E.g., ‘chorea gravidarum’ should not be connected to ‘female reproductive system disease’, while ‘placenta disease’ should.
We may want to adopt a similar strategy for 'puerperal disorder', i.e.:
- [ ] Replace the current link to ‘pregnancy disorder’ with a link to ’disease’;
- [ ] Add an axiom to link to ‘female’;
- [ ] Create a term for ‘puerperium’ and add a (temporal) link to it;
- [ ] Revise parentage of its children.
Stemming from https://github.com/EBISPOT/efo/issues/396. In EFO, 'pregnancy disorder' and 'puerperal disorder' were added for ICD10 mapping purposes, and were modelled after MONDO. However, placement of both terms may need revision, see monarch-initiative/mondo#652.