Remove all instances of 'directly regulates', 'directly positively regulates' and 'directly negatively regulates

geneontology / go-shapes

Schema for Gene Ontology Causal Activity Models defined using RDF Shapes

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Remove all instances of 'directly regulates', 'directly positively regulates' and 'directly negatively regulates #255

Open pgaudet opened 3 years ago

pgaudet commented 3 years ago

We have decided not to use those.

Can we remove? Or will that break something ?

vanaukenk commented 3 years ago

Do we have a mechanism to update all the existing models that use these relations, as well as 'directly activates' and 'directly inhibits'?

If not, we will now have a lot of models that are invalid. It'd be good to be able to update things like this programmatically before we remove the relations.

ukemi commented 3 years ago

We also need to do at least one other mass replacement of relations. We need to change stand-alone CC annotations that are to cellular anatomical entities to located_in rather than part_of. Annotations to complexes can stay as they are.

cmungall commented 3 years ago

@pgaudet can you add more context - what meeting was this decided on? What was the rationale? how will models we updated

Will we use causally_upstream_of_[{negative,positive}]_effect in place?

pgaudet commented 3 years ago

This was decided on GO-CAM modeling calls. We decided that there was no case when we needed to distinguish

regulates and directly regulates (and same for positive and negative regulates). I dont know how models can be updated, this was also the question @vanaukenk was asking https://github.com/geneontology/go-shapes/issues/255#issuecomment-777666490

Thanks, Pascale