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

[Karen Christie]

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.

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.

-Karen



On Mon, 15 Sep 2008, Jennifer Deegan (nee Clark) wrote:

> Hi,
>
> I just read through this all again (after getting back from holiday) and also 
> visited the bfo and read about their understanding of function and process, 
> and it all makes sense to me now. I think that part of the problem in 
> discussing these things is often that the discussion is done in ontology 
> language rather than biology language. If anybody is going to present this at 
> the meeting, could I ask that we try to make the language biologist-friendly? 
> I think this would really help. I often find at consortium meetings that 
> people start talking about function*ing* with a special meaningful tone of 
> voice, but without enough preamble to let everybody understand what they are 
> all on about. I'd be happy to volunteer for idiot-proofing duties.
>
> Thanks,
>
> Jen
>
>
>
> Amelia Ireland wrote:
>
>> 
>> Back in Gotham City on 2 Sep 2008, at 03:42, Jane Lomax wrote:
>> 
>>> I'm all for this proposal. I think the exercise of splitting the 
>>> molecular processes in MF from the molecular 'functions' will in  itself 
>>> be a useful one in improving the broad structure of the node.
>>> 
>>> David, I think there are more 'dirty' functions (heh) than you 
>>> think...Amelia and I once had a discussion where we came to the 
>>> conclusion that the only true molecular processes in MF are  catalysis, 
>>> transporter & regulator and their children (and I agree  that 'regulator 
>>> activity' is probably redundant with the regulation  BP terms). I think 
>>> that's probably still true, will be interested to  see!
>>> 
>>> Should we take this to the Montreal meeting? Or is this something  that we 
>>> can agree on now?
>> 
>> 
>> Could this be done in small steps? E.g. classify some/all of the  "true" 
>> functions as is-a bfo:Process first, based on criteria that  your average 
>> GO person can understand without having to venture into  the territory of 
>> words like 'realizables' and 'occurrents' that they  don't use in everyday 
>> life. I think that the full proposal is too big  and scary, but broken down 
>> into small, logical steps, people will be  able to handle it and see that 
>> they're not going to have to undergo a  huge paradigm shift in either their 
>> thinking or working practices.
>> 
>> I definitely think that we should bring up the topic before the  meeting so 
>> that people are aware of the issues and any basic  misunderstandings can be 
>> cleared up without taking up meeting time.
>> 
>> Cheers,
>> Amelia.
>> 
>> PS: Can I be added to the ontology-editors list?
>> 
>> -- 
>> Amelia Ireland
>> GO Editorial Office
>> http://www.ebi.ac.uk || http://www.berkeleybop.org
>> BBOP Plant Project: http://bbopgarden.blogspot.com
>> 
>> 
>> 
>> 
>> 
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>
> -- 
> Jennifer Deegan (nee Clark)
> EMBL-European Bioinformatics Institute
> Gene Ontology Consortium
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