Package org.molgenis.ontology.sorta.service

Interface SortaService

  • All Known Implementing Classes:
    SortaServiceImpl
    public interface SortaService

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      java.lang.Iterable<org.molgenis.data.Entity> findOntologyTermEntities​(java.lang.String ontologyIri, org.molgenis.data.Entity inputEntity)
      Find a list of relevant ontologyterm typed entities using lexical matching (elasticsearch + ngram) in generic type based on given ontologyIri and a set of query inputs (name, synonym, ontology database id, e.g.
      java.lang.Iterable<org.molgenis.data.Entity> getAllOntologyEntities()
      Get all ontology entities in generic type
      org.molgenis.data.Entity getOntologyEntity​(java.lang.String ontologyIri)
      Get a specified ontology entity in generic type based on the given ontologyIri
      org.molgenis.data.Entity getOntologyTermEntity​(java.lang.String ontologyTermIri, java.lang.String ontologyIri)
      Get a specified ontologyterm in generic type based on the given ontologyIri and ontologyTermIri

    • Method Detail

      • getAllOntologyEntities

        java.lang.Iterable<org.molgenis.data.Entity> getAllOntologyEntities()
        Get all ontology entities in generic type
        Returns:
        list of untyped ontology entities

      • getOntologyEntity

        org.molgenis.data.Entity getOntologyEntity​(java.lang.String ontologyIri)
        Get a specified ontology entity in generic type based on the given ontologyIri
        Returns:
        specified ontology entity in generic type

      • getOntologyTermEntity

        org.molgenis.data.Entity getOntologyTermEntity​(java.lang.String ontologyTermIri,
                                               java.lang.String ontologyIri)
        Get a specified ontologyterm in generic type based on the given ontologyIri and ontologyTermIri
        Returns:
        specifieid ontologyterm entity in a generic type

      • findOntologyTermEntities

        java.lang.Iterable<org.molgenis.data.Entity> findOntologyTermEntities​(java.lang.String ontologyIri,
                                                                      org.molgenis.data.Entity inputEntity)
        Find a list of relevant ontologyterm typed entities using lexical matching (elasticsearch + ngram) in generic type based on given ontologyIri and a set of query inputs (name, synonym, ontology database id, e.g. hpo, omim)
        Returns:
        a list of ontologyterm entities in generic type