Package ubic.gemma.core.ontology.providers

Interface GeneOntologyService

    • 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

      • 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

      • 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<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

      • 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
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​(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.