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[go-friends] UniProtKB-GOA release [2011-06-09]

Tony Sawford tonys at ebi.ac.uk
Thu Jun 9 06:18:38 PDT 2011


UniProtKB-GOA release: 06 June 2011
===================================

UniProtKB-GOA (UniProtKB GO Annotation at EBI) is a project run by the 
European Bioinformatics Institute that provides assignments of gene 
products to the Gene Ontology (GO) resource.

The data can be obtained via:

           EBI FTP: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/

           EBI SRS: http://srs.ebi.ac.uk. Search GOA data library

           GO FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/

           GO CVS: http://www.geneontology.org/GO.CVS.help.html

For further information read: http://www.ebi.ac.uk/GOA or contact
goa at ebi.ac.uk.

Latest News
===========

1. Inferred Cellular Component GO annotations now included in the 
UniProtKB-GOA annotation set.

We are pleased to announce an additional set of Cellular Component GO 
annotations available in this release that have been automatically 
generated from the 'occurs_in' relationship, made available as 
intersection tags in Biological Process terms in the GO OBO v1.2 format.

For example:

[Term]
id: GO:0033579 ! protein amino acid galactosylation in endoplasmic reticulum
intersection_of: GO:0042125 ! protein amino acid galactosylation
intersection_of: occurs_in GO:0005783 ! endoplasmic reticulum

This information is used to describe Biological Processes that occur in 
a specific Cellular Component.  As many GO users do not currently reason 
over the GO inter-ontology relationships, the set of inferred 
annotations has been generated to improve the consistency of the 
annotation set. Such GO annotations are produced when an annotation has 
been made (either manually or electronically) to a process term that, 
either directly or via one of its parent terms, has an 'occurs_in' 
relationship to a component term and where the component term (or one of 
its children) has not already been used in the annotation set for the 
same gene product identifier. The generated inferred annotations apply 
the same gene product identifier, reference and evidence code as the 
asserted Processs annotation and are generated from all sources of GO 
annotations, with only 'NOT'-qualified annotations being excluded. All 
such inferred GO annotations can be identified by the 'GOC' value in the 
'assigned_by' field (column 15).

These relationships are also visible in the QuickGO Ancestor Chart 
display, for example: 
http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0033579#term=ancchart

2.  Annotations that apply the new manual GO evidence codes IBA, IBD, 
IKR and IRD are now available in the UniProtKB-GOA annotation set.
For further information on these recently created manual evidence codes, 
please consult the GO website for code definitions: 
http://www.geneontology.org/GO.evidence.shtml. These types of  evidenced 
GO annotations are currently being created by the GO Consortium's 
Reference Genome project, identified by the 'RefGenome' value in the 
assigned_by field (column 15).



Regards,
UniProtKB-GOA Production



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