[MOBY-l] New GO service at BDGP.

[Simon Twigger]

Brad, Mark

Can I pass a GO ID to this script as well as a keyword? Im in the 
process of working on a bunch of new GO annotations from RGD and as part 
of the QC I want to check the GO terms our curators typed/copied in 
against the current terms (to see if any have been made obsolete, to 
avoid any typos at our end, etc) and whilst I can do this from a flat 
file, it might be fun to try and use your service as the source of 
current GO terms. I'd want to pass in the GO ID and get back the GO info 
as you showed in the example. If it does take GO IDs, what would happen 
if I entered one that was obsolete?

Simon.

On Tuesday, July 30, 2002, at 05:34 PM, Bradley Marshall wrote:

> I've got a new service up that outputs GO terms.  Here's the info from 
> the
> registration script:
>
> my $reg = $Central->registerService(
>  "RetrieveGOFromKeywords",    # subroutine name called by SOAP server
>  "Retrieve",      # serviceType
>  '"flybase.org', # Authority URI
>  ["Object"],    # input object
>  ["GO_Term"],     # output object
>  ["Generic/Keyword"],    # namespace
>  "http://toy.lbl.gov:8088/cgi-bin/moby/go_service.cgi",  # URL of SOAP 
> server
> CGI script
>  "Returns all GO_term objects related to input keyword(s)", # service
> description
>  );
>
> Most of this was done by
> Mark, I just installed the script and made a simple client script.  
> SInce I'm
> still learning the nuts and bolts I imagine some of this info will 
> change.  For
> examaple, is 'Generic/Keyword' really an appropriate namespace for this
> service? I've attatched the client script.  Here's a simple example:
>
> ./brads_moby_client.pl transcription 'transcription factor'
>
> You can also search with a wildcard, like 'transcription*'. Here's the 
> output
> of the above example:
>
> ################## begin output
>
> I guess I'm looking for any services that search by keyword?  So far 
> only GO?
>
> Found:
>         From: flybase.org
>         Name: RetrieveGOFromKeywords
>         Type: Retrieve
>         Desc: GO_Term;'Returns all GO_term objects related to input 
> keyword(s)'
>
> Executing Service: RetrieveGOFromKeywords with GO_term=neuroligin
> <MOBY
> AuthURI='http://flybase.org'>
>  <GO_Term namespace='GO/Acc' id='GO:0006350'>
>   <Term>transcription</Term>
>   <Definition></Definition>
>   <Type>biological_process</Type>
>  </GO_Term>
>  <GO_Term namespace='GO/Acc' id='GO:0003700'>
>   <Term>transcription factor</Term>
>   <Definition>Any protein required to initiate or regulate 
> transcription;
> includes both gene regulatory proteins as well as the general 
> transcription
> factors.</Definition>
>   <Type>molecular_function</Type>
>  </GO_Term>
> </MOBY>
>
> ############################ end output
>
> Brad
> --
>
--------------------------------------------------------------------------------------------------
Simon Twigger, Ph.D.
Assistant Professor, Bioinformatics Research Center

Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, 53226
tel. 414-456-8802, fax 414-456-6595