[Go] Advice on adding an enzyme function

[Chris Mungall]

On May 21, 2008, at 10:38 AM, Pankaj Jaiswal wrote:

> Well, it boils down to the level of specific annotation one wants.  
> If preciseness is not the buzzword in annotation, then as I have  
> seen it many times, it becomes very difficult to automate the  
> annotation and associations e.g. a MetaCyc based pathways database  
> built using GO annotations. Reason they store variants of a  
> reaction catalyzed by enzymes based on the substrate specifics as  
> well as species specificity, compared to KEGG which is winner takes  
> all. EC does the same as KEGG and e.g. even fails to identify the  
> F0F1 ATPase of a mitochondria from plastid. I agree it is a messy  
> situation, but if we do add the specific children terms, generic  
> parent term will always be there to suffice ones requirements. Any  
> specific instances (children) is for the precise annotation.

You mean is_a children, not instances.

> Use of ChEBI for creating Xrefs is a good idea and I am sure Chris  
> is working on it.

Actually, Mike Bada has done the majority of the work here. There is  
a summary of progress on the wiki:

http://wiki.geneontology.org/index.php/XP:biological_process_xp_chebi

In general, I support the addition of specific terms where required,  
together with a cross-product definition (e.g. to CHEBI), but I don't  
know the biochemistry well enough to know how explosive this could be  
in this case.

Jim appears to be suggesting dynamic annotation-time cross-products  
rather than explicitly realizing the terms in the GO. See http:// 
wiki.geneontology.org/index.php/Annotation_Cross_Products

This could be an option if for example there are cases where the  
number of substrates is large and the mechanism is essentially the  
same. Do you want to add it as a use case Jim?

> Pankaj
>
>
> Rama Balakrishnan wrote:
>> I am not very enthusiastic either about substrate specific terms.
>> I am not sure if we have consistently added substrate-specific  
>> terms. Long time back (really long time back) I was told that if  
>> the mechanism of catalysis is the same between substrates, then we  
>> don't want to create substrate specific terms.
>> Rama
>> On May 21, 2008, at 9:26 AM, Jim Hu wrote:
>>> Hi guys,
>>>
>>> I'm not enthusiastic about substrate-specific child terms.  There  
>>> are too many possible substrates and it seems like this would be  
>>> better as a with CheBI.  Substrate class specific child terms,  
>>> sure - leaving aside what makes a group of substrates members of  
>>> a class.  I'd also hate to get bogged down in arguments about  
>>> whether a particular substrate is physiologically significant.
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