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" |
getOntologyNoReasoning | Returns an instance of the ontology parser created from OWL or OBO file without reasining |
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" |