Package ubic.gemma.core.ontology

Interface OntologyService

All Known Implementing Classes:

OntologyServiceImpl

public interface OntologyService

Author:

Paul

Method Summary

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	findExperimentsCharacteristicTags(String searchQuery, boolean useNeuroCartaOntology)	Deprecated.
Map<Characteristic,Long>	findObsoleteTermUsage()	Locates usages of obsolete terms in Characteristics, ignoring Gene Ontology annotations.
Collection<OntologyTerm>	findTerms(String query)	Given a search string will look through the loaded ontologies for terms that match the search term.
Collection<CharacteristicValueObject>	findTermsInexact(String givenQueryString, Taxon taxon)	Given a search string will first look through the characteristic database for any entries that have a match.
Set<OntologyTerm>	getCategoryTerms()	Obtain terms which are allowed for use in the category of a Characteristic.
Set<OntologyTerm>	getChildren(Collection<OntologyTerm> matchingTerms, boolean direct, boolean includeAdditionalProperties)	Obtain the children of a collection of terms.
String	getDefinition(String uri)	Obtain a definition for the given URI.
Set<OntologyTerm>	getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties)	Obtain the parents of a collection of terms.
Set<OntologyProperty>	getRelationTerms()	Obtain terms allowed for the predicate (relationship) in a Statement.
OntologyTerm	getTerm(String uri)	Obtain a term for the given URI.
Set<OntologyTerm>	getTerms(Collection<String> uris)	Return all the terms matching the given URIs.
void	reindexAllOntologies()	Recreate the search indices, for ontologies that are loaded.
void	reinitializeAndReindexAllOntologies()	Reinitialize (and reindex) all the ontologies "from scratch".

Method Detail

findObsoleteTermUsage

Map<Characteristic,Long> findObsoleteTermUsage()

Locates usages of obsolete terms in Characteristics, ignoring Gene Ontology annotations. Requires the ontologies are loaded into memory.

Will also find terms that are no longer in an ontology we use.

Returns:

map of value URI to a representative characteristic using the term. The latter will contain a count of how many occurrences there were.

findExperimentsCharacteristicTags

@Deprecated
Collection<CharacteristicValueObject> findExperimentsCharacteristicTags(String searchQuery,
                                                                        boolean useNeuroCartaOntology)
                                                                 throws SearchException

Deprecated.

Using the ontology and values in the database, for a search searchQuery given by the client give an ordered list of possible choices

Parameters:

searchQuery - search query

useNeuroCartaOntology - use neurocarta ontology

Returns:

characteristic vos

Throws:

SearchException

findTerms

Collection<OntologyTerm> findTerms(String query)
                            throws SearchException

Given a search string will look through the loaded ontologies for terms that match the search term. If the query looks like a URI, it just retrieves the term. For other queries, this a lucene backed search, is inexact and for general terms can return a lot of results.

Parameters:

query - search query

Returns:

returns a collection of ontologyTerm's

Throws:

SearchException

findTermsInexact

Collection<CharacteristicValueObject> findTermsInexact(String givenQueryString,
                                                       @Nullable
                                                       Taxon taxon)
                                                throws SearchException

Given a search string will first look through the characteristic database for any entries that have a match. If a ontologyTermURI is given it will add all the individuals from that URI that match the search term criteria to the returned list also.

Parameters:

taxon - Only used if we're going to search for genes or taxon is otherwise relevant; if null, restriction is not used.

givenQueryString - query string

Returns:

characteristic vos

Throws:

SearchException

getCategoryTerms

Set<OntologyTerm> getCategoryTerms()

Obtain terms which are allowed for use in the category of a Characteristic.

getRelationTerms

Set<OntologyProperty> getRelationTerms()

Obtain terms allowed for the predicate (relationship) in a Statement.

getParents

Set<OntologyTerm> getParents(Collection<OntologyTerm> terms,
                             boolean direct,
                             boolean includeAdditionalProperties)

Obtain the parents of a collection of terms.

See Also:

OntologyTerm.getParents(boolean, boolean)

getChildren

Set<OntologyTerm> getChildren(Collection<OntologyTerm> matchingTerms,
                              boolean direct,
                              boolean includeAdditionalProperties)

Obtain the children of a collection of terms.

See Also:

OntologyTerm.getChildren(boolean, boolean)

getDefinition

@Nullable
String getDefinition(String uri)

Obtain a definition for the given URI.

getTerm

@Nullable
OntologyTerm getTerm(String uri)

Obtain a term for the given URI.

getTerms

Set<OntologyTerm> getTerms(Collection<String> uris)

Return all the terms matching the given URIs.

reindexAllOntologies

void reindexAllOntologies()

Recreate the search indices, for ontologies that are loaded.

reinitializeAndReindexAllOntologies

void reinitializeAndReindexAllOntologies()

Reinitialize (and reindex) all the ontologies "from scratch". This is necessary if indices are old etc. This should be admin-only.