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

[Jane Lomax]

Hi - as it stands, I don't actually think we have anything to bring to 
the meeting with this. For the time being, all we're talking about is 
creating a mapping file for the BFO people that states "GO:molecular 
function is-a bfo:Process". This will have no implications for GO so 
there's no need to take to Montreal (right, Chris?).

If in the future we do decide to do some work cleaning up the function 
ontology, we can take a proposal then...

Jane


Jennifer Deegan (nee Clark) wrote:
> 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
>
>
>
>
>


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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