[Go] ec2go question

[Midori Harris]

Hi Doug,

I've looked at the CVS repository, and the ec2go file didn't include the 
"partial" EC xrefs (the ones with hyphens) prior to revision 1.79, 
committed on Nov. 4th.

It looks as though the procedure for generating and committing the file 
also changed with that revision, because it and subsequent revisions were 
committed by Amelia, whereas Dan Barrell committed older revisions. I 
think we should go back to excluding the partial ECs from ec2go, and I 
rashly assume it would be a small quick fix to do so (but perhaps Amelia 
or another software person should speak up).

Midori

On Fri, 14 Nov 2008, Doug wrote:

> Does anyone know if the format/content of the ec2go translation file changed 
> recently (past few weeks)?  I am seeing some strange IEA annotations in our 
> set which derive from ec2go.
> See our sult1st2 gene for example:
>
> http://zfin.org/cgi-bin/webdriver?MIval=aa-markergoview.apg&OID=ZDB-GENE-030804-27
>
> the EC:2.8.2.- was translated, as shown in the ec2go file, to a whole host of 
> sulfotransferase activities.  Is this a problem with ec2go, or has something 
> gone wild on our end?
>
> Here are the ec2go lines which were translated:
> EC:2.8.2.- > GO:N-acetylglucosamine 6-O-sulfotransferase activity ; 
> GO:0001517
> EC:2.8.2.- > GO:N-acetylgalactosamine 4-O-sulfotransferase activity ; 
> GO:0001537
> EC:2.8.2.- > GO:heparan sulfate 2-O-sulfotransferase activity ; GO:0004394
> EC:2.8.2.- > GO:HNK-1 sulfotransferase activity ; GO:0016232
> EC:2.8.2.- > GO:heparan sulfate 6-O-sulfotransferase activity ; GO:0017095
> EC:2.8.2.- > GO:trans-9R,10R-dihydrodiolphenanthrene sulfotransferase 
> activity ; GO:0018721
> EC:2.8.2.- > GO:1-phenanthrol sulfotransferase activity ; GO:0018722
> EC:2.8.2.- > GO:3-phenanthrol sulfotransferase activity ; GO:0018723
> EC:2.8.2.- > GO:4-phenanthrol sulfotransferase activity ; GO:0018724
> EC:2.8.2.- > GO:trans-3,4-dihydrodiolphenanthrene sulfotransferase activity ; 
> GO:0018725
> EC:2.8.2.- > GO:9-phenanthrol sulfotransferase activity ; GO:0018726
> EC:2.8.2.- > GO:2-phenanthrol sulfotransferase activity ; GO:0018727
> EC:2.8.2.- > GO:phenanthrol sulfotransferase activity ; GO:0019111
> EC:2.8.2.- > GO:1-hydroxypyrene sulfotransferase activity ; GO:0034930
> EC:2.8.2.- > GO:galactose 3-O-sulfotransferase activity ; GO:0050694
> EC:2.8.2.- > GO:proteoglycan sulfotransferase activity ; GO:0050698
> EC:2.8.2.- > GO:cholesterol sulfotransferase activity ; GO:0051922
>
> I assume that the assignment of EC:2.8.2.- to this gene product does not mean 
> that it has all of those sulfotransferase activities..but instead means it 
> should have at least one of them???
>
>
> Doug Howe, Ph.D.
> Scientific Curator
> Zebrafish Nomenclature Coordinator
> Zebrafish Information Network
> 541-346-0120
> dhowe at cs.uoregon.edu
>
>
>
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