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source for GO annotations

camon at ebi.ac.uk camon at ebi.ac.uk
Fri Apr 30 03:05:28 PDT 2004


Dear Carl,

The GO annotations that you download from the most recent GOA release will
be the most up-to-date GO annotation dataset. We have never had our
releases synchronised with UniProt/Swiss-Prot/TrEMBL flatfile releases.
UniProt is not the most up-to-date source of GO annotations. GOA is curated
in a separate database and used to supplement the information in the
UniProt flatfiles at intervals. There are lots of reasons for the
differences.
InterPro to GO annotations change. InterPro cross references to UniProt
Accessions change. Keywords are removed /added during de-merging and
merging of TrEMBL flatfiles.  QuickGO is the browser with the most
up-to-date view of GO annotations, we update QuickGO weekly. We try to
release
GOA monthly. I understand that the big UniProt releases are quarterly but
Daniel Barrell the GOA developer will confirm this to you.


It may also be of interest to you that UniProt-Swiss-Prot will only
display manual GO annotations but UniProt-TrEMBL will display electronic
if manual
is not available. We are currently trying to update the new UniProt
flatfiles on www.uniprot.org with links to QuickGO so that users can
always access the most up-to-date GO annotations.

I hope that helps,
you may here more for Daniel

If you have any further queries please e-mail goa at ebi.ac.uk

kind regards
Evelyn Camon (GOA Coordinator)




> 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
>
>
>
>
>
>




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