[MOBY-l] TAIR service

[Lukas Mueller]

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
>>>
>>
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>
> --
> --------------------------------
> "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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