Package ubic.gemma.core.ontology.providers

Interface GeneOntologyService

All Superinterfaces:

AutoCloseable, OntologyService

All Known Implementing Classes:

GeneOntologyServiceImpl

public interface GeneOntologyService
extends OntologyService

Author:

paul

Nested Class Summary

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

OntologyService.InferenceMode, OntologyService.LanguageLevel

Method Summary

Modifier and Type	Method	Description
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> masterOntos, Collection<OntologyTerm> comparisonOntos)
Set<OntologyTerm>	getAllParents(Collection<OntologyTerm> entries)
Set<OntologyTerm>	getAllParents(Collection<OntologyTerm> entries, boolean includePartOf)
Collection<Gene>	getGenes(String goId, Taxon taxon)	Find genes for a given GO term by GO ID.
Collection<Gene>	getGenes(OntologyTerm goTerm, 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.
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.
Collection<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.
boolean	isBiologicalProcess(OntologyTerm term)

Methods inherited from interface java.lang.AutoCloseable

close

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

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

Method Detail

calculateGoTermOverlap

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. 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.

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

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

Parameters:

queryGene1 - query gene 1

queryGene2 - query gene 2

Returns:

Collection>OntologyEntries<s

calculateGoTermOverlap

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

computeOverlap

Collection<OntologyTerm> computeOverlap(Collection<OntologyTerm> masterOntos,
                                        Collection<OntologyTerm> comparisonOntos)

getAllParents

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

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

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

getResource

@Nullable
OntologyResource getResource(String goId)

Retrieve a GO resource by ID or URI.

Specified by:

getResource in interface OntologyService

getTerm

@Nullable
OntologyTerm getTerm(String goId)

Retrieve a GO term by ID or URI.

Specified by:

getTerm in interface OntologyService

getTermIndividuals

Collection<OntologyIndividual> getTermIndividuals(String goId)

Retrieve a GO individuals by ID or URI.

Specified by:

getTermIndividuals in interface OntologyService

getGenes

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

Find genes for a given of GO term.

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

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

Find genes for a given GO term by GO ID.

Parameters:

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

See Also:

getGenes(OntologyTerm, Taxon)

getGOTerms

Collection<OntologyTerm> getGOTerms(Gene gene)

Parameters:

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

Returns:

ontology terms

getGOTerms

Collection<OntologyTerm> getGOTerms(Gene gene,
                                    boolean includePartOf,
                                    @Nullable
                                    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.

Parameters:

gene - gene

includePartOf - include part of

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

Returns:

ontology terms

getTermAspect

@Nullable
GeneOntologyServiceImpl.GOAspect getTermAspect(Characteristic goId)

getTermAspect

@Nullable
GeneOntologyServiceImpl.GOAspect getTermAspect(String goId)

Parameters:

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

Returns:

aspect if found, null otherwise

getTermDefinition

@Nullable
String getTermDefinition(String goId)

Return a definition for a GO ID.

Parameters:

goId - e.g. GO:0094491 or URI

Returns:

Definition or null if there is no definition.

getValueObject

GeneOntologyTermValueObject getValueObject(OntologyTerm term)

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

Parameters:

term - the term to be converted.

Returns:

value object representing the given term.

getValueObjects

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

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

Parameters:

terms - the terms to be converted.

Returns:

collection of value objects representing the given terms.

getValueObjects

List<GeneOntologyTermValueObject> getValueObjects(Gene gene)

Returns GO Terms VOs for the given Gene.

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

boolean isBiologicalProcess(OntologyTerm term)

clearCaches

void clearCaches()

Primarily here for testing, to recover memory.