[MOBY-l] SGD IDs

[Ken Steube]

I believe that Genbank/gi is NCBI_gi.

Many of our namespaces come from the Gene Ontology Cross-reference
Abbreviations List.  I don't personally know which of the three for SGD
you should use, but looking that list might help.

Ken

On Mon, 12 Apr 2004, Berriz, Gabriel F. wrote:

> I'm trying to prototype a service that takes a single gene ID as
> input.  For starters I want to limit myself to yeast genes IDs, and
> more specifically to SGD IDs, which match the Perl pattern
> /^[SL]\d{7}$/.  I'm trying to determine the right syntax for the
> service's input object.  My *guess* is that it will be something like:
>
>   <Object namespace="SGD" id="S1234567"/>
>
> but I have not been able to confirm this guess.  The list returned by
> retrieveNamespaces includes at least three plausible candidates: SGD,
> SGD_LOCUS, and SGD_ORF.  The description that comes along with these
> entries is not enough to disambiguate this choice.
>
> I am also confused by the fact that the namespace "Genbank/gi", which
> is used in several examples in MOBY-S's documentation, does not appear
> in the list returned by retrieveNamespaces.
>
> (It is possible that answers to some or all of the questions above are
> in some part of the documentation that I have missed; if so, please
> let me know.)

>
> Thanks, and regards,
>
> Gabriel
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>

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Ken Steube
San Diego Supercomputer Center
University of California, San Diego, MC 0505
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