NIX THAT - Re: [MOBY-l] TAIR service

Fri Jul 26 14:30:04 UTC 2002

Sorry Lukas!!

Ignore what I just said about the second service not being registered - I see
it now.  The output is still wonky from *both* of your services, however.
The verbatim output from your Sequence retrieval service is:

 <Sequence namespace="TAIR/Locus" id="AT1G56520"><SequenceString/></Sequence>

So it is missing the Length element altogether, and the SequenceString
content.  Similarly, your VitualSequence retrieval output is missing the
content of the <Length> element.  Why not hard-code your output until the
MOBYObject code becomes more stable/reliable?... at least until after the
ISMB and I3C demonstrations next week...

M

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
>
> On Thursday, July 25, 2002, at 02:51 , mwilkinson at gene.pbi.nrc.ca wrote:
>
> > My users don't want Virtual Sequences... they want **REAL**
> > sequences!!  ;-)
> >
> > Actually, a service to retrieve Sequences based on TAIR/Locus would be
> > really
> > useful to me right now, as we are working with Arabidopsis microarrays
> > and it
> > would be nice to retrieve the sequence for the spotted gene (not
> > coincidentally identified by TAIR Locus) using MOBY... just because we
> > can...  That, together with the GO_Term retrieval that you have running
> > already would really be a wonderful tool for us as we could build a
> > filter
> > that screened out spots on the array based on TAIR's GO-annotations!!
> > VERY
> > cool...
> >
> > Mark
> >
> >
> >
> > Lukas Mueller wrote:
> >
> >> Hi all,
> >>
> >> just want to let the list know that TAIR has a service up and running
> >> now. It returns VirtualSequences for GO_Terms. It is available from the
> >> MOBY_client.cgi at:
> >> http://bioinfo.pbi.nrc.ca:8099/cgi-bin/MOBY-Client.cgi
> >> Setting up the service was quite straightforward, but there also were
> >> some minor problems. If you are working on a service and experience
> >> problems, let me know, I may be able to help you!
> >>
> >> Cheers
> >> Lukas
> >>
> >> On Monday, July 22, 2002, at 09:56 , mwilkinson at gene.pbi.nrc.ca wrote:
> >>
> >>> Hi all,
> >>>
> >>> Now that there are a handful of services up and running, the issues
> >>> around dealing with our wonderful Object/Service ontologies are
> >>> becoming
> >>> clearer to me.  I'm wondering if anyone has opinions about whether
> >>> ontologies should be a Client/Service issue, or if they should be
> >>> dealt
> >>> with at MOBY-Central?
> >>>
> >>> e.g. I query MOBY central with an input Object-type.  Does it respond
> >>> only with the services that deal with that object type, or does it
> >>> track
> >>> down the parentage of that Object and tell me the services that deal
> >>> with that object type and its parents?  Similarly, does a Service
> >>> accept
> >>> *any* type of object, and skim-off the information that it understands
> >>> based on the ontology, or does it restrict itself to only dealing with
> >>> *exactly* the type of object that it is registererd to deal with, and
> >>> reject everything else?
> >>>
> >>> I think these questions arise whether or not we have a separate
> >>> ontology-server (i.e. rip ontology-awareness out of the MOBY-Central
> >>> itself - which seems like a good idea in any case), as it remains
> >>> ambiguous who has the responsibility for dealing with the ontologies -
> >>> server, client, or Central?
> >>>
> >>> How does myGrid deal with this?  other opinions?  I'd like to keep
> >>> things as far away from the Server end as possible, since one of the
> >>> "founding principles" was that service-creation should be mindless...
> >>> At
> >>> the same time, I worry that there is going to be too much pounding on
> >>> MOBY-Central...
> >>>
> >>> These seem like important questions which we need to address *soon*,
> >>> since we are already building both clients and services, and the pace
> >>> at
> >>> which Services are appearing is increasing daily!!  Making a decision
> >>> now, even if it is viewed as an experiment, would be a good thing.
> >>>
> >>> M
> >>>
> >>>
> >>>
> >>> --
> >>> --------------------------------
> >>> "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
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> moby-l mailing list
> >>> moby-l at biomoby.org
> >>> http://biomoby.org/mailman/listinfo/moby-l
> >>>
> >>
> >> _______________________________________________
> >> moby-l mailing list
> >> moby-l at biomoby.org
> >> http://biomoby.org/mailman/listinfo/moby-l
> >
> > --
> > --------------------------------
> > "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
> >
> >
> >
> > _______________________________________________
> > moby-l mailing list
> > moby-l at biomoby.org
> > http://biomoby.org/mailman/listinfo/moby-l
> >
>
> _______________________________________________
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> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l

--
--------------------------------
"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