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source for GO annotations

Daniel Barrell dbarrell at ebi.ac.uk
Fri Apr 30 01:48:16 PDT 2004


Hi,

UniProt incorporates GO annotation from gene_association.goa_uniprot.gz 
  on a semi-regular basis but is not updated with every release of GOA. 
  This is something we are striving to fix but concurrency will always 
be a problem.  The master source for all UniProt GOA annnotation should 
always be the Gene Association files.

Additionally, Swiss-Prot entries never include IEA annotation whereas 
TrEMBL entries do - another reason to go straight to 
gene_association.goa_uniprot.gz.

Regards

Daniel

(GOA and UniProt)

Schaefer, Carl (NIH/NCI) wrote:
> Any idea why the annotations in 
> http://www.geneontology.org/cgi-bin/GO/downloadGOGA.pl/gene_association.goa_uniprot.gz 
> are not consistent with annotations in the SP/TrEMBL flat files. For 
> example, in 
> ftp://us.expasy.org/databases/trembl/release_compressed/hum.dat.gz, 
> accession Q96RE8 has annotations:
> 
>  
> 
> DR   GO; GO:0016021 <http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0016021>; C:integral to membrane; IEA.
> 
> DR   GO; GO:0019028 <http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0019028>; C:viral capsid; IEA.
> 
> DR   GO; GO:0004937 <http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0004937>; F:alpha1-adrenergic receptor activity; IEA.
> 
> DR   GO; GO:0004872 <http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0004872>; F:receptor activity; IEA.
> 
> DR   GO; GO:0001584 <http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0001584>; F:rhodopsin-like receptor activity; IEA.
> 
> DR   GO; GO:0005198 <http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0005198>; F:structural molecule activity; IEA.
> 
> DR   GO; GO:0007186 <http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0007186>; P:G-protein coupled receptor protein signalin...; IEA.
> 
>  
> 
> But gene_association.goa_uniprot has annotations
> 
>  
> 
> Q96RE8      GO:0001584  GOA:interpro      IEA  
> 
> Q96RE8      GO:0004872  GOA:spkw    IEA  
> 
> Q96RE8      GO:0004930  GOA:spkw    IEA  
> 
> Q96RE8      GO:0004937  GOA:interpro      IEA  
> 
> Q96RE8      GO:0007186  GOA:interpro      IEA  
> 
> Q96RE8      GO:0007186  GOA:spkw    IEA  
> 
> Q96RE8      GO:0016021  GOA:interpro      IEA  
> 
> Q96RE8      GO:0016021  GOA:spkw    IEA  
> 
>  
> 
> So hum.dat has 0019028 and 0005198, which are not in the goa file, while 
> the goa file has 0004930, which is not in hum.dat.
> 
>  
> 
> Carl Schaefer
> 
> National Cancer Institute
> 
> Center for Bioinformatics

-- 

Daniel Barrell
EMBL - The EBI
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Phone: +44 (0)1223 492551
Email: dbarrell at ebi.ac.uk


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