Gemma Web Services

See also : Understanding the Gemma API.

Available services

The Gemma WSDL is at

Currently there are about 18 services, some of which are primarily designed to provide parameter values for use in the more interesting services. The major functionality includes:

  • Getting gene coexpression information.
  • Retrieving expression profiles for genes in given data sets.
  • Getting GO terms for a gene.

Data formats

The output returned from the Gemma web services are just standard xml files. Although the help says that the output and the input are integers and longs and such they are actually just string representations of these types. Casting will be a necessary step.


Some web services take ‘taxon id’ as a parameter. Rather than provide a service which provides these, here is a reference:

  • human = 1
  • mouse = 2
  • rat = 3


We have been testing our web services with Matlab. For a sample session see the end of the page.

Methods api

For the latest documentation see the generated pages

Sample matlab session

Here is an example of a session in Matlab using a web service to retrieve gene coexpression information.

>> createClassFromWsdl('')

ans =
>> methods(gemmaService)
Methods for class gemmaService:
arrayDesignIdentifierByName        experimentName geneIDbyTaxon
arrayDesignUsed                    experimentNumSamples geneId
dEDVRank                           expressionExperimentSetIDs geneName
dEDVfromEEIDGeneID                 gemmaService geneOverlap
differentialExpressionProbeResult  gene2GOdescription goTerm2Gene
display                            gene2Go physicalLocation
experimentAnnotation               gene2Probe probe2Gene
experimentDEDV                     geneByNCBIId
experimentIDbyTaxon                geneCoexpression
experimentId                       geneDetailsByGeneID
>> geneName(gemmaService,406791)
ans =
                 gene_id: '406791'
    gene_official_symbol: 'PDE12'
>> help geneName
 --- help for gemmaService/geneName ---
        gene_ids{:} = (integer)
        gene_name_results{:} = (geneNames)
>> dEDVfromEEIDGeneID(gemmaService,[373513 37298],[2628])
ans =
          dedv: {2x1 cell}
    geneIdList: {2x1 cell}
      eeIdList: {2x1 cell}

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