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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" |
| 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" |