Using both ChEBI and SO in axioms

geneontology / go-ontology

Source ontology files for the Gene Ontology

http://geneontology.org/page/download-ontology

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Using both ChEBI and SO in axioms #12867

Closed ukemi closed 7 years ago

ukemi commented 7 years ago

Yesterday I made a term 'tRNA folding' fully assuming that its logical definition would classify it as a tRNA metabolic process. To my surprise this didn't happen. The reason is that for some terms in the ontology, we create axioms using the ChEBI term 'transfer RNA' and for some terms we use the SO term 'tRNA'. I suspect that we want the ChEBI term since it refers to the molecule whereas the SO term is a sequence feature. We need to go through and clean this up one way or the other.

ValWood commented 7 years ago

Hi David,

I don't think tRNA foldng is metabolic is it? (protein folding isn't metabolic either)

hdrabkin commented 7 years ago

If folding is a part of trna biosynthesis (term doesn't exit; should it ? If so, would it not have something in it that says ... resulting in a fuctional/mature tRNA). I would think the same might need to be true of protein... ?

ukemi commented 7 years ago

RNA folding is_a RNA metabolic process in GO.

ValWood commented 7 years ago

I don't think they should be based on previous discussions. The tRNA isn't "metabolised" during folding? So chromosome condensation isn't DNA metabolism.....

ukemi commented 7 years ago

Hi Val,

If you think this is an issue, please open a separate ticket. This ticket should stick to the use of SO and ChEBI in the axioms. It would be simple enough to just put RNA folding under cellular process.

-D

dosumis commented 7 years ago

Draft bridging ontology with relevant axioms is here: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/ontology/extensions/go_bridge.owl?view=log (see also #12341).

Try importing this into a Protege session and checking for inferences.

TODO

[x] Add appropriate import statements to gene_ontology_write.obo/owl + redirects to catalog xml files.
[ ] Set up BFO minimal import generation

Warning - file has some equivalence axioms between named classes. May cause Jenkins build to fail. If this is the case, we could potentially be relaxed to subclassing axioms until build issues are fixed.

dosumis commented 7 years ago

See discussions on #12341. Minimal BFO import is duplicated with item on #12341.