Modifications to regulates terms

[pgaudet]

In the course of the work that GO is doing to ensure that we can correctly represent all relations for molecular function in GO annotations, we have noticed an inconsistency in the regulation branch:

1. There are two sets of terms that appear redundant:
   • 'directly negatively regulates' & 'directly inhibits' (has alt name directly negatively regulates)
   • 'directly positively regulates' & 'directly activates' (has alt name: directly positively regulates)
2. There is 'indirectly inhibits' and' indirectly activates' (with alt names indirectly negatively regulates and indirectly positively regulates, respectively), but not indirectly negatively regulates and indirectly positively regulates.

In GO we used to have the notion of 'activates' and 'inhibits' as children of positively and negatively regulates; however we have found this difficult to use from experimental data in papers and have merged these terms quite a while ago.

In OntoBee some ontologies are shown as using 'directly activates' : https://ontobee.org/ontology/RO?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002406

and directly inhibits https://ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002408

But if you look at the ontologies, there are no terms using these relations, for example: https://ontobee.org/ontology/VO?iri=http://purl.obolibrary.org/obo/RO_0002408

These ontology seem to just have the entire RO in them, without necessarily using all relations.

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We propose to

• [x] obsolete 'directly inhibits' with replaced_by 'directly negatively regulates';
• [x] new def: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
• [x] obsolete 'directly activates' with replaced_by 'directly positively regulates'
• [x] new def: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
• [x] change the label of 'indirectly inhibits' to indirectly negatively regulates
• [x] new def: p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
• [x] change the label of indirectly activates' to indirectly positively regulates
• [x] new def: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
• [x] create parent class indirectly regulates
• [x] add children: indirectly negatively regulates and indirectly positively regulates
• [x] def: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.

Thanks, Pascale

@ukemi @vanaukenk

[pgaudet]

Related to #630