Man pages for Bioconductor-mirror/ontoCAT
Ontology traversal and search

getAccessionReturns accession of the ontology term
getAllTermChildrenReturns all children of term of interest
getAllTermChildrenByIdReturns all children of term of interest
getAllTermIdsReturns accessions of all ontology terms
getAllTermParentsReturns set of all parents of the term of interest
getAllTermParentsByIdReturns set of all parents of the term of interest
getAllTermsReturns all ontology terms
getEFOReturns an instance of the EFO ontology parser
getEFOBranchRootIdsReturns all term's parents
getLabelReturns label of the ontology term
getOntologyReturns an instance of the ontology parser created from OWL...
getOntologyAccessionReturns ontology accession
getOntologyDescriptionReturns ontology description
getOntologyNoReasoningReturns an instance of the ontology parser created from OWL...
getOntologyRelationNamesReturns list of relations used in ontology
getRootIdsReturns root terms of ontology
getRootsReturns root terms of ontology
getTermAndAllChildrenReturns accessions of all term's parents and term itself
getTermAndAllChildrenByIdReturns accessions of all term's parents and term itself
getTermByIdReturns ontology term
getTermChildrenReturns direct children of term of interest
getTermChildrenByIdReturns direct children of term of interest
getTermDefinitionsReturns set of ontology term's definitions
getTermDefinitionsByIdReturns set of ontology term's definitions
getTermNameByIdReturns ontology term's label
getTermParentsReturns set of direct parents of the term of interest
getTermParentsByIdReturns set of direct parents of the term of interest
getTermRelationNamesReturns list of relation names available for the term
getTermRelationNamesByIdReturns list of relation names available for the term
getTermRelationsReturns set of terms that are in defined relation with term...
getTermRelationsByIdReturns set of terms that are in defined relation with term...
getTermSynonymsReturns set of ontology term's synonyms
getTermSynonymsByIdReturns set of ontology term's synonyms
hasTermReturns true if term is in ontology
isEFOBranchRootReturns true if term is the branch root in EFO
isEFOBranchRootByIdReturns true if term is the branch root in EFO
isRootReturns true if term is the root in the ontology hierarchy
isRootByIdReturns true if term is the root in the ontology hierarchy
ontoCAT-packageThe ontoCAT package provides a simple interface to the...
Ontology-classClass "Ontology"
OntologyTerm-classClass "OntologyTerm"
searchTermSearches term by its name in ontology
searchTermPrefixSearches for term by prefix in ontology
showHierarchyDownToTermReturns tree representation of term's parents
showHierarchyDownToTermByIdReturns tree representation of term's parents
showPathsToTermReturns paths to the term
showPathsToTermByIdReturns paths to the term
Bioconductor-mirror/ontoCAT documentation built on June 1, 2017, 1:47 p.m.