[Ontology-editors] [Go-fp] notes from MF-BP skype (Re: MF-BP links & managers call)

[Jennifer Deegan (nee Clark)]

Hi Chris,

The next day we discussed this on the managers' call. It was decided 
that when there were two species that did the same process differently 
we should make two different process terms with informative non-taxon 
names and put the appropriate functions underneath.

I have started discussing this with the electron transport working group 
and it is being met with strong opinions, both for and against. We 
haven't actually made any new terms to test it, but I am hoping to have 
an example put together to present at the meeting.

Jen


Chris Mungall wrote:

> Just wondering where we were with this - last commit in the fp-links  
> directory is April...
> 
> On Jun 17, 2008, at 10:42 AM, Midori Harris wrote:
> 
>> Hi,
>>
>> Minutes from today's impromptu Skpe conference, such as they are ...
>>
>> Present: Midori, Chris, David, Tanya, Pascale, Harold, Amelia
>>
>> Conclusions:
>> - None of us could see a big problem with the MF-BP approach; we  
>> think Jen's concerrns reflect the fact that electron transport is a  
>> fairly thorny area of biochemistry, rather than a general problem  
>> with making MF-BP links.
>>
>> - We want to continue capturing MF-BP links essentially as Harold  and 
>> Jen have started. Go for low-hanging fruit -- emphasize  metabolic 
>> pathways for now, because there should be a lot of  straightforward 
>> links there.
>>
>> - Don't worry about the occasional "error" of asserting a link that  
>> may not hold in some obscure species. The people working on the  
>> oddballs are, by and large, the same groups who most want GO to have  
>> the MF-BP links (e.g. JGI, TIFKAT*, other groups working on proks).  
>> They'll tell us if we get it wrong, and then we can fix it.
>>
>> - Also continue looking at Reactome for links. Show our links to  
>> Reactome curators (Peter d'E, and maybe others).
>>
>> - Keep collecting links in tab-delimited format for now (Chris  parses 
>> into OBO format). Time frame for asserting links directly in  OBO 
>> format: weeks. Time frame for including links in the ontology:  months.
>>
>> - Present this summary at tomorrow's managers' call.
>>
>> - We had fun!
>>
>> Additions, corrections, comments, etc. welcome (not to mention  
>> charitable contributions). Also, feel free to plunk this on a wiki  or 
>> tell me where to do so.
>>
>> thanks!
>> m
>>
>> *The Institute Formerly Know As TIGR
>>
> 
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-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium