Package ubic.gemma.core.ontology

Interface FactorValueOntologyService

All Known Implementing Classes:
FactorValueOntologyServiceImpl
public interface FactorValueOntologyService
Ontology service for factor values and their annotations.

There are two kind of entities represented in his ontologies:

  • Factor values (i.e. http://gemma.msl.ubc.ca/ont/TGFVO/1)
  • Factor value annotations (i.e. http://gemma.msl.ubc.ca/ont/TGFVO/1/2) which can be either a subject, object or a characteristic
TODO: fully implement the OntologyService interface.

  • Method Details

    • getIndividual

      @Nullable OntologyIndividual getIndividual(String uri)
      Obtain an individual from the ontology by URI.

    • getFactorValues

      Slice<OntologyIndividual> getFactorValues(int offset, int limit)
      Obtain all the factor value in the ontology.

    • getFactorValueUris

      Collection<String> getFactorValueUris()

    • getFactorValueUris

      Slice<String> getFactorValueUris(int offset, int limit)
      Obtain all the factor value URIs in the ontology.

    • getFactorValueAnnotations

      Set<OntologyIndividual> getFactorValueAnnotations(String uri)
      Obtain annotations belonging to the given URI representing a factor value.

    • getFactorValueStatements

      Set<OntologyStatement> getFactorValueStatements(String uri)
      Obtain statements related to the given URI representing a factor value.

    • writeToRdf

      void writeToRdf(Collection<String> uri, Writer writer)
      Write multiple individuals represented by the given URIs to RDF.

    • writeToRdfIgnoreAcls

      void writeToRdfIgnoreAcls(Collection<String> uri, Writer writer)
      Write multiple individuals represented by the given URIs to RDF, ignoring ACLs.

      use this only if the FVs were prefiltered with getFactorValueUris() or getFactorValues(int, int)