org.molgenis.ontology.matching

Interface OntologyService

All Known Implementing Classes:

OntologyServiceImpl

public interface OntologyService

Makes Ontology trees manageable

Author:

chaopang

Method Summary

Modifier and Type	Method and Description
Iterable<OntologyTerm>	findOntologyTerms(String queryTerm, String ontologyIri)
Iterable<Ontology>	getAllOntologies()
Iterable<Entity>	getAllOntologyEntities()
Iterable<Entity>	getAllOntologyTermEntities(String ontologyIri)
Iterable<OntologyTerm>	getAllOntologyTerms(String ontologyIri)
Iterable<Entity>	getChildOntologyTermEntities(String ontologyIri, String ontologyTermIri)
Iterable<OntologyTerm>	getChildOntologyTerms(String ontologyIri, String ontologyTermIri)
Ontology	getOntology(String ontologyIri)
Entity	getOntologyEntity(String ontologyIri)
OntologyTerm	getOntologyTerm(String ontologyTermIri, String ontologyIri)
Entity	getOntologyTermEntity(String ontologyTermIri, String ontologyIri)
List<String>	getOntologyTermSynonyms(String ontologyTermIri, String ontologyIri)
Iterable<Entity>	getRootOntologyTermEntities(String ontologyIri)
Iterable<OntologyTerm>	getRootOntologyTerms(String ontologyIri)
OntologyServiceResult	search(String ontologyUrl, String queryString)
OntologyServiceResult	searchEntity(String ontologyIri, Entity entity)

Method Detail

getAllOntologies

Iterable<Ontology> getAllOntologies()

Returns:

a list of all available ontologies

getAllOntologyEntities

Iterable<Entity> getAllOntologyEntities()

Returns:

a list of untyped ontology entities

getOntology

Ontology getOntology(String ontologyIri)

Parameters:

ontologyIri -

Returns:

an ontology based on the ontologyIri

getOntologyEntity

Entity getOntologyEntity(String ontologyIri)

Parameters:

ontologyIri -

Returns:

an untyped ontology based on the ontologyIri

findOntologyTerms

Iterable<OntologyTerm> findOntologyTerms(String queryTerm,
                                         String ontologyIri)

Parameters:

queryTerm -

ontologyIri -

Returns:

a list of ontology terms sorted based on the relevance

getOntologyTerm

OntologyTerm getOntologyTerm(String ontologyTermIri,
                             String ontologyIri)

Parameters:

ontologyTermIRI -

ontologyIri -

Returns:

an ontologyTerm based on specified ontologyTermIri in particular ontology

getOntologyTermEntity

Entity getOntologyTermEntity(String ontologyTermIri,
                             String ontologyIri)

Parameters:

ontologyTermIri -

ontologyIri -

Returns:

an untyped ontologyTerm entity based on specified ontologyTermIri in particular ontology

getOntologyTermSynonyms

List<String> getOntologyTermSynonyms(String ontologyTermIri,
                                     String ontologyIri)

Parameters:

ontologyTermIri -

ontologyIri -

Returns:

a list of synonyms for ontology term provided

getAllOntologyTerms

Iterable<OntologyTerm> getAllOntologyTerms(String ontologyIri)

Parameters:

ontologyIri -

Returns:

a list of ontologyterms from specified ontology

Throws:

NullPointerException - if the ontologyIri is not known

getAllOntologyTermEntities

Iterable<Entity> getAllOntologyTermEntities(String ontologyIri)

Parameters:

ontologyIri -

Returns:

a list of untyped ontologyterm entities from specified ontology

getRootOntologyTerms

Iterable<OntologyTerm> getRootOntologyTerms(String ontologyIri)

Parameters:

ontologyIri -

Returns:

a list of root ontologyterms from specified ontology

Throws:

NullPointerException - if the ontologyIri is not known

getRootOntologyTermEntities

Iterable<Entity> getRootOntologyTermEntities(String ontologyIri)

Parameters:

ontologyIri -

Returns:

a list of untyped root ontologyterm entities from specified ontology

Throws:

NullPointerException - if the ontologyIri is not known

getChildOntologyTerms

Iterable<OntologyTerm> getChildOntologyTerms(String ontologyIri,
                                             String ontologyTermIri)

Parameters:

ontologyIri -

ontologyTerm -

Returns:

a list of child ontologyTerms from current ontologyTerm in specified ontology

Throws:

NullPointerException - if the ontologyIri is not known

NullPointerException - if the ontologyTermIri is not known

getChildOntologyTermEntities

Iterable<Entity> getChildOntologyTermEntities(String ontologyIri,
                                              String ontologyTermIri)

Parameters:

ontologyIri -

ontologyTerm -

Returns:

a list of untyped child ontologyTerm entities from current ontologyTerm in specified ontology

Throws:

NullPointerException - if the ontologyIri is not known

NullPointerException - if the ontologyTermIri is not known

searchEntity

OntologyServiceResult searchEntity(String ontologyIri,
                                   Entity entity)

Parameters:

ontologyIri -

entity - input for storing the query information

Returns:

a list of relevant ontologyTerms based on the given input stored in an entity

Throws:

NullPointerException - if the ontologyIri is not known

search

OntologyServiceResult search(String ontologyUrl,
                             String queryString)

Parameters:

ontologyUrl -

queryString -

Returns:

a list of relevant ontologyTerms based on give queryString