Package org.biojava.nbio.ontology

Class OntoTools

java.lang.Object
org.biojava.nbio.ontology.OntoTools
public final class OntoTools extends Object
Tools for manipulating ontologies.
Author:
Matthew Pocock

  • Field Details

    • RELATION

      public static final Term RELATION

    • ANY

      public static final Term ANY

    • NONE

      public static final Term NONE

    • IS_A

      public static final Term IS_A

    • PART_OF

      public static final Term PART_OF

    • REFLEXIVE

      public static final Term REFLEXIVE

    • SYMMETRIC

      public static final Term SYMMETRIC

    • TRANSITIVE

      public static final Term TRANSITIVE

    • EQUIVALENCE

      public static final Term EQUIVALENCE

    • PARTIAL_ORDER

      public static final Term PARTIAL_ORDER

  • Method Details

    • getCoreOntology

      public static Ontology getCoreOntology()
      Get the Ontology that defines our core "central dogma".

      This contains definitions that we have to have, such as any, predicate, is-a and transient. These are our axioms, upon which the default interpreters build.

      Returns:
      the "core" Ontology

    • getIntegerOntology

      public static IntegerOntology getIntegerOntology()
      Get the Ontology that defines integers.

      This contains a term for each and every integer. I haven't decided yet if it contains terms for arithmatic.

      Returns:
      the integer Ontology

    • getDefaultFactory

      public static OntologyFactory getDefaultFactory()