org.biojava.ontology
Interface Ontology

All Superinterfaces:

Changeable

All Known Subinterfaces:

ComparableOntology

All Known Implementing Classes:

IntegerOntology, Ontology.Impl, SimpleComparableOntology

public interface Ontology
extends Changeable

An ontology.

This is just a set of Term objects, and a set of Triple objects describing relationships between these terms. This class does not itself contain any reasoning functionality. Ontology is a collection of facts, or axioms.

Since:

1.4

Author:

Thomas Down, Matthew Pocock

See Also:

ComparableOntology

Nested Class Summary

static class

Ontology.Impl A basic in-memory implementation of an ontology

Field Summary

static ChangeType	TERM
static ChangeType	TRIPLE

Method Summary

boolean	containsTerm(String name) Determines if this ontology currently contains a term named name
boolean	containsTriple(Term subject, Term object, Term predicate) See if a triple exists in this ontology
Term	createTerm(String name, String description) Create a new term in this ontology.
Term	createTerm(String name, String description, Object[] synonyms) Create a new term in this ontology.
Triple	createTriple(Term subject, Term object, Term predicate, String name, String description) Creates a new Triple.
Variable	createVariable(String name, String description) Create a new term in this ontology that is used as a variable.
void	deleteTerm(Term t) Remove a term from an ontology, together with all triples which refer to it.
String	getDescription() Return a human-readable description of this ontology, or the empty string if none is available
String	getName() Return the name of this ontology
OntologyOps	getOps() Return the associated OntologyOps.
Term	getTerm(String s) Fetch the term with the specified name.
Set	getTerms() Return all the terms in this ontology
Set	getTriples(Term subject, Term object, Term predicate) Return all triples from this ontology which match the supplied pattern.
Term	importTerm(Term t, String localName) Create a view of a term from another ontology.

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

TERM

static final ChangeType TERM

TRIPLE

static final ChangeType TRIPLE

Method Detail

getName

String getName()

Return the name of this ontology

getDescription

String getDescription()

Return a human-readable description of this ontology, or the empty string if none is available

getTerms

Set getTerms()

Return all the terms in this ontology

getTerm

Term getTerm(String s)
             throws NoSuchElementException

Fetch the term with the specified name.

Returns:

The term named name

Throws:

NoSuchElementException - if no term exists with that name

getTriples

Set getTriples(Term subject,
               Term object,
               Term predicate)

Return all triples from this ontology which match the supplied pattern. If any of the parameters of this method are null, they are treated as wildcards.

Parameters:

subject - The subject to search for, or null

object - The object to search for, or null

predicate - The relationship to search for, or null.

getOps

OntologyOps getOps()

Return the associated OntologyOps.

Returns:

the OntologyOps instance associated with this instance.

For developers:

This method should be implemented by ontology implementors to allow OntoTools to get optimized access to some usefull ontology operations. It is not intended that users will ever invoke this. A sensible dumb implementation of this would return a per-ontology instance of DefaultOps.

createTerm

Term createTerm(String name,
                String description)
                throws AlreadyExistsException,
                       ChangeVetoException,
                       IllegalArgumentException

Create a new term in this ontology.

Parameters:

name - The name of the term (must be unique)

description - A human-readable description (may be empty)

Returns:

The newly created term.

Throws:

IllegalArgumentException - if either name or description is null, or violates some other constraint of this implementation.

AlreadyExistsException - if a term of this name already exists

ChangeVetoException

createTerm

Term createTerm(String name,
                String description,
                Object[] synonyms)
                throws AlreadyExistsException,
                       ChangeVetoException,
                       IllegalArgumentException

Create a new term in this ontology.

Parameters:

name - The name of the term (must be unique)

description - A human-readable description (may be empty)

synonyms - Some synonyms for this term.

Returns:

The newly created term.

Throws:

IllegalArgumentException - if either name or description is null, or violates some other constraint of this implementation.

AlreadyExistsException - if a term of this name already exists

ChangeVetoException

createVariable

Variable createVariable(String name,
                        String description)
                        throws AlreadyExistsException,
                               ChangeVetoException,
                               IllegalArgumentException

Create a new term in this ontology that is used as a variable.

Parameters:

name - The name of the term (must be unique)

description - A human-readable description (may be empty)

Returns:

The newly created term.

Throws:

IllegalArgumentException - if either name or description is null, or violates some other constraint of this implementation.

AlreadyExistsException - if a term of this name already exists

ChangeVetoException

importTerm

Term importTerm(Term t,
                String localName)
                throws ChangeVetoException,
                       IllegalArgumentException

Create a view of a term from another ontology. If the requested term has already been imported under that name, this method returns the existing RemoteTerm object. If the term that is being imported is itself a RemoteTerm instance then first unwrap the term back to the orriginal term it represents and then produce a RemoteTerm from that. If the term being imported orriginated from this ontology, then return that term unaltered.

Parameters:

t - the Term to import

localName - the local name to import it under, optionally null

Throws:

ChangeVetoException

IllegalArgumentException

createTriple

Triple createTriple(Term subject,
                    Term object,
                    Term predicate,
                    String name,
                    String description)
                    throws AlreadyExistsException,
                           ChangeVetoException

Creates a new Triple.

Parameters:

subject - the subject Term

object - the object Term

predicate - the predicate Term

name - the name of the triple, or null

description - the description of the triple, or null

Returns:

a new Triple over these three terms

Throws:

AlreadyExistsException - if a triple already exists with the same subject, object and predicate, regardless of the name and description

ChangeVetoException

NullPointerException - if subject, object or predicate are null

IllegalArgumentException - if subject, object or predicate are not all from the same ontology

containsTriple

boolean containsTriple(Term subject,
                       Term object,
                       Term predicate)

See if a triple exists in this ontology

deleteTerm

void deleteTerm(Term t)
                throws ChangeVetoException

Remove a term from an ontology, together with all triples which refer to it.

Throws:

ChangeVetoException

containsTerm

boolean containsTerm(String name)

Determines if this ontology currently contains a term named name