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

[Jennifer Deegan (nee Clark)]

Hi Chris,

Don't worry, it's all really fine. :-) I just wanted to mention.

Thanks,

Jen


 Chris Mungall wrote:
>
> 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
>>
>>