Ontology-class          Class "Ontology"
OntologyTerm-class      Class "OntologyTerm"
getAccession            Returns accession of the ontology term
getAllTermChildren      Returns all children of term of interest
getAllTermChildrenById
                        Returns all children of term of interest
getAllTermIds           Returns accessions of all ontology terms
getAllTermParents       Returns set of all parents of the term of
                        interest
getAllTermParentsById   Returns set of all parents of the term of
                        interest
getAllTerms             Returns all ontology terms
getEFO                  Returns an instance of the EFO ontology parser
getEFOBranchRootIds     Returns all term's parents
getLabel                Returns label of the ontology term
getOntology             Returns an instance of the ontology parser
                        created from OWL or OBO file. Reasoning over
                        ontologies and extracting relationships is
                        supported by using HermiT reasoner.
getOntologyAccession    Returns ontology accession
getOntologyDescription
                        Returns ontology description
getOntologyNoReasoning
                        Returns an instance of the ontology parser
                        created from OWL or OBO file without reasining
getOntologyRelationNames
                        Returns list of relations used in ontology
getRootIds              Returns root terms of ontology
getRoots                Returns root terms of ontology
getTermAndAllChildren   Returns accessions of all term's parents and
                        term itself
getTermAndAllChildrenById
                        Returns accessions of all term's parents and
                        term itself
getTermById             Returns ontology term
getTermChildren         Returns direct children of term of interest
getTermChildrenById     Returns direct children of term of interest
getTermDefinitions      Returns set of ontology term's definitions
getTermDefinitionsById
                        Returns set of ontology term's definitions
getTermNameById         Returns ontology term's label
getTermParents          Returns set of direct parents of the term of
                        interest
getTermParentsById      Returns set of direct parents of the term of
                        interest
getTermRelationNames    Returns list of relation names available for
                        the term
getTermRelationNamesById
                        Returns list of relation names available for
                        the term
getTermRelations        Returns set of terms that are in defined
                        relation with term of interest
getTermRelationsById    Returns set of terms that are in defined
                        relation with term of interest
getTermSynonyms         Returns set of ontology term's synonyms
getTermSynonymsById     Returns set of ontology term's synonyms
hasTerm                 Returns true if term is in ontology
isEFOBranchRoot         Returns true if term is the branch root in EFO
isEFOBranchRootById     Returns true if term is the branch root in EFO
isRoot                  Returns true if term is the root in the
                        ontology hierarchy
isRootById              Returns true if term is the root in the
                        ontology hierarchy
ontoCAR-package         The ontoCAT package provides a simple interface
                        to the Experimental Factor Ontology (EFO) and
                        to any other ontology described in OWL or OBO
                        format.
searchTerm              Searches term by its name in ontology
searchTermPrefix        Searches for term by prefix in ontology
showHierarchyDownToTerm
                        Returns tree representation of term's parents
showHierarchyDownToTermById
                        Returns tree representation of term's parents
showPathsToTerm         Returns paths to the term
showPathsToTermById     Returns paths to the term
