Package org.biojava.nbio.ontology

Interface Term

All Superinterfaces:
Annotatable
All Known Subinterfaces:
OntologyTerm, RemoteTerm, Triple, Variable
All Known Implementing Classes:
AbstractTerm, IntegerOntology.IntTerm, OntologyTerm.Impl, RemoteTerm.Impl, Term.Impl, Triple.Impl, Variable.Impl
public interface Term extends Annotatable
A term in an ontology. This has an Annotation which can be used for storing additional human-displayable information. It is strongly recommended that the Annotation is not used for any machine-readable data -- this should be represented by relations in the ontology instead.

Terms are things that represent things. They are the same sort of thing as a Java object or a prolog atom. A sub-set of terms are themselves relations. This means that they are used to describe associations between pairs of terms. Since all terms can be described, it is possible (and indeed encouraged) to describe relations. As a minimum, you should consider saying if they are identity or partial order relations, or if they are transitive, reflexive, symmetrical, anti-symmetrical or anything else you know about them. This gives the inference engine some chance of working out what is going on.

Since:
1.4
Author:
Thomas Down, Matthew Pocock
See Also:
  • org.biojavax.ontology.ComparableTerm

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Interface
    Description
    static class 
    Term.Impl
    Simple in-memory implementation of an ontology term.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addSynonym(Object synonym)
    Add a synonym for this term.
    String
    getDescription()
    Return a human-readable description of this term, or the empty string if none is available.
    String
    getName()
    Return the name of this term.
    Ontology
    getOntology()
    Return the ontology in which this term exists.
    Object[]
    getSynonyms()
    Return the synonyms for this term.
    void
    removeSynonym(Object synonym)
    Remove a synonym for this term.
    void
    setDescription(String description)
    set the description of the term;

    Methods inherited from interface org.biojava.nbio.ontology.utils.Annotatable

    getAnnotation

  • Method Details

    • getName

      String getName()
      Return the name of this term.
      Returns:
      the name of the term

    • getDescription

      String getDescription()
      Return a human-readable description of this term, or the empty string if none is available.
      Returns:
      the description of the term

    • setDescription

      void setDescription(String description)
      set the description of the term;
      Parameters:
      description -

    • getOntology

      Ontology getOntology()
      Return the ontology in which this term exists.
      Returns:
      the ontology

    • getSynonyms

      Object[] getSynonyms()
      Return the synonyms for this term.
      Returns:
      the synonyms

    • addSynonym

      void addSynonym(Object synonym)
      Add a synonym for this term.
      Parameters:
      synonym - the synonym

    • removeSynonym

      void removeSynonym(Object synonym)
      Remove a synonym for this term.
      Parameters:
      synonym -