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[Gofriends] Second Announcement: Introduction of cross-product definitions in extended GO on January 18, 2010

Midori Harris midori at ebi.ac.uk
Mon Jan 4 02:27:04 PST 2010


Dear GO Friends,

The plan to add cross-product definitions to the extended GO is on track, 
and will be implemented on January 18th as announced:

---------- Forwarded message ----------

Dear GO Friends,

We are pleased to announce that we are about to introduce cross-product 
definitions, in the form of intersection_of tags, into the "extended" version 
of GO (ontology/obo_format_1_2/gene_ontology_ext.obo). The target date for this 
addition is January 18, 2010.

This addition may have considerable impact on your tools and analyses because:

  1. Loading scripts that use gene_ontology_ext.obo will need to be modified to 
take the intersection_of tags into account by January 18, 2010.

  2. GO analysis tools that use gene_ontology_ext.obo will need to be modified 
to take the intersection_of tags into account by January 18, 2010.

  3. Some intersection_of tags will use new relationship types that will not be 
used elsewhere in the GO, and scripts and tools will have to be modified to 
take these new relationship types into account.

The first cross-products in GO will be "internal"; that is, they reference only 
terms within the GO. For example, the Biological Process (BP) ontology term 
"regulation of mitotic recombination" references two other BP terms, 
"biological regulation" and "mitotic recombination". Internal cross-products 
may also link branches of the GO, as in "nucleotide-excision repair complex", a 
Cellular Component (CC) term that references a CC term ("protein complex") and 
a BP term ("nucleotide-excision repair").

The addition of cross-product definitions to GO will enabel many ontology 
maintenance tasks to be automated, allowing curators to make additions and 
corrections more quickly and accurately. In the future, cross-products will 
also support improved querying and visualization of the ontology, and can be 
used to increase annotation coverage in GO through alignment with pathway 
databases and probabilistic inference.

The principles of cross-products are documented at:

http://www.geneontology.org/GO.ontology.structure.shtml#xp

The intersection_of tag is documented in the OBO Format specifications:

http://www.geneontology.org/GO.format.obo-1_2.shtml

Please let us know if you have questions or comments about this plan.

On behalf of the GO Consortium,
Midori Harris

============================
Midori A. Harris, Ph.D.
GO Editor
EMBL - EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

Tel: +44 (0) 1223 494667
Fax: +44 (0) 1223 494468
Email: midori at ebi.ac.uk
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