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

[Midori Harris]

For that we probably want a nupdate from Harold. Is he on this list?

m

On Fri, 15 Aug 2008, Chris Mungall wrote:

>
> 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
>>>> 
>>> _______________________________________________
>>> Go-fp mailing list
>>> Go-fp at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go-fp
>> 
>> -- 
>> Jennifer Deegan (nee Clark)
>> EMBL-European Bioinformatics Institute
>> Gene Ontology Consortium
>> 
>
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors