Examples of org.biojava.ontology.Term

org.biojava.ontology.Term
A term in an ontology. This has an {@link org.biojava.bio.Annotation 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.
@author Thomas Down @author Matthew Pocock @since 1.4 @see org.biojavax.ontology.ComparableTerm

            StringTokenizer toke = new StringTokenizer(line);
            String subject = toke.nextToken();
            String predicate = toke.nextToken();
            String object = toke.nextToken();


            Term subT = resolveTerm(subject, onto);
            Term objT = resolveTerm(object, onto);
            Term relT = resolveTerm(predicate, onto);


            Triple trip = resolveTriple(subT, objT, relT, onto);
            trip = trip==null?null:trip; // prevent unused field error
          } catch (StringIndexOutOfBoundsException e) {
            throw new IOException("Could not parse line: " + line);

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          String source = termName.substring(1, c1);
          String target = termName.substring(c2 + 1, termName.length() - 1);
          String predicate = termName.substring(c1 + 1, c2);


          Term st = resolveTerm(source, onto);
          Term tt = resolveTerm(target, onto);
          Term rt = resolveTerm(predicate, onto);


          return onto.createTriple(st, tt, rt, null, null);
        } else {
          return onto.createTerm(termName, "");
        }

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          key.equals(RELATIONSHIP) || 
          key.equals(DISJOINT_FROM) ||
          key.equals(INTERSECTION_OF) ||
          key.equals(SUBSET)) {
        try {
          Term object = ontology.containsTerm(value) ?
            object = ontology.getTerm(value): ontology.createTerm(value);
          Term predicate = ontology.containsTerm(key) ? ontology.getTerm(key) : ontology.createTerm(key);
                 ontology.createTriple(currentTerm, object, predicate, currentTerm + " " + predicate + " " + object, key+"-relationship");              
        } catch (AlreadyExistsException ex) {
        }
                
      } else if (key.equals(COMMENT)){

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Related Classes of org.biojava.ontology.Term

org.biojava.bio.SmallAnnotation

org.biojava.ontology.io.TabDelimParser

org.biojava.ontology.obo.OboFileHandler

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