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 Summary

Constructors

Constructor	Description
GeneWebService(GeneService geneService, GeneCoexpressionSearchService geneCoexpressionSearchService, GeneArgService geneArgService)	Constructor for service autowiring

Method Summary

Modifier and Type	Method	Description
ResponseDataObject<List<GeneEvidenceValueObject>>	getGeneEvidence(GeneArg<?> geneArg)	Deprecated.
ResponseDataObject<List<CoexpressionValueObjectExt>>	getGeneGeneCoexpression(GeneArg<?> geneArg, GeneArg<?> with, LimitArg limit, Integer stringency)	Retrieves the coexpression of two given genes.
ResponseDataObject<List<GeneOntologyTermValueObject>>	getGeneGoTerms(GeneArg<?> geneArg)	Retrieves the GO terms of the given gene.
ResponseDataObject<List<PhysicalLocationValueObject>>	getGeneLocations(GeneArg<?> geneArg)	Retrieves the physical location of the given gene.
PaginatedResponseDataObject<CompositeSequenceValueObject>	getGeneProbes(GeneArg<?> geneArg, OffsetArg offset, LimitArg limit)	Retrieves the probes (composite sequences) with this gene.
ResponseDataObject<List<GeneValueObject>>	getGenes(GeneArrayArg genes)	Retrieves all genes matching the identifier.
PaginatedResponseDataObject<GeneValueObject>	getGenes(OffsetArg offsetArg, LimitArg limitArg)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GeneWebService

@Autowired
public GeneWebService(GeneService geneService,
                      GeneCoexpressionSearchService geneCoexpressionSearchService,
                      GeneArgService geneArgService)

Constructor for service autowiring

Method Detail

getGenes

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

getGenes

@GET
@Path("/{genes}")
@Produces("application/json")
public ResponseDataObject<List<GeneValueObject>> getGenes(@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.

getGeneEvidence

@GET
@Path("/{gene}/evidence")
@Produces("application/json")
@Deprecated
public ResponseDataObject<List<GeneEvidenceValueObject>> getGeneEvidence(@PathParam("gene")
                                                                         GeneArg<?> geneArg)

Deprecated.

Retrieves gene evidence for 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.

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.

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.