# Ontology traversal and search

## Documentation for package ‘ontoCAT’ version 1.6.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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