search

geneontology / amigo

AmiGO is the public interface for the Gene Ontology.
http://amigo.geneontology.org
BSD 3-Clause "New" or "Revised" License
29 stars 17 forks source link

BUG when including "regulates" #702

Closed ValWood closed 7 months ago

ValWood commented 8 months ago

In the AmiGO filtering, one option is GO class direct, this works as I expect and gives me all of the terms which are directly annotated (i.e. descendants).

I expected "GO class including regulates" to do exactly the same but include the regulates descendants. It doesn't do this, it gives me all of the annotated ancestors?

There does not seem to be a way to access the decedent annotations and regulation annotations?

Here is an example:

Screenshot 2023-10-31 at 17 31 53

my search term is meiotic sister chromatid cohesion, centromeric

kltm commented 8 months ago

Repeating, while trying to remove any textual ambiguity:

I'm assuming those are the "correct" answers.

The issue then is the different counts of the isa_partof_label link; i.e. that https://amigo.geneontology.org/amigo/search/annotation?q=*:*&fq=isa_partof_closure_label:%22maintenance%20of%20meiotic%20sister%20chromatid%20cohesion,%20centromeric%22&sfq=document_category:%22annotation%22 gives a large undercount (47 vs 343)?

ValWood commented 7 months ago

Yes, I aways forget that "[GO class (including "regulates)" has a different meaning, and that I need to use GO class direct but ensure I am using regulates closure.