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 enable 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 - write to the GO helpdesk at gohelp.geneontology.org .