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MOBY namespaces and the GO xrefs

Midori Harris midori at
Tue Jun 24 06:20:28 PDT 2003


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:
> 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>, 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

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 A. Harris, Ph.D.
GO Editor
Wellcome Trust Genome Campus
Cambridge CB10 1SD UK

Tel: +44 (0) 1223 494667
Fax: +44 (0) 1223 494468
Email: midori at

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