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

[Chris Mungall]

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
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>>
>> < 
>> BindingTermDocumentation 
>> .doc>_______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>
> =====================================
> 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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