Package ubic.gemma.core.ontology.providers

Class GeneOntologyServiceImpl

java.lang.Object

ubic.basecode.ontology.jena.AbstractOntologyService

ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService

ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl

All Implemented Interfaces:

DisposableBean, InitializingBean, OntologyService, GeneOntologyService

@Service
public class GeneOntologyServiceImpl
extends AbstractOntologyMemoryBackedService
implements GeneOntologyService, InitializingBean, DisposableBean

Holds a complete copy of the GeneOntology. This gets loaded on startup.

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

Field Summary

Fields inherited from interface ubic.gemma.core.ontology.providers.GeneOntologyService

BASE_GO_URI

Constructor Summary

Constructors

Constructor	Description
GeneOntologyServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()
static String	asRegularGoId(String uri)
static String	asRegularGoId(OntologyTerm term)
static String	asRegularGoId(Characteristic term)
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)
void	destroy()
Collection<OntologyTerm>	findTerm(String queryString)	Search by inexact string
Set<OntologyTerm>	getAllParents(Collection<OntologyTerm> entries)
Set<OntologyTerm>	getAllParents(Collection<OntologyTerm> entries, boolean includePartOf)
Collection<Gene>	getGenes(String goId, Taxon taxon)
Collection<OntologyTerm>	getGOTerms(Long gene, boolean includePartOf, GeneOntologyServiceImpl.GOAspect goAspect)
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()
GeneOntologyServiceImpl.GOAspect	getTermAspect(String goId)
GeneOntologyServiceImpl.GOAspect	getTermAspect(Characteristic goId)
String	getTermDefinition(String goId)	Return a definition for a GO Id.
OntologyTerm	getTermForId(String goId)
String	getTermName(String goId)	Return human-readable term ("protein kinase") for a GO Id.
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)

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

loadModel, loadModelFromStream

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

cancelInitializationThread, findIndividuals, findResources, findTerm, findUsingAlternativeId, getAdditionalPropertyUris, getAllURIs, getCacheName, getChildren, getDescription, getInferenceMode, getLanguageLevel, getName, getParents, getProcessImports, getResource, getTerm, getTermIndividuals, index, initialize, isEnabled, isInitializationThreadAlive, isInitializationThreadCancelled, isOntologyLoaded, isSearchEnabled, loadTermsInNameSpace, setAdditionalPropertyUris, 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.gemma.core.ontology.providers.GeneOntologyService

getTerm

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

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

Constructor Detail

GeneOntologyServiceImpl

public GeneOntologyServiceImpl()

Method Detail

asRegularGoId

public static String asRegularGoId(Characteristic term)

Parameters:

term - the term

Returns:

Usual formatted GO id, e.g., GO:0039392

asRegularGoId

public static String asRegularGoId(OntologyTerm term)

Parameters:

term - ontology term

Returns:

Usual formatted GO id, e.g., GO:0039392

asRegularGoId

public static String asRegularGoId(String uri)

getOntologyName

protected String getOntologyName()

Specified by:

getOntologyName in class AbstractOntologyService

getOntologyUrl

protected String getOntologyUrl()

Overrides:

getOntologyUrl in class AbstractOntologyMemoryBackedService

afterPropertiesSet

public void afterPropertiesSet()
                        throws InterruptedException

Specified by:

afterPropertiesSet in interface InitializingBean

Throws:

InterruptedException

destroy

public void destroy()
             throws Exception

Specified by:

destroy in interface DisposableBean

Throws:

Exception

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<OntologyTerm> findTerm(String queryString)
                                  throws OntologySearchException

Description copied from interface: GeneOntologyService

Search by inexact string

Specified by:

findTerm in interface GeneOntologyService

Specified by:

findTerm in interface OntologyService

Parameters:

queryString - query string

Returns:

ontology terms

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

getGenes

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

Specified by:

getGenes in interface GeneOntologyService

Parameters:

goId - go id

taxon - taxon

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

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,
                                           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

getGOTerms

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

Parameters:

gene - gene

goAspect - go aspect

includePartOf - include part of

Returns:

collection of 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 (not 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

Returns:

Definition or null if there is no definition.

getTermForId

public OntologyTerm getTermForId(String goId)

Specified by:

getTermForId in interface GeneOntologyService

Parameters:

goId - e.g. GO_0001312

Returns:

null if not found

getTermName

public String getTermName(String goId)

Description copied from interface: GeneOntologyService

Return human-readable term ("protein kinase") for a GO Id.

Specified by:

getTermName in interface GeneOntologyService

Parameters:

goId - go id

Returns:

term name

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