Ontology traversal and search


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Documentation for package ‘ontoCAT’ version 1.4.2

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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"
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"