[Gofriends] New inter- and intra-ontology links in GO

[Tanya Berardini]

On Feb. 17, 2009,  the Gene Ontology Consortium added 'regulates' links

       -  within the molecular function (MF) ontology
       -  between the biological process (BP) and MF ontologies.

A special 'extended' version of the ontology, gene_ontology_ext.obo,
contains these new intra-MF and inter-ontology links. The file is available
at the following URL:

       http://geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo

It is recommended that production databases and tools do *not* switch to
this URL until they are capable of handling these new links.

Please note that the new links get filtered out from the standard GO
releases available from the usual locations:

       http://geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo
       http://geneontology.org/ontology/obo_format_1_0/gene_ontology.1_0.obo

This is to give software developers additional time to adapt their tools.

Note that the regulates relationships *within* BP will continue to be
present in the above files, as they have been for the past 1 year. No action
needs to be taken - the structure of the GO available at the standard URLs
has not changed substantially.  More information is available here:
http://wiki.geneontology.org/index.php/Overview_of_Function-Process_regulates_links

If you have any questions, please mail this list or
gohelp at genome.stanford.edu

Regards,
The GO Consortium
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