When doing GO queries, and display consider F-P part of links

ValWood commented 7 years ago

When curating, for some "single-step biological processes" like protein phosphorylation

(protein kinase activity -> protein phosphorylation)

we do not explicitly make (or display) the "protein phosphorylation" because its obvious to a biologist that a kinase is involved in "phosphorylation" and it isn't a useful process to display on the gene pages (unless explicitly annotated for some reason).

However, if you do a query on "protein phosphorylation" you would wan't to retrieve all of the protein kinases.

This should be possible if, when a BP query is performed , part_of links between functions and processes are followed:

http://www.ebi.ac.uk/QuickGO-Old/GTerm?id=GO:0004672#term=ancchart

If this doesn't make sense, add dicuss label

kimrutherford commented 7 years ago

Does this need to be just for the query builder or should the BP term pages show all annotation by following the part_of links?

ValWood commented 7 years ago

Term pages too actually....

kimrutherford commented 6 years ago

Where are the F-P links?

We get our term relationships from go-basic.obo and it doesn't have those links.

ValWood commented 6 years ago

I guess including them even longer term, will be difficult because we would need full GO with all of the external stuff? What is the difference in size, and the impact. Is there another way ?

ValWood commented 6 years ago

e,g. GO:0065009

kimrutherford commented 5 years ago

This issue has been around a while. I've added the discuss label because I don't know what to do next.

ValWood commented 3 years ago

"This will become necessary if GO removes single step processes, until then, future.

pombase / website

When doing GO queries, and display consider F-P part of links #485