[Ontology-editors] What does the MF ontology represent?

[Jennifer Deegan (nee Clark)]

Hi,

> I've been thinking about this thread too, along similar lines to Jen, 
> but I hadn't quite gotten my ideas into words yet. Jen has said it very 
> nicely and I agree completely.

Yay!

> The only thing I'd like to add is that I think that some of the language 
> (e.g., "gloss" or "dirty functions") used previously can come across as 
> antagonistic to the biological perspective. Since I think we all agree 
> that we need to address ontological concerns as well as biological ones, 
> perhaps for future discussions we could come up with language that gives 
> equal merit to both the ontological and biological perspectives. For 
> example, as an annotator, the part of the definition that I generally 
> find most helpful in identifying the correct term is not the logical 
> definition, but what Barry Smith dismissed as "gloss". To me, the 
> "gloss" is the substance of the definition that allows me to correlate 
> the paper I'm reading to the appropriate GO term. So, I'd prefer to 
> refer to this part of the definition as the "description definition" or 
> something similar. I don't have a suggestion at the moment for "dirty 
> function", but I think it would be good to come up with something less 
> potentially antagonistic, so that people can listen to the proposal with 
> an open mind.

Yes I also agree very much about this. I think there is a lot of 
resistance amongst the ontology experts to using non-technical language 
to communicate with the biologists, but I think that often it is the 
technical language that gets in the way of necessary changes being 
adopted, rather than the actual substance of the proposals.

Jen





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