[Go] 'binding issues' item listed on the GO Consortium meeting agenda

[Harold Drabkin]

 From one of Jim's earlier comments, I think a big problem is parentage: 
if Chebi has a relationship between, say glucose-6 phosphate and glucose 
(child parent or something) , and we have a protein that binds 
glucose-6-phosphate, we don't want to imply any binding to glucose ( it 
might, but it might not). Chebi may have relationships between, for 
example, for  ATP, ADP, and AMP, but a protein may bind very 
specifically to  one of them. And I suppose there are many cases where a 
protein can bind related chemicals with different non-zero affinities, 
so that if one annotated binding to one there may be a good chance it 
would bind another. Should there be a rule in how one interprets the 
annotation line so as to not read any relationships among things in the 
target ontology to the actual single term designated as the target for 
the GO annotation? (hope this is clear).fcc

Harold



Chris Mungall wrote:
> I have added this example to the col16 page:
> http://wiki.geneontology.org/index.php/Annotation_Cross_Products#Binding
>
> I think the use of CHEBI in annotation-time cross-products poses 
> specific problems
>
> * It's often not clear (to me anyway) which CHEBI term to use. Jim's 
> example (linked to in the above page) has "PEP binding". CHEBI has two 
> terms in which PEP is a RELATED synonym: "phosphoenolpyruvic acid" and 
> "phosphoenolpyruvate". neither of these are defined in the traditional 
> OBO sense. It's not clear if the InChi strings count as they are under 
> RELATED synonym too.
>
> (Jim/Debbie - since you provided this example can you comment on this, 
> I'm too lazy to read the PMID, thanks!)
>
> * Many CHEBI terms do not have is_a parents. It's extremely important 
> for there to be correct is_a parentage. For example, if the 
> post-composed term is "phosphoenolpyruvic acid binding" then this can 
> be inferred to be a subtype of GO:0042301 ! phosphate binding, based 
> on is_a parentage in CHEBI.
>
> * CHEBI has other relations, but their semantics are unclear
>
> This gives me reason for caution. However, I am optimistic - CHEBI are 
> willing to fix these things in their ontology.
>
> In particular I would propose the following guidelines for use of 
> CHEBI in annotation time cross-products
>
> * The CHEBI term *should* preferably have a definition. The GO 
> annotator who uses a CHEBI ID in col 16 should propose a definition on 
> the CHEBI tracker
> * The CHEBI term *must* have is_a ancestry to CHEBI:24431 ! molecular 
> structure. If a GO annotator wishes to use a CHEBI ID in col 16, and 
> there is no such ancestry, the annotator should send a request on the 
> CHEBI tracker
> * The CHEBI term *should* have the correct synonym assignment. For 
> example, if the GO curator thinks the correct post-composed term is 
> "PEP binding" then PEP *must* be either an EXACT synonym or a primary 
> term name.
>
> On Mar 18, 2009, at 7:53 AM, Jim Hu wrote:
>
>> Hi Pascale,
>>
>> I think this is also potentially related to the discussion of 
>> whether/how the cross-product system can/should be used for 
>> post-composition of binding annotations.
>>
>> Jim
>>
>> On Mar 18, 2009, at 8:46 AM, Pascale Gaudet wrote:
>>
>>> Hi Emily,
>>>
>>> I am attaching the summary Debby Siegele put together about some of 
>>> the issues we've been having with substrate binding. (This was sent 
>>> to the ref genome list).
>>>
>>> Pascale
>>>
>>> Emily Dimmer wrote:
>>>>
>>>> Hi,
>>>>
>>>> I noticed that the GO Consortium meeting agenda for Monday 30th 
>>>> March has a item entitled 'binding issues'. However there is no 
>>>> indication of who added this topic.Could someone please give a bit 
>>>> more detail about why this item has been added?
>>>>
>>>> I do agree that it is an area that is probably worth discussing 
>>>> (particularly with regards ISSing 'protein binding' annotations). 
>>>> Its just that I feel that agenda items which deal with annotation 
>>>> issues are more easily resolved when the meeting participants have 
>>>> had advanced notice as to the background of the discussion topic, 
>>>> so to be able to review their database's annotation sets/collect 
>>>> their thoughts!
>>>>
>>>> Thanks,
>>>> Emily
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------
>>>>    Emily Dimmer Ph.D.
>>>>    GOA Coordinator
>>>>    EMBL-EBI
>>>>    Wellcome Trust Genome Campus
>>>>    Hinxton
>>>>    Cambridge CB10 1SD, U.K.
>>>>    Tel:     +44 1223 494654
>>>>    Fax:    +44 1223 494468
>>>>    email:  edimmer at ebi.ac.uk
>>>>    URL:    http://www.ebi.ac.uk/goa
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>> <BindingTermDocumentation.doc>_______________________________________________ 
>>>
>>> Go mailing list
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>>
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>>
>>
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>
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