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MOBY namespaces and the GO xrefs

Midori Harris midori at ebi.ac.uk
Tue Jun 24 06:20:28 PDT 2003


Hi,

Just a bit from a GO perspective...

> Now that we have a ~stable MOBY API (touch wood) I'd like to "seed" the
> MOBY Central registry with a set of standard "namespaces" (e.g. a
> genbank GI number is a namespace, and a genbank Accession is another
> namespace) before things get chaotic.  The GO has database xref
> abbreviations that are already nicely defined, so clearly it would be a
> good idea to take advantage of this resource:
> http://www.geneontology.org/doc/GO.xrf_abbs
> 
> Q1)  GO friends - Is there a way to request inclusion of new xref
> abbreviations into this list?  In MOBY, *every* piece of data will have
> a namespace, so the list may blossom quickly...  

We've handled it by email to the GO list <go at geneontology.org>, and I'm
happy to continue to do so. Help from MOBY folks would be welcome, though;
one way to help would be to ferret out the bits to put in each field of
the xref document (the specifications are laid out in
http://www.geneontology.org/doc/GO.xrf_abbs_spec).

As for how big the list grows, I doubt that storage is a big issue, since
it's just a text file. If managing it is likely to become a nightmare,
we'll rethink who maintains it and how.

I can't help with questions about LSID's...

> Q4)  Before we start building services using these abbreviations, are
> there any "issues" with this list that you are aware of that should be
> addressed prior to us using them "In Anger"? ((c) M.A.  ;-) )  e.g. Have
> they been of sufficient granularity, or do you know of some that need to
> be subdivided?

The granularity is sufficient for GO's purposes; we've subdivided once or
twice when we felt the need, and could subdivide further as long as we
keep the existing abbreviations.

Midori

============================
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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