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:
There are two sets of terms that appear redundant:
'directly negatively regulates' & 'directly inhibits' (has alt name directly negatively regulates)
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 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:
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.
We propose to
Thanks, Pascale
@ukemi @vanaukenk