Query binding MF

[pombase-admin]

I'd like to know all instances where I have used a binding MF term I suspect many of these can be migrated to activated_by / inhibited by extensions (these may have extension required_for, but don't think it is true for all cases)

Original comment by: Antonialock

[pombase-admin]

Do you mean GO:0005515 protein binding? of specific children like children of GO:0019899 (enzyme binding)

Annotations to GO:0005515 protein binding are fine, but you might want to add qualifiers (and only use this if the interaction is direct).

Note that eventually we will "hide" most of the children (except for the ones which are linked to specific processes, like the specific RNA pol II transcription factor binding terms, which are describing a very specific function of a gene product).

We "ignore" all of the specific "types" of protein specified by the children (which are specified completely adequately by the with column).

(for now I'll put your request to low priority, will raise next time Kim is doing chado stuff. Once the data is loaded we may be able to access this through AmiGO (if you mean the children of protein binding these will stand out), or Midori might want to try to hone here SQL query skills...

Original comment by: ValWood

[pombase-admin]

I should add something about binding annotation to the documentation

Original comment by: ValWood

[pombase-admin]

not protein binding....

I've been using the binding terms when co-factors of catalytic activities have been characterized....sometimes but not always I've added a "required for GO:catalytic activity' but not always. I was going to change these to GO:catalytic activity annotation_extension=activated_by(chebi:xxx)

Original comment by: Antonialock

[ValWood]

Is this still valid? @Antonialock

[Antonialock]

I can't remember this. I'm sure we can spot them if there is anything that needs fixing.