Package org.biojava.nbio.ontology

Interface Ontology

All Known Implementing Classes:

IntegerOntology, Ontology.Impl

public interface Ontology

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:

org.biojavax.ontology.ComparableOntology

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	Ontology.Impl	A basic in-memory implementation of an ontology

Method Summary

Modifier and Type	Method	Description
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)	Create a new term 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 name)	Fetch the term with the specified name.
Set<Term>	getTerms()	Return all the terms in this ontology
Set<Triple>	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.
void	setDescription(String description)	set the description of this ontology
void	setName(String name)	Set the name for this ontology

Method Detail

getName

String getName()

Return the name of this ontology

Returns:

the name of the ontology

setName

void setName(String name)

Set the name for this ontology

Parameters:

name - - the name

getDescription

String getDescription()

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

Returns:

the description of the term

setDescription

void setDescription(String description)

set the description of this ontology

Parameters:

description -

getTerms

Set<Term> getTerms()

Return all the terms in this ontology

Returns:

a Set of all Terms of the ontology.

getTerm

Term getTerm(String name)
      throws NoSuchElementException

Fetch the term with the specified name.

Parameters:

name - the name of the term

Returns:

The term named name

Throws:

NoSuchElementException - if no term exists with that name

getTriples

Set<Triple> 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.

Returns:

a Set of triples

getOps

OntologyOps getOps()

Return the associated OntologyOps. 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.

Returns:

the OntologyOps instance associated with this instance.

createTerm

Term createTerm(String name)
         throws AlreadyExistsException,
                IllegalArgumentException

Create a new term in this ontology.

Parameters:

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

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)
         throws AlreadyExistsException,
                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,
                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,
                        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 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

Returns:

a Term

Throws:

ChangeVetoException

IllegalArgumentException

createTriple

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

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

Parameters:

subject -

object -

predicate -

Returns:

true if contained

deleteTerm

void deleteTerm(Term t)

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

Parameters:

t -

Throws:

ChangeVetoException

containsTerm

boolean containsTerm(String name)

Determines if this ontology currently contains a term named name

Parameters:

name -

Returns:

true is contained