Ontology parsing


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Documentation for package ‘ontoCAT’ version 1.0.0

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ontoCAR-package The ontoCAT package provides a simple interface to the Experimental
getAccession Returns accession of the ontology term
getAccession-method Class "OntologyTerm"
getAllTermChildren Returns all term's children
getAllTermChildren-method Class "OntologyParser"
getAllTermIds Returns accessions of all ontology terms
getAllTermIds-method Class "OntologyParser"
getAllTermParents Returns all term's parents
getAllTermParents-method Class "OntologyParser"
getAllTerms Returns all ontology terms
getAllTerms-method Class "OntologyParser"
getDefinitions Returns set of ontology term's definitions
getDefinitions-method Class "OntologyParser"
getEFOBranchRootIds Returns all term's parents
getEFOBranchRootIds-method Class "OntologyParser"
getEFOParser Returns an instance of the EFO ontology parser
getLabel Returns label of the ontology term
getLabel-method Class "OntologyTerm"
getOntologyAccession Returns ontology accession
getOntologyAccession-method Class "OntologyParser"
getOntologyDescription Returns ontology description
getOntologyDescription-method Class "OntologyParser"
getOntologyParser Returns an instance of the ontology parser created from OWL or OBO file
getRootIds Returns root terms of ontology
getRootIds-method Class "OntologyParser"
getRoots Returns root terms of ontology
getRoots-method Class "OntologyParser"
getSynonyms Returns set of ontology term's synonyms
getSynonyms-method Class "OntologyParser"
getTermAndAllChildrenIds Returns accessions of all term's parents and term itself
getTermAndAllChildrenIds-method Class "OntologyParser"
getTermById Returns ontology term
getTermById-method Class "OntologyParser"
getTermChildren Returns direct children of term of interest
getTermChildren-method Class "OntologyParser"
getTermNameById Returns ontology term's label
getTermNameById-method Class "OntologyParser"
getTermParents Returns set of direct parents of the term of interest
getTermParents-method Class "OntologyParser"
getTreeDownTo Returns all term's parents
getTreeDownTo-method Class "OntologyParser"
hasTerm Returns true if term is in ontology
hasTerm-method Class "OntologyParser"
isEFOBranchRoot Returns true if term is the branch root in EFO
isEFOBranchRoot-method Class "OntologyParser"
isRoot Returns true if term is the root in the ontology hierarchy
isRoot-method Class "OntologyParser"
ontoCAR The ontoCAT package provides a simple interface to the Experimental
OntologyParser-class Class "OntologyParser"
OntologyTerm-class Class "OntologyTerm"
searchTerm Searches term by its name in ontology
searchTerm-method Class "OntologyParser"
searchTermPrefix Searches for term by prefix in ontology
searchTermPrefix-method Class "OntologyParser"
show-method Class "OntologyTerm"