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Using BioMOBY Web Services from G-language GAE

You can search for web services by

help -w

in G-language Shell, just like searching for other documentations.

For example, searching for web services related to KEGG gives the following:

  G > help -w kegg
      Found keyword "kegg" in the following web services (13 hits).
  
 RINGStest                          : Testing the query for a KEGG Glycan ID given a KCF...
 convertIdentifier2KeggID           : This service consumes an identifier from the follo...
 convertKeggGeneId2PDBId            : This service consumes an identifier under the KEGG...
 convertKeggGeneId2ProtId           : This service consumes an identifier under the KEGG...
 getColoredKeggPathwayOfKeggIds     : This service takes as input a KEGG pathway and KEG...
 getKeggCompoundsOnKeggPathway      : This service, given a KEGG pathway, searches for a...
 getKeggIdsByKeggPathway            : This service, given a KEGG pathway, searches for a...
 getKeggPathwayAsGif                : This service, given a KEGG pathway, returns a Gif ...
 getKeggPathwaysByKeggID            : This service, given a KEGG identifier, attempts to...
 getPubChemSubstanceIdByKeggCompound: This service, given a KEGG compound, returns the a...
 getUniprotDescriptorsByKeyword     : Gets the uniprot identifier and description from a...
 getUniprotIdentifierByGeneName     : This service takes in a gene name, as an identifie...
 getUniprotIdentifiersByKeyword     : Gets uniprot identifiers by keyword using the bfin...

Descriptions of the service can be browsed by giving service name to help -w

G > help -w getKeggPathwayAsGif
  
   Name: getKeggPathwayAsGif
  
   Description:
       This service, given a KEGG pathway, returns a Gif image of the pathway if it exists.
       For example, the <Object, KEGG_PATHWAY, 'hsa00053')
       returns a diagram of the pathway 'ASCORBATE AND ALDRATE METABOLISM'.
  
  
   Input:
       pathway
                    Object:   Object
                 Namespace:   KEGG_PATHWAY
  
  Output:
       image
                    Object:   b64_encoded_gif
                 Namespace:
  
  Authority : bioinfo.icapture.ubc.ca
  Contact   : ekawas@mrl.ubc.ca
  Type      : Conversion
  Category  : moby
  URL       : http://bioinfo.icapture.ubc.ca:8090/mobyservices/services/getKeggPathwayAsGif
  LSID      : urn:lsid:biomoby.org:serviceinstance:bioinfo.icapture.ubc.ca,
              getKeggPathwayAsGif:2007-12-03T19-38-05Z

To run the service, use ws() as follows:

  ws("getKeggPathwayAsGif", 'hsa00053'=>'KEGG_PATHWAY');
biomobyenglish.txt · Last modified: 2014/01/18 07:44 (external edit)