Hello! In GORULE:0000015, we check that when a GAF has two taxon IDs, that they are formed correctly. I had a couple questions to clarify what the intention is. Here's the link to the rule: https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000015.md
Is this rule saying that 1) the first taxon should be attached to the gp, and 2) the second should be the interacting species (is that just what it means, or is there a way to verify this?) 3) the 2 allowed terms that can be used with dual taxons ('GO:0044419 : interspecies interaction between organisms', and 'GO:0044215 : other organism'), is that to mean only those terms are allowed? Or are children terms also allowed?
involved_inshould be allowed. But http://geneontology.org/docs/go-annotations/#annotation-qualifiers says only
colocalizes_withare allowed. I'm making corrections in ontobio to catch the space issue, but I'm not sure how to proceed given the new information here
@dustine32 @vanaukenk I'm looking at the gpad 2.0 spec. For with/from:
Pipe-separated entries represent independent evidence; comma-separated entries represent grouped evidence, e.g. two of three genes in a triply mutant organism
We currently only model with/from as a list. Could/should the pipes be treated as different annotations? Like if I had withfrom
a|b, this would be the same as 1:
b? Do we need to update how this is modeled internally?