[Go] addition of localization specific process terms ?

[Jennifer Deegan (nee Clark)]

Hi,

> 
> I previously addressed this from an end-user point of view. But as Jim  
> mentions in the sf tracker item about binding, it's also important to  
> consider this from the curation point of view.
> 
> Jim's point is that increased pre-coordination in the ontology makes  it 
> harder for curators, because it will take longer to hone in on the  most 
> appropriate term for an annotation.
> 
> Whilst I can see that obviously there is some correlation between  
> ontology size and time to find a term, I'm wondering the extent to  
> which this is a problem. I would have expected that most annotation  
> systems used at the MODs and UniProtKB would utilize some kind of term  
> completion rather than the curator manually traversing down the graph.  
> Also, if the curators are expected to post-compose using col 16, then  
> they have *two* terms to find: for example to annotate "PEP binding"  
> they would find the most specific term in GO *and* the relevant CHEBI  
> terms (and finding terms in CHEBI is probably harder than finding  terms 
> in GO)
> 
> But I don't annotate so I'm not sure.
> 
> I would like to hear the opinion of some of the annotators here. Is  
> excessive pre-coordination a concern for curation?
> 

For some parts of the ontology I have often thought that less 
pre-composition would be a good thing. It would simplify ontology 
management a lot for the editors, and at least one annotator has 
mentioned to me that it would make requesting new terms much simpler.

I think it would also avoid logic errors. For example in the development 
area we pre-compose a lot by just combining anatomy and process terms:

Anatomy:
[i]heart
---[p]heart valve

Process:
[i]development
---[p]morphogenesis

Pre-combined terms:
[i]heart development
---[p]heart valve development
etc.

but what if there are cases where this rule does not hold:

Anatomy:
[i]A
---[p]B

Process:
[i]X

Pre-combined terms:
[i]AX
---[p]BX

for example, where the development of a part of an organ does not take 
place as part of the development of the organ. Perhaps that part 
develops elsewhere and migrates into the organ. Maybe this is a rare 
thing, but it seems to me that we don't currently bother to think much 
about this, and that avoiding pre-composition would allow annotators 
much more flexibility to capture what actually happens.

The risk is that it would push the burden of capturing difficult ideas 
onto the annotation step (which is done multiple times) rather than 
keeping it with the ontology development step (which is done once-ish). 
It may just make sense to have better tool support for the more 
difficult pre-composition problems faced by ontology developers.

I would be interested to hear this discussed at the consortium meeting, 
and I am also particularly interested to hear what the annotators think.

Jennifer









-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium