ubic.gemma.core.ontology

Interface OntologyService

All Superinterfaces:

InitializingBean

All Known Implementing Classes:

OntologyServiceImpl

public interface OntologyService
extends InitializingBean

Author:

Paul

Method Summary

Modifier and Type	Method and 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<OntologyIndividual>	findIndividuals(String givenSearch)
Collection<Characteristic>	findTermAsCharacteristic(String search) Given a search string will look through the Mged, birnlex, obo Disease Ontology and FMA Ontology for terms that match the search term.
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()
CellLineOntologyService	getCellLineOntologyService()
CellTypeOntologyService	getCellTypeOntologyService()
ChebiOntologyService	getChebiOntologyService()
DiseaseOntologyService	getDiseaseOntologyService()
ExperimentalFactorOntologyService	getExperimentalFactorOntologyService()
GemmaOntologyService	getGemmaOntologyService()
HumanDevelopmentOntologyService	getHumanDevelopmentOntologyService()
HumanPhenotypeOntologyService	getHumanPhenotypeOntologyService()
MammalianPhenotypeOntologyService	getMammalianPhenotypeOntologyService()
MouseDevelopmentOntologyService	getMouseDevelopmentOntologyService()
ObiService	getObiService()
OntologyResource	getResource(String uri)
SequenceOntologyService	getSequenceOntologyService()
OntologyTerm	getTerm(String uri)
UberonOntologyService	getUberonService()
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
void	sort(List<CharacteristicValueObject> characteristics)
Collection<Characteristic>	termsToCharacteristics(Collection<? extends OntologyResource> terms)

Methods inherited from interface org.springframework.beans.factory.InitializingBean

afterPropertiesSet

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 OntologySearchException

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:

OntologySearchException

findIndividuals

Collection<OntologyIndividual> findIndividuals(String givenSearch)
                                        throws OntologySearchException

Throws:

OntologySearchException

findTermAsCharacteristic

Collection<Characteristic> findTermAsCharacteristic(String search)
                                             throws OntologySearchException

Given a search string will look through the Mged, birnlex, obo Disease Ontology and FMA Ontology for terms that match the search term. this a lucene backed search, is inexact and for general terms can return a lot of results.

Parameters:

search - search

Returns:

a collection of Characteristics that are backed by the corresponding found OntologyTerm

Throws:

OntologySearchException

findTerms

Collection<OntologyTerm> findTerms(String search)
                            throws OntologySearchException

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:

OntologySearchException

findTermsInexact

Collection<CharacteristicValueObject> findTermsInexact(String givenQueryString,
                                                       Taxon taxon)
                                                throws OntologySearchException,
                                                       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. Then will search the loaded ontologies for OntologyResources (Terms and Individuals) that match the search term exactly

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:

OntologySearchException

SearchException

getCategoryTerms

Collection<OntologyTerm> getCategoryTerms()

Returns:

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

getCellLineOntologyService

CellLineOntologyService getCellLineOntologyService()

Returns:

the cellLineOntologyService

getCellTypeOntologyService

CellTypeOntologyService getCellTypeOntologyService()

getChebiOntologyService

ChebiOntologyService getChebiOntologyService()

Returns:

the chebiOntologyService

getDiseaseOntologyService

DiseaseOntologyService getDiseaseOntologyService()

Returns:

the diseaseOntologyService

getExperimentalFactorOntologyService

ExperimentalFactorOntologyService getExperimentalFactorOntologyService()

Returns:

the experimentalFactorOntologyService

getGemmaOntologyService

GemmaOntologyService getGemmaOntologyService()

getHumanDevelopmentOntologyService

HumanDevelopmentOntologyService getHumanDevelopmentOntologyService()

getHumanPhenotypeOntologyService

HumanPhenotypeOntologyService getHumanPhenotypeOntologyService()

Returns:

the HumanPhenotypeOntologyService

getMammalianPhenotypeOntologyService

MammalianPhenotypeOntologyService getMammalianPhenotypeOntologyService()

Returns:

the MammalianPhenotypeOntologyService

getMouseDevelopmentOntologyService

MouseDevelopmentOntologyService getMouseDevelopmentOntologyService()

getObiService

ObiService getObiService()

Returns:

the ObiService

getResource

OntologyResource getResource(String uri)

Parameters:

uri - uri

Returns:

the OntologyResource

getSequenceOntologyService

SequenceOntologyService getSequenceOntologyService()

getTerm

OntologyTerm getTerm(String uri)

Parameters:

uri - uri

Returns:

the OntologyTerm for the specified URI.

getUberonService

UberonOntologyService getUberonService()

Returns:

UberonService

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

sort

void sort(List<CharacteristicValueObject> characteristics)

termsToCharacteristics

Collection<Characteristic> termsToCharacteristics(Collection<? extends OntologyResource> terms)