[Go] Advice on adding an enzyme function

[Pankaj Jaiswal]

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.

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

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.