Package ubic.gemma.core.ontology

Class OntologyConfig

java.lang.Object
ubic.gemma.core.ontology.OntologyConfig
@Configuration @Profile("!test") public class OntologyConfig extends Object

  • Constructor Details

    • OntologyConfig

      public OntologyConfig()

  • Method Details

    • ontologyTaskExecutor

      @Bean public org.springframework.core.task.TaskExecutor ontologyTaskExecutor()
      Executor used for loading ontologies in background.

    • excludedWordsFromStemming

      @Bean public TextResourceToSetOfLinesFactoryBean excludedWordsFromStemming()

    • ontologyExternalLinks

      @Bean public OntologyExternalLinks ontologyExternalLinks(org.springframework.core.env.Environment environment) throws IOException
      Throws:
      IOException

    • unifiedOntologyService

      @Bean public OntologyServiceFactory<?> unifiedOntologyService(@Value("${gemma.ontology.unified.enabled}") boolean enabled, @Value("${gemma.ontology.unified.tdb.dir}") Path tdbDir)
      This ontology encompasses all the ontologies declared below.

    • gemmaOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<GemmaOntologyService> gemmaOntologyService()

    • experimentalFactorOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<ExperimentalFactorOntologyService> experimentalFactorOntologyService()

    • obiService

      @Bean public org.springframework.beans.factory.FactoryBean<ObiService> obiService()

    • cellTypeOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<CellTypeOntologyService> cellTypeOntologyService()

    • chebiOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<ChebiOntologyService> chebiOntologyService()

    • mammalianPhenotypeOntologyServiceOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<MammalianPhenotypeOntologyService> mammalianPhenotypeOntologyServiceOntologyService()

    • humanPhenotypeOntologyServiceOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<HumanPhenotypeOntologyService> humanPhenotypeOntologyServiceOntologyService()

    • mouseDevelopmentOntologyServiceOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<MouseDevelopmentOntologyService> mouseDevelopmentOntologyServiceOntologyService()

    • humanDevelopmentOntologyServiceOntologyService

      @Bean @Deprecated public org.springframework.beans.factory.FactoryBean<HumanDevelopmentOntologyService> humanDevelopmentOntologyServiceOntologyService()
      Deprecated.

    • sequenceOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<SequenceOntologyService> sequenceOntologyService()

    • cellLineOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<CellLineOntologyService> cellLineOntologyService()

    • uberonOntologyServiceOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<UberonOntologyService> uberonOntologyServiceOntologyService()

    • patoOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<PatoOntologyService> patoOntologyService()

    • mondoOntologyServiceOntologyService

      @Bean public org.springframework.beans.factory.FactoryBean<MondoOntologyService> mondoOntologyServiceOntologyService()