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EBISPOT / efo

Github repo for the Experimental Factor Ontology (EFO)
https://www.ebi.ac.uk/efo/
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Release EFO simple version #1583

Open dosumis opened 2 years ago

dosumis commented 2 years ago

EFO-base is not safe to use for generating import modules for other (application) ontologies or merging into KnowledgeBases. However, we have strong use-cases for re-use, given that some parts of EFO are used as a reference ontology.

I suggest we release a -simple version:

This would only have

dosumis commented 2 years ago

CC @matentzn

matentzn commented 2 years ago

Do you mean like

  1. reason
  2. relax
  3. remove --select "EFO:" --select complement --select classes --preserve-structure true (remove all classes not in EFO namespace, keeps OPs in existential of the type EFO:1 sub R some EFO:2)
  4. reduce

? Note that EFO has plenty of non-OBO classes like ORDO ids in it, but probably better not to include in ubergraph.

I expected a few disconnected nodes with such a cutting procedure, but maybe this is ok?

dosumis commented 2 years ago

I expected a few disconnected nodes with such a cutting procedure, but maybe this is ok?

I think that's fine. It would give us a safe way to re-use EFO reference ontology bits elsewhere (ubergraph; scAtlas, CAP).

dosumis commented 2 years ago

Should probably take pains to make clear specialised use cases in release notes and description on release product.