[MOBY-l] TAIR service

[mwilkinson at gene.pbi.nrc.ca]

Good morning Lukas!

Um... It doesn't appear that you added "another" service...  Here's a full
run-down of the symptoms:

1) You have a *single* service running at www.arabidopsis.org
2) The service takes GO_Term objects as input and outputs Sequence objects
3) The service uses the GO/Acc namespace
4) Using the MOBY-Client.cgi, your Sequence retrieval service is discovered
correctly
5)  BUT!!! when executed, it returns **VirtualSequence** objects, not
Sequence objects
6)  AND these VirtualSequence objects are malformed anyway in that they don't
have a length

I'd guess it is the MOBYObjects.pm code that is causing the problems (in
answer to your question yesterday, no, I don't use that module in my services
yet).

How did you register this new service?  I hope you didn't edit the database
by hand ;-)  ;-)  ;-)

I have a more fundamental objection to the way your service is registered.  I
am guessing (but am not sure) that you don't actually use the payload of the
GO_Term object to perform your service... right?  You just take the GO/Acc
namespace and ID and then do a lookup on the TAIR database with that ID.   If
so, then you should not be registering your service as being limited to
GO_Term objects - better register it as taking base Objects in the namespace
GO/Acc.  That will allow it to be discovered (by the ontology) anytime
someone has an object in that namespace, regardless of what object type they
have.

Does that seem reasonable to you?

Cheers!

Mark



Lukas Mueller wrote:

> Hi there,
> I added another TAIR service that gives the Sequence object for an
> Object with a TAIR/Locus namespace. The DNA sequence is given right now.
> I'll implement different services that return DNASequence and
> ProteinSequence objects later. The Sequence itself is not displayed in
> the MOBY_client.cgi. Is this a bug or a feature?
> Cheers
> Lukas

--
--------------------------------
"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson, RA Bioinformatics
National Research Council, Plant Biotechnology Institute
110 Gymnasium Place, Saskatoon, SK, Canada

phone : (306) 975 5279
pager : (306) 934 2322
mobile: markw_mobile at illuminae.com


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