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

[Chris Mungall]

Exactly.

I'm really sorry this thread has stirred up some hard feelings. As I  
said before, I understand "gloss" purely in the technical sense as in  
glossary, no antagonism intended. We all agree on the utility of the  
different parts of the definition in different roles. I'm more than  
happy to call this the "descriptive part of the definition".

And can we just drop the "dirty function" thing? The term has been  
used once since St Croix in a clearly ironic context, it's not like  
there is a gang of ontologists trying to force this term down poor  
biologists throats.

On Sep 16, 2008, at 6:42 AM, Jane Lomax wrote:

> 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
>
> p: +44 1223 492516
> f: +44 1223 494468
>
>