[Ontology-editors] draft cross-product announcement email

[Tanya Berardini]

For extra security, we should add a sentence that all other .obo files will
NOT have these new features yet.

Tanya

On Wed, Jul 1, 2009 at 8:28 AM, Midori Harris <midori at ebi.ac.uk> wrote:

> Hi,
>
> This is my first draft of an email to GO friends about adding xps to the
> go_ext file. It could use some reasons why xps are wonderful (there's a
> placeholder right now); other edits welcome too.
>
> m
>
> subject:
> Announcement: Introduction of cross-product definitions in extended GO
> ([date])
>
> body:
> 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 [date].
>
> 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 [date].
>  2. GO analysis tools that use gene_ontology_ext.obo will need to be
> modified to take the intersection_of tags into account by [date].
>  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").
>
> [reasons for xps]
>
> The principles of cross-products are documented at:
>
> [linky]
>
> 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,
> [name(s)]
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>



-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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