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ontoCAT (version 1.24.0)

Ontology traversal and search

Description

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

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Version

Version

1.24.0

License

Apache License 2.0

Maintainer

Natalja Kurbatova

Last Published

February 15th, 2017

Functions in ontoCAT (1.24.0)

getAllTermChildren

Returns all children of term of interest
OntologyTerm-class

Class "OntologyTerm"
getRootIds

Returns root terms of ontology
getTermSynonyms

Returns set of ontology term's synonyms
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.
getRoots

Returns root terms of ontology
getTermAndAllChildrenById

Returns accessions of all term's parents and term itself
getTermDefinitions

Returns set of ontology term's definitions
getOntologyNoReasoning

Returns an instance of the ontology parser created from OWL or OBO file without reasining
isEFOBranchRootById

Returns true if term is the branch root in EFO
getOntologyRelationNames

Returns list of relations used in ontology
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.
getAllTerms

Returns all ontology terms
getOntologyAccession

Returns ontology accession
getTermParentsById

Returns set of direct parents of the term of interest
getAllTermChildrenById

Returns all children of term of interest
getEFO

Returns an instance of the EFO ontology parser
getTermDefinitionsById

Returns set of ontology term's definitions
getTermChildrenById

Returns direct children of term of interest
getTermRelationNames

Returns list of relation names available for the term
showHierarchyDownToTermById

Returns tree representation of term's parents
isRootById

Returns true if term is the root in the ontology hierarchy
hasTerm

Returns true if term is in ontology
showPathsToTermById

Returns paths to the term
getAllTermIds

Returns accessions of all ontology terms
getEFOBranchRootIds

Returns all term's parents
getTermChildren

Returns direct children of term of interest
getTermRelations

Returns set of terms that are in defined relation with term of interest
getTermRelationNamesById

Returns list of relation names available for the term
getTermRelationsById

Returns set of terms that are in defined relation with term of interest
searchTerm

Searches term by its name in ontology
getOntologyDescription

Returns ontology description
getTermNameById

Returns ontology term's label
Ontology-class

Class "Ontology"
searchTermPrefix

Searches for term by prefix in ontology
showPathsToTerm

Returns paths to the term
getTermParents

Returns set of direct parents of the term of interest
getAllTermParents

Returns set of all parents of the term of interest
getTermById

Returns ontology term
isEFOBranchRoot

Returns true if term is the branch root in EFO
isRoot

Returns true if term is the root in the ontology hierarchy
getTermSynonymsById

Returns set of ontology term's synonyms
getTermAndAllChildren

Returns accessions of all term's parents and term itself
getAllTermParentsById

Returns set of all parents of the term of interest
getAccession

Returns accession of the ontology term
showHierarchyDownToTerm

Returns tree representation of term's parents