ontoCAT: Ontology traversal and search
Version 1.28.0

The ontoCAT R package provides a simple interface to ontologies described in widely used standard formats, stored locally in the filesystem or accessible online.

Browse man pages Browse package API and functions Browse package files

AuthorNatalja Kurbatova, Tomasz Adamusiak, Pavel Kurnosov, Morris Swertz, Misha Kapushevsky
Bioconductor views Classification DataRepresentation
Date of publicationNone
MaintainerNatalja Kurbatova <natalja@ebi.ac.uk>
LicenseApache License 2.0
Version1.28.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ontoCAT")

Man pages

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...
getOntologyAccession: Returns ontology accession
getOntologyDescription: Returns ontology description
getOntologyNoReasoning: Returns an instance of the ontology parser created from OWL...
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...
getTermRelationsById: Returns set of terms that are in defined relation with term...
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
ontoCAT-package: The ontoCAT package provides a simple interface to the...
Ontology-class: Class "Ontology"
OntologyTerm-class: Class "OntologyTerm"
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

Functions

Ontology-class Man page
OntologyTerm-class Man page
getAccession Man page
getAccession,OntologyTerm-method Man page
getAllTermChildren Man page
getAllTermChildren,Ontology,OntologyTerm-method Man page
getAllTermChildrenById Man page
getAllTermChildrenById,Ontology,character-method Man page
getAllTermIds Man page
getAllTermIds,Ontology-method Man page
getAllTermParents Man page
getAllTermParents,Ontology,OntologyTerm-method Man page
getAllTermParentsById Man page
getAllTermParentsById,Ontology,character-method Man page
getAllTerms Man page
getAllTerms,Ontology-method Man page
getEFO Man page Source code
getEFOBranchRootIds Man page
getEFOBranchRootIds,Ontology-method Man page
getLabel Man page
getLabel,OntologyTerm-method Man page
getOntology Man page Source code
getOntologyAccession Man page
getOntologyAccession,Ontology-method Man page
getOntologyDescription Man page
getOntologyDescription,Ontology-method Man page
getOntologyNoReasoning Man page Source code
getOntologyRelationNames Man page
getOntologyRelationNames,Ontology-method Man page
getRootIds Man page
getRootIds,Ontology-method Man page
getRoots Man page
getRoots,Ontology-method Man page
getTermAndAllChildren Man page
getTermAndAllChildren,Ontology,OntologyTerm-method Man page
getTermAndAllChildrenById Man page
getTermAndAllChildrenById,Ontology,character-method Man page
getTermById Man page
getTermById,Ontology,character-method Man page
getTermChildren Man page
getTermChildren,Ontology,OntologyTerm-method Man page
getTermChildrenById Man page
getTermChildrenById,Ontology,character-method Man page
getTermDefinitions Man page
getTermDefinitions,Ontology,OntologyTerm-method Man page
getTermDefinitionsById Man page
getTermDefinitionsById,Ontology,character-method Man page
getTermNameById Man page
getTermNameById,Ontology,character-method Man page
getTermParents Man page
getTermParents,Ontology,OntologyTerm-method Man page
getTermParentsById Man page
getTermParentsById,Ontology,character-method Man page
getTermRelationNames Man page
getTermRelationNames,Ontology,OntologyTerm-method Man page
getTermRelationNamesById Man page
getTermRelationNamesById,Ontology,character-method Man page
getTermRelations Man page
getTermRelations,Ontology,OntologyTerm,character-method Man page
getTermRelationsById Man page
getTermRelationsById,Ontology,character,character-method Man page
getTermSynonyms Man page
getTermSynonyms,Ontology,OntologyTerm-method Man page
getTermSynonymsById Man page
getTermSynonymsById,Ontology,character-method Man page
hasTerm Man page
hasTerm,Ontology,character-method Man page
isEFOBranchRoot Man page
isEFOBranchRoot,Ontology,OntologyTerm-method Man page
isEFOBranchRootById Man page
isEFOBranchRootById,Ontology,character-method Man page
isRoot Man page
isRoot,Ontology,OntologyTerm-method Man page
isRootById Man page
isRootById,Ontology,character-method Man page
onLoad Source code
ontoCAR Man page
ontoCAR-package Man page
searchTerm Man page
searchTerm,Ontology,character-method Man page
searchTermPrefix Man page
searchTermPrefix,Ontology,character-method Man page
show,OntologyTerm-method Man page
showHierarchyDownToTerm Man page
showHierarchyDownToTerm,Ontology,OntologyTerm-method Man page
showHierarchyDownToTermById Man page
showHierarchyDownToTermById,Ontology,character-method Man page
showPathsToTerm Man page
showPathsToTerm,Ontology,OntologyTerm-method Man page
showPathsToTermById Man page
showPathsToTermById,Ontology,character-method Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
NOTICE
R
R/onLoad.R
R/ontoCAT.R
build
build/vignette.rds
inst
inst/doc
inst/doc/ontoCAT.R
inst/doc/ontoCAT.Rnw
inst/doc/ontoCAT.pdf
inst/extdata
inst/extdata/bodysystem.owl
inst/extdata/cell.obo
inst/jars
inst/jars/log4j.xml
inst/jars/ontocat-bioconductor.jar
man
man/Ontology-class.Rd
man/OntologyTerm-class.Rd
man/getAccession.Rd
man/getAllTermChildren.Rd
man/getAllTermChildrenById.Rd
man/getAllTermIds.Rd
man/getAllTermParents.Rd
man/getAllTermParentsById.Rd
man/getAllTerms.Rd
man/getEFO.Rd
man/getEFOBranchRootIds.Rd
man/getLabel.Rd
man/getOntology.Rd
man/getOntologyAccession.Rd
man/getOntologyDescription.Rd
man/getOntologyNoReasoning.Rd
man/getOntologyRelationNames.Rd
man/getRootIds.Rd
man/getRoots.Rd
man/getTermAndAllChildren.Rd
man/getTermAndAllChildrenById.Rd
man/getTermById.Rd
man/getTermChildren.Rd
man/getTermChildrenById.Rd
man/getTermDefinitions.Rd
man/getTermDefinitionsById.Rd
man/getTermNameById.Rd
man/getTermParents.Rd
man/getTermParentsById.Rd
man/getTermRelationNames.Rd
man/getTermRelationNamesById.Rd
man/getTermRelations.Rd
man/getTermRelationsById.Rd
man/getTermSynonyms.Rd
man/getTermSynonymsById.Rd
man/hasTerm.Rd
man/isEFOBranchRoot.Rd
man/isEFOBranchRootById.Rd
man/isRoot.Rd
man/isRootById.Rd
man/ontoCAT-package.Rd
man/searchTerm.Rd
man/searchTermPrefix.Rd
man/showHierarchyDownToTerm.Rd
man/showHierarchyDownToTermById.Rd
man/showPathsToTerm.Rd
man/showPathsToTermById.Rd
vignettes
vignettes/ontoCAT.Rnw
ontoCAT documentation built on May 20, 2017, 10:11 p.m.