ubic.gemma.core.ontology.providers

Interface GeneOntologyService

All Superinterfaces:

ubic.basecode.ontology.providers.OntologyService

All Known Implementing Classes:

GeneOntologyServiceImpl

public interface GeneOntologyService
extends ubic.basecode.ontology.providers.OntologyService

Author:

paul

Field Summary

Fields

Modifier and Type	Field and Description
static String	BASE_GO_URI

Method Summary

Modifier and Type	Method and Description
Map<Long,Collection<ubic.basecode.ontology.model.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<ubic.basecode.ontology.model.OntologyTerm>	calculateGoTermOverlap(Gene queryGene1, Gene queryGene2)
Map<Long,Collection<ubic.basecode.ontology.model.OntologyTerm>>	calculateGoTermOverlap(Long queryGene, Collection<Long> geneIds)
void	clearCaches() Primarily here for testing, to recover memory.
Collection<ubic.basecode.ontology.model.OntologyTerm>	computeOverlap(Collection<ubic.basecode.ontology.model.OntologyTerm> masterOntos, Collection<ubic.basecode.ontology.model.OntologyTerm> comparisonOntos)
Collection<ubic.basecode.ontology.model.OntologyTerm>	findTerm(String queryString) Search by inexact string
Set<ubic.basecode.ontology.model.OntologyTerm>	getAllParents(Collection<ubic.basecode.ontology.model.OntologyTerm> entries)
Set<ubic.basecode.ontology.model.OntologyTerm>	getAllParents(Collection<ubic.basecode.ontology.model.OntologyTerm> entries, boolean includePartOf)
Collection<Gene>	getGenes(String goId, Taxon taxon)
Collection<ubic.basecode.ontology.model.OntologyTerm>	getGOTerms(Gene gene)
Collection<ubic.basecode.ontology.model.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.
ubic.basecode.ontology.model.OntologyTerm	getTerm(String uri)
GeneOntologyServiceImpl.GOAspect	getTermAspect(Characteristic goId)
GeneOntologyServiceImpl.GOAspect	getTermAspect(String goId)
String	getTermDefinition(String goId) Return a definition for a GO Id.
ubic.basecode.ontology.model.OntologyTerm	getTermForId(String value)
String	getTermName(String goId) Return human-readable term ("protein kinase") for a GO Id.
GeneOntologyTermValueObject	getValueObject(ubic.basecode.ontology.model.OntologyTerm term) Converts the given Ontology Term to a Gene Ontology Value Object.
Collection<GeneOntologyTermValueObject>	getValueObjects(Collection<ubic.basecode.ontology.model.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(ubic.basecode.ontology.model.OntologyTerm term)

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

cancelInitializationThread, findIndividuals, findIndividuals, findResources, findResources, findTerm, findUsingAlternativeId, getAllURIs, getChildren, getChildren, getParents, getParents, getResource, getTermIndividuals, index, initialize, initialize, isEnabled, isInitializationThreadAlive, isInitializationThreadCancelled, isOntologyLoaded, loadTermsInNameSpace, startInitializationThread, waitForInitializationThread

Field Detail

BASE_GO_URI

static final String BASE_GO_URI

See Also:

Constant Field Values

Method Detail

calculateGoTermOverlap

Map<Long,Collection<ubic.basecode.ontology.model.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<ubic.basecode.ontology.model.OntologyTerm> calculateGoTermOverlap(Gene queryGene1,
                                                                             Gene queryGene2)

Parameters:

queryGene1 - query gene 1

queryGene2 - query gene 2

Returns:

Collection>OntologyEntries<s

calculateGoTermOverlap

Map<Long,Collection<ubic.basecode.ontology.model.OntologyTerm>> calculateGoTermOverlap(Long queryGene,
                                                                                       Collection<Long> geneIds)

computeOverlap

Collection<ubic.basecode.ontology.model.OntologyTerm> computeOverlap(Collection<ubic.basecode.ontology.model.OntologyTerm> masterOntos,
                                                                     Collection<ubic.basecode.ontology.model.OntologyTerm> comparisonOntos)

findTerm

Collection<ubic.basecode.ontology.model.OntologyTerm> findTerm(String queryString)
                                                        throws ubic.basecode.ontology.search.OntologySearchException

Search by inexact string

Specified by:

findTerm in interface ubic.basecode.ontology.providers.OntologyService

Parameters:

queryString - query string

Returns:

ontology terms

Throws:

ubic.basecode.ontology.search.OntologySearchException

getAllParents

Set<ubic.basecode.ontology.model.OntologyTerm> getAllParents(Collection<ubic.basecode.ontology.model.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<ubic.basecode.ontology.model.OntologyTerm> getAllParents(Collection<ubic.basecode.ontology.model.OntologyTerm> entries,
                                                             boolean includePartOf)

getGenes

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

Parameters:

taxon - taxon

goId - go id

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

Collection<ubic.basecode.ontology.model.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<ubic.basecode.ontology.model.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

getTerm

@Nullable
ubic.basecode.ontology.model.OntologyTerm getTerm(String uri)

Specified by:

getTerm in interface ubic.basecode.ontology.providers.OntologyService

Parameters:

uri - of the term

Returns:

term if found or null otherwise.

getTermAspect

@Nullable
GeneOntologyServiceImpl.GOAspect getTermAspect(Characteristic goId)

getTermAspect

@Nullable
GeneOntologyServiceImpl.GOAspect getTermAspect(String goId)

Parameters:

goId - GO ID e.g. GO:0038128 (not 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

Returns:

Definition or null if there is no definition.

getTermForId

@Nullable
ubic.basecode.ontology.model.OntologyTerm getTermForId(String value)

Parameters:

value - e.g. GO:0038128

Returns:

term or null if not found

getTermName

String getTermName(String goId)

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

Parameters:

goId - go id

Returns:

term name

getValueObject

GeneOntologyTermValueObject getValueObject(ubic.basecode.ontology.model.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<ubic.basecode.ontology.model.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(ubic.basecode.ontology.model.OntologyTerm term)

clearCaches

void clearCaches()

Primarily here for testing, to recover memory.