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

[Chris Mungall]

Ah, I guess my question was about what's happening with F-P links in  
general, specifically the low hanging fruit part (there is the P->F  
regulation terms which are really LHF of course, but there must be  
more LHF..)

On Aug 15, 2008, at 2:20 AM, Jennifer Deegan (nee Clark) wrote:

> 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
>