Class GoTermsWebService

java.lang.Object

ubic.gemma.rest.GoTermsWebService

@Service
@Path("/goTerms")
public class GoTermsWebService
extends Object

RESTful interface for reverse GO-term lookup: GO term URI → genes annotated with it. Companion to GET /genes/{id}/goTerms (gene → its GO terms).

Drives the dataset Visualize tab's "pick genes by GO term" mode — visitor types a GO term, the UI calls /goTerms/{termUri}/genes and renders the candidate gene list for selection.

GO-term TYPEAHEAD is not a new endpoint; the existing GET /annotations/search?query=...&prefixes=GO_ already covers it (filters the Lucene index to GO URIs, ranks by Lucene score).

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	GoTermsWebService.GoTermGeneCountValueObject	Wire payload for GET /goTerms/{termUri}/genes/count.

Constructor Summary

Constructors

Constructor	Description
GoTermsWebService()

Method Summary

Modifier and Type	Method	Description
ResponseDataObject<GoTermsWebService.GoTermGeneCountValueObject>	countGenesByGoTerm(String termUri, TaxonArg<?> taxonArg, boolean propagate, int maxTerms)	Distinct-gene count for the given GO term, optionally including descendants.
PaginatedResponseDataObject<GeneValueObject>	getGenesByGoTerm(String termUri, TaxonArg<?> taxonArg, OffsetArg offsetArg, LimitArg limitArg, boolean propagate, int maxTerms)	Reverse lookup: genes annotated with the given GO term.

Methods inherited from class Object

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

Constructor Details

GoTermsWebService

public GoTermsWebService()

Method Details

getGenesByGoTerm

@GET
@Path("/{termUri}/genes")
@Produces("application/json")
public PaginatedResponseDataObject<GeneValueObject> getGenesByGoTerm(@PathParam("termUri")
 String termUri,
 @QueryParam("taxon")
 TaxonArg<?> taxonArg,
 @QueryParam("offset") @DefaultValue("0")
 OffsetArg offsetArg,
 @QueryParam("limit") @DefaultValue("100")
 LimitArg limitArg,
 @QueryParam("propagate") @DefaultValue("false")
 boolean propagate,
 @QueryParam("maxTerms") @DefaultValue("0")
 int maxTerms)

Reverse lookup: genes annotated with the given GO term. termUri is the full OBO-style URI (http://purl.obolibrary.org/obo/GO_0006915); URL-encoded into the path segment.

When propagate=true (default false) the lookup also includes the union of genes annotated to any subClassOf descendant of termUri — the natural semantic for a parent term like "regulation of apoptotic process" where the caller wants every gene under that umbrella. propagate=true requires the GO ontology to be loaded in the OntologyService; if it isn't, the call falls back to exact-term-only and logs a warning rather than 503-ing.

countGenesByGoTerm

@GET
@Path("/{termUri}/genes/count")
@Produces("application/json")
public ResponseDataObject<GoTermsWebService.GoTermGeneCountValueObject> countGenesByGoTerm(@PathParam("termUri")
 String termUri,
 @QueryParam("taxon")
 TaxonArg<?> taxonArg,
 @QueryParam("propagate") @DefaultValue("false")
 boolean propagate,
 @QueryParam("maxTerms") @DefaultValue("0")
 int maxTerms)

Distinct-gene count for the given GO term, optionally including descendants. Cheap — goes through countByGOTermUris, which runs COUNT(DISTINCT gene.id) without materializing Gene rows. Use this in place of fetching the full gene list just to display "N genes annotated to {term}" badges.