Package ubic.gemma.core.ontology.providers

Class GeneOntologyServiceImpl

java.lang.Object

ubic.basecode.ontology.jena.AbstractOntologyService

ubic.basecode.ontology.providers.AbstractOntologyService

ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, OntologyService, GeneOntologyService

@Service
@ParametersAreNonnullByDefault
public class GeneOntologyServiceImpl
extends AbstractOntologyService
implements GeneOntologyService, org.springframework.beans.factory.InitializingBean

Gene Ontology

Author:

pavlidis

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	GeneOntologyServiceImpl.GOAspect

Nested classes/interfaces inherited from interface ubic.basecode.ontology.providers.OntologyService

OntologyService.InferenceMode, OntologyService.LanguageLevel

Constructor Summary

Constructors

Constructor	Description
GeneOntologyServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()
Map<Long,Collection<OntologyTerm>>	calculateGoTermOverlap(Long queryGene, Collection<Long> geneIds)
Map<Long,Collection<OntologyTerm>>	calculateGoTermOverlap(Gene queryGene, Collection<Long> geneIds)	Given a query Gene, and a collection of gene ids calculates the go term overlap for each pair of queryGene and gene in the given collection.
Collection<OntologyTerm>	calculateGoTermOverlap(Gene queryGene1, Gene queryGene2)
void	clearCaches()	Primarily here for testing, to recover memory.
Collection<OntologyTerm>	computeOverlap(Collection<OntologyTerm> masterTerms, Collection<OntologyTerm> comparisonTerms)
Collection<OntologySearchResult<OntologyTerm>>	findTerm(String queryString, int maxResults)
Set<OntologyTerm>	getAllParents(Collection<OntologyTerm> entries)
Set<OntologyTerm>	getAllParents(Collection<OntologyTerm> entries, boolean includePartOf)
protected String	getCacheName()
Collection<Gene>	getGenes(String goId, Taxon taxon)	Find genes for a given GO term by GO ID.
Collection<Gene>	getGenes(OntologyTerm term, Taxon taxon)	Find genes for a given of GO term.
Collection<OntologyTerm>	getGOTerms(Gene gene)
Collection<OntologyTerm>	getGOTerms(Gene gene, boolean includePartOf, GeneOntologyServiceImpl.GOAspect goAspect)	Get all GO terms for a gene, including parents of terms via is-a relationships; and optionally also parents via part-of relationships.
protected String	getOntologyName()
protected String	getOntologyUrl()
OntologyResource	getResource(String goId)	Retrieve a GO resource by ID or URI.
OntologyTerm	getTerm(String goId)	Retrieve a GO term by ID or URI.
GeneOntologyServiceImpl.GOAspect	getTermAspect(String goId)
GeneOntologyServiceImpl.GOAspect	getTermAspect(Characteristic goId)
String	getTermDefinition(String goId)	Return a definition for a GO ID.
Collection<OntologyIndividual>	getTermIndividuals(String goId)	Retrieve a GO individuals by ID or URI.
GeneOntologyTermValueObject	getValueObject(OntologyTerm term)	Converts the given Ontology Term to a Gene Ontology Value Object.
List<GeneOntologyTermValueObject>	getValueObjects(Collection<OntologyTerm> terms)	Converts the given collection of Ontology Terms to Gene Ontology Value Objects.
List<GeneOntologyTermValueObject>	getValueObjects(Gene gene)	Returns GO Terms VOs for the given Gene.
void	initialize(InputStream stream, boolean forceIndexing)
boolean	isBiologicalProcess(OntologyTerm term)
protected boolean	isOntologyEnabled()

Methods inherited from class ubic.basecode.ontology.jena.AbstractOntologyService

cancelInitializationThread, findIndividuals, findResources, findTerm, findUsingAlternativeId, getAdditionalPropertyUris, getAllURIs, getChildren, getDescription, getExcludedWordsFromStemming, getInferenceMode, getLanguageLevel, getName, getParents, getProcessImports, index, initialize, isEnabled, isInitializationThreadAlive, isInitializationThreadCancelled, isOntologyLoaded, isSearchEnabled, loadModel, loadModelFromStream, loadTermsInNameSpace, setAdditionalPropertyUris, setExcludedWordsFromStemming, setInferenceMode, setLanguageLevel, setProcessImports, setSearchEnabled, startInitializationThread, toString, waitForInitializationThread

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface ubic.basecode.ontology.providers.OntologyService

cancelInitializationThread, findIndividuals, findIndividuals, findResources, findResources, findTerm, findUsingAlternativeId, getAdditionalPropertyUris, getAllURIs, getChildren, getChildren, getDescription, getExcludedWordsFromStemming, getInferenceMode, getLanguageLevel, getName, getParents, getParents, getProcessImports, index, initialize, isEnabled, isInitializationThreadAlive, isInitializationThreadCancelled, isOntologyLoaded, isSearchEnabled, loadTermsInNameSpace, setAdditionalPropertyUris, setExcludedWordsFromStemming, setInferenceMode, setLanguageLevel, setProcessImports, setSearchEnabled, startInitializationThread, waitForInitializationThread

Constructor Detail

GeneOntologyServiceImpl

public GeneOntologyServiceImpl()

Method Detail

getOntologyName

protected String getOntologyName()

Specified by:

getOntologyName in class AbstractOntologyService

getOntologyUrl

protected String getOntologyUrl()

Specified by:

getOntologyUrl in class AbstractOntologyService

isOntologyEnabled

protected boolean isOntologyEnabled()

Specified by:

isOntologyEnabled in class AbstractOntologyService

getCacheName

@Nullable
protected String getCacheName()

Specified by:

getCacheName in class AbstractOntologyService

afterPropertiesSet

public void afterPropertiesSet()

Specified by:

afterPropertiesSet in interface org.springframework.beans.factory.InitializingBean

calculateGoTermOverlap

public Map<Long,Collection<OntologyTerm>> calculateGoTermOverlap(Gene queryGene,
                                                                       Collection<Long> geneIds)

Description copied from interface: GeneOntologyService

Given a query Gene, and a collection of gene ids calculates the go term overlap for each pair of queryGene and gene in the given collection. Returns a Map<Gene,Collection<OntologyEntries>>. The key is the gene (from the [queryGene,gene] pair) and the values are a collection of the overlapping ontology entries.

Specified by:

calculateGoTermOverlap in interface GeneOntologyService

Parameters:

queryGene - query gene

geneIds - gene ids

Returns:

map of gene ids to collections of ontologyTerms. This will always be populated but collection values will be empty when there is no overlap.

calculateGoTermOverlap

public Collection<OntologyTerm> calculateGoTermOverlap(Gene queryGene1,
                                                       Gene queryGene2)

Specified by:

calculateGoTermOverlap in interface GeneOntologyService

Parameters:

queryGene1 - query gene 1

queryGene2 - query gene 2

Returns:

Collection>OntologyEntries<s

calculateGoTermOverlap

public Map<Long,Collection<OntologyTerm>> calculateGoTermOverlap(Long queryGene,
                                                                       Collection<Long> geneIds)

Specified by:

calculateGoTermOverlap in interface GeneOntologyService

computeOverlap

public Collection<OntologyTerm> computeOverlap(Collection<OntologyTerm> masterTerms,
                                               Collection<OntologyTerm> comparisonTerms)

Specified by:

computeOverlap in interface GeneOntologyService

findTerm

public Collection<OntologySearchResult<OntologyTerm>> findTerm(String queryString,
                                                               int maxResults)
                                                        throws OntologySearchException

Specified by:

findTerm in interface OntologyService

Throws:

OntologySearchException

getAllParents

public Set<OntologyTerm> getAllParents(Collection<OntologyTerm> entries)

Specified by:

getAllParents in interface GeneOntologyService

Parameters:

entries - NOTE terms that are in this collection are NOT explicitly included; however, some of them may be included incidentally if they are parents of other terms in the collection.

Returns:

ontology terms

getAllParents

public Set<OntologyTerm> getAllParents(Collection<OntologyTerm> entries,
                                       boolean includePartOf)

Specified by:

getAllParents in interface GeneOntologyService

getResource

public OntologyResource getResource(String goId)

Description copied from interface: GeneOntologyService

Retrieve a GO resource by ID or URI.

Specified by:

getResource in interface GeneOntologyService

Specified by:

getResource in interface OntologyService

Overrides:

getResource in class AbstractOntologyService

getTerm

public OntologyTerm getTerm(String goId)

Description copied from interface: GeneOntologyService

Retrieve a GO term by ID or URI.

Specified by:

getTerm in interface GeneOntologyService

Specified by:

getTerm in interface OntologyService

Overrides:

getTerm in class AbstractOntologyService

getTermIndividuals

public Collection<OntologyIndividual> getTermIndividuals(String goId)

Description copied from interface: GeneOntologyService

Retrieve a GO individuals by ID or URI.

Specified by:

getTermIndividuals in interface GeneOntologyService

Specified by:

getTermIndividuals in interface OntologyService

Overrides:

getTermIndividuals in class AbstractOntologyService

getGenes

public Collection<Gene> getGenes(OntologyTerm term,
                                 @Nullable
                                 Taxon taxon)

Description copied from interface: GeneOntologyService

Find genes for a given of GO term.

Specified by:

getGenes in interface GeneOntologyService

Returns:

Collection of all genes in the given taxon that are annotated with the given id, including its child terms in the hierarchy, or null if the GO term is not found

getGenes

public Collection<Gene> getGenes(String goId,
                                 @Nullable
                                 Taxon taxon)

Description copied from interface: GeneOntologyService

Find genes for a given GO term by GO ID.

Specified by:

getGenes in interface GeneOntologyService

Parameters:

goId - a GO ID (i.e. GO:000001) or URI

See Also:

GeneOntologyService.getGenes(OntologyTerm, Taxon)

getGOTerms

public Collection<OntologyTerm> getGOTerms(Gene gene)

Specified by:

getGOTerms in interface GeneOntologyService

Parameters:

gene - Take a gene and return a set of all GO terms including the parents of each GO term

Returns:

ontology terms

getGOTerms

public Collection<OntologyTerm> getGOTerms(Gene gene,
                                           boolean includePartOf,
                                           @Nullable
                                           GeneOntologyServiceImpl.GOAspect goAspect)

Description copied from interface: GeneOntologyService

Get all GO terms for a gene, including parents of terms via is-a relationships; and optionally also parents via part-of relationships.

Specified by:

getGOTerms in interface GeneOntologyService

Parameters:

gene - gene

includePartOf - include part of

goAspect - limit only to the given aspect (pass null to use all)

Returns:

ontology terms

getTermAspect

public GeneOntologyServiceImpl.GOAspect getTermAspect(Characteristic goId)

Specified by:

getTermAspect in interface GeneOntologyService

getTermAspect

public GeneOntologyServiceImpl.GOAspect getTermAspect(String goId)

Specified by:

getTermAspect in interface GeneOntologyService

Parameters:

goId - GO ID e.g. GO:0038128 or URI

Returns:

aspect if found, null otherwise

getTermDefinition

public String getTermDefinition(String goId)

Description copied from interface: GeneOntologyService

Return a definition for a GO ID.

Specified by:

getTermDefinition in interface GeneOntologyService

Parameters:

goId - e.g. GO:0094491 or URI

Returns:

Definition or null if there is no definition.

getValueObject

public GeneOntologyTermValueObject getValueObject(OntologyTerm term)

Description copied from interface: GeneOntologyService

Converts the given Ontology Term to a Gene Ontology Value Object.

Specified by:

getValueObject in interface GeneOntologyService

Parameters:

term - the term to be converted.

Returns:

value object representing the given term.

getValueObjects

public List<GeneOntologyTermValueObject> getValueObjects(Collection<OntologyTerm> terms)

Description copied from interface: GeneOntologyService

Converts the given collection of Ontology Terms to Gene Ontology Value Objects.

Specified by:

getValueObjects in interface GeneOntologyService

Parameters:

terms - the terms to be converted.

Returns:

collection of value objects representing the given terms.

getValueObjects

public List<GeneOntologyTermValueObject> getValueObjects(Gene gene)

Description copied from interface: GeneOntologyService

Returns GO Terms VOs for the given Gene.

Specified by:

getValueObjects in interface GeneOntologyService

Parameters:

gene - the Gene to retrieve GO Terms for and convert them to VOs.

Returns:

Gene Ontology VOs representing all GO Terms associated with the given gene.

isBiologicalProcess

public boolean isBiologicalProcess(OntologyTerm term)

Specified by:

isBiologicalProcess in interface GeneOntologyService

clearCaches

public void clearCaches()

Description copied from interface: GeneOntologyService

Primarily here for testing, to recover memory.

Specified by:

clearCaches in interface GeneOntologyService

initialize

public void initialize(InputStream stream,
                       boolean forceIndexing)

Specified by:

initialize in interface OntologyService

Overrides:

initialize in class AbstractOntologyService