Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

GO Update from SWISS-PROT/TrEMBL/InterPro

Evelyn Camon camon at ebi.ac.uk
Tue Nov 13 03:11:59 PST 2001


Hi,

On behalf of SWISS-PROT I would like to answer a question that
appears to come up again and again....

******************************************************
*Will SWISS-PROT records add GO term or link to GO soon?*
******************************************************

The official answer is that we will first provide association files for
all SWISS-PROT + TrEMBL records, as well as for all complete
proteome sets (http://www.ebi.ac.uk/proteome/) in the way we
do it now for the human data (see below).
-------------------------------------------------------------------------

Access to Association Files:

GO:  ftp://ftp.geneontology.org/pub/go/doc/goa.README
ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.goa

 EBI: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/README
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa
-------------------------------------------------------------------------

In the long run we hope to link from SWISS-PROT + TrEMBL to GO and
eventually include the GO terms directly in SWISS-PROT + TrEMBL records.

Via the Sequence Retrieval System, SRS (http://srs.ebi.ac.uk/)
you can already view GO term assignments in the XML formated display of
InterPro entries. XML formated versions of SWISS-PROT and TrEMBL are
currently being developed.

Indirectly you can view GO mappings to SWISS-PROT/TrEMBL and InterPro
records using our QuickGO browser (http://www.ebi.ac.uk/ego/)

For example search SWISS-PROT acession number P00001 will display
the GO terms associated to that product as well as displaying the source

of the mapping.  At the moment QuickGO does not display the evidence
codes this will happen at a later date.

And here are some recent stats on the number of distinct protein
accession numbers in SWISS-PROT and TrEMBL with GO assignments
(data from 29-OCT-2001):

Evidence code:---SWISS-PROT(%)----TrEMBL(%)
-------------------101,602(100%)------483,802(100%)
IEA----------------84,671(83%)------- 237,297(49%)
Non-IEA:-----------6,628(6.5%)----------3,310(0.7%)

We are currently working on incorporating the NON-IEA  associations from

consortium databases into our records.

Thats all fow now hope this information helps..

Evelyn Camon
GO Curation Coordinator (SWISS-PROT/TrEMBL/InterPro)

EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD,
United Kingdom
URL:http://www.ebi.ac.uk/

E-mail:camon at ebi.ac.uk
Phone:+44 (0)1223 494 465






--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



More information about the go-friends mailing list