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

[Jennifer Deegan (nee Clark)]

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