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BioJava core module
There is a newer version: 1.9.7
package org.biojava.ontology;

import java.io.BufferedReader;
import java.io.InputStreamReader;

import org.biojava.bio.BioError;
import org.biojava.ontology.io.TabDelimParser;
import org.biojava.utils.ClassTools;

/**
 * Tools for manipulating ontologies.
 *
 * @author Matthew Pocock
 */
public final class OntoTools {
  private static final Ontology CORE_ONTOLOGY;
  private static final OntologyFactory DEFAULT_FACTORY;
  private static final IntegerOntology CORE_INTEGER;
  //private static final Ontology CORE_STRING;

  // public static final Term TYPE;
  public static final Term RELATION;
  public static final Term ANY;
  public static final Term NONE;
  public static final Term IS_A;
  public static final Term PART_OF;
  // public static final Term SUB_TYPE_OF;
  // public static final Term INSTANCE_OF;
  // public static final Term DOMAIN;
  // public static final Term CO_DOMAIN;
  // public static final Term HAS_DOMAIN;
  // public static final Term HAS_CO_DOMAIN;

  // public static final Term BOOLEAN;
  // public static final Term TRUE;
  // public static final Term FALSE;
  // public static final Term PREDICATE;

  // public static final Term AND;
  // public static final Term OR;
  // public static final Term XOR;
  // public static final Term EQUAL;
  // public static final Term NOT_EQUAL;
  // public static final Term IMPLIES;

  public static final Term REFLEXIVE;
  public static final Term SYMMETRIC;
  public static final Term TRANSITIVE;
  public static final Term EQUIVALENCE;
  public static final Term PARTIAL_ORDER;

  static {
    DEFAULT_FACTORY = new OntologyFactory() {
      public Ontology createOntology(String name, String desc)
      throws OntologyException {
        return new Ontology.Impl(name, desc);
      }
    };

    try {
      BufferedReader reader = new BufferedReader(
        new InputStreamReader(
          ClassTools.getClassLoader(OntoTools.class).getResourceAsStream(
            "org/biojava/ontology/core.onto"
          )
        )
      );

      CORE_INTEGER = new IntegerOntology();
      CORE_ONTOLOGY = new TabDelimParser().parse(
              reader,
              DEFAULT_FACTORY
      );

      // TYPE = CORE_ONTOLOGY.getTerm("type");
      RELATION = CORE_ONTOLOGY.getTerm("relation");
      ANY = CORE_ONTOLOGY.getTerm("any");
      NONE = CORE_ONTOLOGY.getTerm("none");
      IS_A = CORE_ONTOLOGY.getTerm("is-a");
      PART_OF = CORE_ONTOLOGY.getTerm("part-of");
      
      // SUB_TYPE_OF = CORE_ONTOLOGY.getTerm("sub_type_of");
      // INSTANCE_OF = CORE_ONTOLOGY.getTerm("instance_of");
      // DOMAIN = CORE_ONTOLOGY.getTerm("domain");
      // CO_DOMAIN = CORE_ONTOLOGY.getTerm("co_domain");
      // HAS_DOMAIN = CORE_ONTOLOGY.getTerm("has_domain");
      // HAS_CO_DOMAIN = CORE_ONTOLOGY.getTerm("has_co_domain");

      // BOOLEAN = CORE_ONTOLOGY.getTerm("boolean");
      // TRUE = CORE_ONTOLOGY.getTerm("true");
      // FALSE = CORE_ONTOLOGY.getTerm("false");
      // PREDICATE = CORE_ONTOLOGY.getTerm("predicate");

      // AND = CORE_ONTOLOGY.getTerm("and");
      // OR = CORE_ONTOLOGY.getTerm("or");
      // XOR = CORE_ONTOLOGY.getTerm("xor");
      // EQUAL = CORE_ONTOLOGY.getTerm("equal");
      // NOT_EQUAL = CORE_ONTOLOGY.getTerm("not_equal");
      // IMPLIES = CORE_ONTOLOGY.getTerm("implies");

      REFLEXIVE = CORE_ONTOLOGY.getTerm("reflexive");
      EQUIVALENCE = CORE_ONTOLOGY.getTerm("equivalence");
      SYMMETRIC = CORE_ONTOLOGY.getTerm("symmetric");
      TRANSITIVE = CORE_ONTOLOGY.getTerm("transitive");
      PARTIAL_ORDER = CORE_ONTOLOGY.getTerm("partial-order");

    } catch (Exception e) {
      throw new BioError("Could not initialize OntoTools", e);
    }
  }


  private OntoTools() {}

  /**
   * 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.
   *
   * @return the "core" Ontology
   */
  public static Ontology getCoreOntology() {
    return CORE_ONTOLOGY;
  }

  /**
   * 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.
   *
   * @return the integer Ontology
   */
  public static IntegerOntology getIntegerOntology() {
    return CORE_INTEGER;
  }

  public static OntologyFactory getDefaultFactory() {
    return DEFAULT_FACTORY;
  }
}