Package ubic.gemma.rest

Class GeneWebService

java.lang.Object
ubic.gemma.rest.GeneWebService
@Service @Path("/genes") public class GeneWebService extends Object
RESTful interface for genes. Does not have an 'all' endpoint (no use-cases). Most methods also have a taxon-specific counterpart in the TaxaWebService (useful when using the 'official symbol' identifier, as this class will just return a random taxon homologue).
Author:
tesarst

  • Constructor Details

    • GeneWebService

      public GeneWebService()

  • Method Details

    • getGenes

      @GET @Produces("application/json") public PaginatedResponseDataObject<GeneValueObject> getGenes(@QueryParam("offset") @DefaultValue("0") OffsetArg offsetArg, @QueryParam("limit") @DefaultValue("20") LimitArg limitArg)

    • getGenesByIds

      @GET @Path("/{genes}") @Produces("application/json") public ResponseDataObject<List<GeneValueObject>> getGenesByIds(@PathParam("genes") GeneArrayArg genes)
      Retrieves all genes matching the identifier.
      Parameters:
      genes - a list of gene identifiers, separated by commas (','). Identifiers can be one of NCBI ID, Ensembl ID or official symbol. NCBI ID is the most efficient (and guaranteed to be unique) identifier. Official symbol returns a gene homologue on a random taxon.

      Do not combine different identifiers in one query.

    • getGeneLocations

      @GET @Path("/{gene}/locations") @Produces("application/json") public ResponseDataObject<List<PhysicalLocationValueObject>> getGeneLocations(@PathParam("gene") GeneArg<?> geneArg)
      Retrieves the physical location of the given gene.
      Parameters:
      geneArg - can either be the NCBI ID, Ensembl ID or official symbol. NCBI ID is most efficient (and guaranteed to be unique). Official symbol returns a gene homologue on a random taxon.

    • getGeneProbes

      @GET @Path("/{gene}/probes") @Produces("application/json") public PaginatedResponseDataObject<CompositeSequenceValueObject> getGeneProbes(@PathParam("gene") GeneArg<?> geneArg, @QueryParam("offset") @DefaultValue("0") OffsetArg offset, @QueryParam("limit") @DefaultValue("20") LimitArg limit)
      Retrieves the probes (composite sequences) with this gene.
      Parameters:
      geneArg - can either be the NCBI ID, Ensembl ID or official symbol. NCBI ID is most efficient (and guaranteed to be unique). Official symbol returns a gene homologue on a random taxon.

    • refreshGenesProbes

      @GET @Path("/probes/refresh") @Secured("GROUP_ADMIN") public javax.ws.rs.core.Response refreshGenesProbes()
      Refresh gene-to-probe associations.

    • getGeneGoTerms

      @GET @Path("/{gene}/goTerms") @Produces("application/json") public ResponseDataObject<List<GeneOntologyTermValueObject>> getGeneGoTerms(@PathParam("gene") GeneArg<?> geneArg)
      Retrieves the GO terms of the given gene.
      Parameters:
      geneArg - can either be the NCBI ID, Ensembl ID or official symbol. NCBI ID is most efficient (and guaranteed to be unique). Official symbol returns a gene homologue on a random taxon.

    • getGeneGeneCoexpression

      @GET @Path("/{gene}/coexpression") @Produces("application/json") public ResponseDataObject<List<CoexpressionValueObjectExt>> getGeneGeneCoexpression(@PathParam("gene") GeneArg<?> geneArg, @QueryParam("with") GeneArg<?> with, @QueryParam("limit") @DefaultValue("100") LimitArg limit, @QueryParam("stringency") @DefaultValue("1") Integer stringency)
      Retrieves the coexpression of two given genes.
      Parameters:
      geneArg - can either be the NCBI ID, Ensembl ID or official symbol. NCBI ID is most efficient (and guaranteed to be unique). Official symbol returns a gene homologue on a random taxon.
      with - the gene to calculate the coexpression with. Same formatting rules as with the 'geneArg' apply.
      stringency - optional parameter controlling the stringency of coexpression search. Defaults to 1.