ontoCAT: Ontology traversal and search

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

AuthorNatalja Kurbatova, Tomasz Adamusiak, Pavel Kurnosov, Morris Swertz, Misha Kapushevsky
Date of publicationNone
MaintainerNatalja Kurbatova <natalja@ebi.ac.uk>
LicenseApache License 2.0
Version1.26.0

View on Bioconductor

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

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

Files

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

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