Package ubic.gemma.core.ontology

Interface OntologyService

All Known Implementing Classes:

OntologyServiceImpl

public interface OntologyService

Author:

Paul

Method Summary

Modifier and Type	Method	Description
void	addExpressionExperimentStatement(Characteristic vc, ExpressionExperiment ee)	Will add the give vocab characteristic to the expression experiment.
Map<String,CharacteristicValueObject>	countObsoleteOccurrences(int start, int stop, int step)
Collection<CharacteristicValueObject>	findExperimentsCharacteristicTags(String searchQuery, boolean useNeuroCartaOntology)	Using the ontology and values in the database, for a search searchQuery given by the client give an ordered list of possible choices
Collection<OntologyTerm>	findTerms(String search)	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.
Collection<OntologyTerm>	getCategoryTerms()
Set<OntologyTerm>	getChildren(Collection<OntologyTerm> matchingTerms, boolean direct, boolean includeAdditionalProperties)	Obtain the children of a collection of terms.
String	getDefinition(String uri)
Set<OntologyTerm>	getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties)	Obtain the parents of a collection of terms.
OntologyTerm	getTerm(String uri)
Set<OntologyTerm>	getTerms(Collection<String> uris)	Return all the terms matching the given URIs.
boolean	isObsolete(String uri)
void	reindexAllOntologies()	Recreate the search indices, for ontologies that are loaded.
void	reinitializeAllOntologies()	Reinitialize all the ontologies "from scratch".
void	removeBioMaterialStatement(Long characterId, BioMaterial bm)
void	saveBioMaterialStatement(Characteristic vc, BioMaterial bm)	Will persist the give vocab characteristic to the given biomaterial
Collection<Characteristic>	termsToCharacteristics(Collection<OntologyTerm> terms)

Method Detail

addExpressionExperimentStatement

void addExpressionExperimentStatement(Characteristic vc,
                                      ExpressionExperiment ee)

Will add the give vocab characteristic to the expression experiment. Does NOT handle persisting of the experiment afterwards.

Parameters:

vc - If the evidence code is null, it will be filled in with IC. A category and value must be provided.

ee - ee

countObsoleteOccurrences

Map<String,CharacteristicValueObject> countObsoleteOccurrences(int start,
                                                                     int stop,
                                                                     int step)

findExperimentsCharacteristicTags

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

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 search)
                            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:

search - search

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

Collection<OntologyTerm> getCategoryTerms()

Returns:

terms which are allowed for use in the Category of a Characteristic

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

String getDefinition(String uri)

Parameters:

uri - uri

Returns:

the definition of the associated OntologyTerm. This requires that the ontology be loaded.

getTerm

@Nullable
OntologyTerm getTerm(String uri)

Parameters:

uri - uri

Returns:

the OntologyTerm for the specified URI.

getTerms

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

Return all the terms matching the given URIs.

isObsolete

boolean isObsolete(String uri)

reindexAllOntologies

void reindexAllOntologies()

Recreate the search indices, for ontologies that are loaded.

reinitializeAllOntologies

void reinitializeAllOntologies()

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

removeBioMaterialStatement

void removeBioMaterialStatement(Long characterId,
                                BioMaterial bm)

saveBioMaterialStatement

void saveBioMaterialStatement(Characteristic vc,
                              BioMaterial bm)

Will persist the give vocab characteristic to the given biomaterial

Parameters:

bm - bm

vc - vc

termsToCharacteristics

Collection<Characteristic> termsToCharacteristics(Collection<OntologyTerm> terms)