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.

Author
Natalja Kurbatova, Tomasz Adamusiak, Pavel Kurnosov, Morris Swertz, Misha Kapushevsky
Date of publication
None
Maintainer
Natalja Kurbatova <natalja@ebi.ac.uk>
License
Apache License 2.0
Version
1.26.0

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

Files in this package

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