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

[Harold Drabkin]

Just saw this;

I''ve asked Jen where I need to put some new files. I've been working on 
and off on various "simple" metabolic pathways and have noted that there 
will be instances where the occurance of the functions in a pathway is 
organism specific. That is, for example, with the glyoxylate pathway:: 
the pathway is used by bacterial and plants, not animals, yet it does in 
fact use several TCA cycle enzymes. The "has_part" is fine of course, but
is means that a person might get the wrong impression when the ontology 
is searched. Thus, an annotation to a mamalian TCA cycle enzyme might be 
returned if one searched on glyoxylate pathway, unless there is a way to 
restrict the relationship searches.
What I really do not want to see is a separate MF entry to the enzymes 
that are involved in glyoxylate path, and the ones that don't.
ie

aconitase activity involved in TCA
aconitase activity involved in glyoxylate

it's the same activity.

Note this is sort of the opposite of two organisms doing the same thing 
via different processes.

Harold


Midori Harris wrote:
> <div class="moz-text-flowed" style="font-family: -moz-fixed">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
>>>
>>
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