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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" |