Ontology-class: Class "Ontology"
In ontoCAT: Ontology traversal and search

Description Accessing the ontologies Accessing the EFO Slots Methods Note Author(s) References See Also Examples

Supports basic operations with ontologies: traversal and search

The appropriate way to access ontology is via the helper getOntology function.

The appropriate way to access EFO is via the helper getEFO function.

ontology:: Object of class "jobjRef" No user-serviceable parts inside. Maps to an internal Java Ontology object.

getAllTermChildren: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns list of term's all children
getAllTermChildrenById: signature(object = "Ontology", id = "character"): Returns list of term's all children
getAllTermIds: signature(object = "Ontology"): Returns list of all term accessions
getAllTermParents: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns list of term's all parents
getAllTermParentsById: signature(object = "Ontology", id = "character"): Returns list of term's all parents
getAllTerms: signature(object = "Ontology"): Returns list of all terms
getEFOBranchRootIds: signature(object = "Ontology"): Returns set of branch root accessions. Method specific for EFO ontology
getOntologyAccession: signature(object = "Ontology"): Returns parsed ontology accession
getOntologyDescription: signature(object = "Ontology"): Returns parsed ontology description
getRootIds: signature(object = "Ontology"): Returns list of root terms accessions, if there are any
getRoots: signature(object = "Ontology"): Returns list of root terms, if there are any
getTermAndAllChildren: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns list of accessions of term itself and all its children recursively
getTermAndAllChildrenById: signature(object = "Ontology", id = "character"): Returns list of accessions of term itself and all its children recursively
getTermById: signature(object = "Ontology", id = "character"): Fetch term by accession. Returns external term representation if found in ontology, null otherwise
getTermChildren: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns list of term's direct children
getTermChildrenById: signature(object = "Ontology", id = "character"): Returns list of term's direct children
getTermDefinitions: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns set of term's definitions if there are some
getTermNameById: signature(object = "Ontology", id = "character"): Returns term's label by accession
getTermParents: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns list of term's direct parents
getTermParentsById: signature(object = "Ontology", id = "character"): Returns list of term's direct parents
getTermSynonyms: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns set of term's synonyms if there are some
hasTerm: signature(object = "Ontology", id = "character"): Check if term with specified accession exists in ontology
isEFOBranchRoot: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns true if term is branch root of EFO. Method specific for EFO ontology
isEFOBranchRootById: signature(object = "Ontology", id = "character"): Returns true if term is branch root of EFO. Method specific for EFO ontology
isRoot: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns true if term is root of ontology
isRootById: signature(object = "Ontology", id = "character"): Returns true if term is root of ontology
searchTerm: signature(object = "Ontology", id = "character"): Searches for term in ontology by name
searchTermPrefix: signature(object = "Ontology", prefix = "character"): Searches for prefix in ontology
showHierarchyDownToTerm: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns set of terms that represent ontology "opened" down to specified term, hence displaying all its parents first and then a tree level, containing specified term
showHierarchyDownToTermById: signature(object = "Ontology", id = "character"): Returns set of terms that represent ontology "opened" down to specified term, hence displaying all its parents first and then a tree level, containing specified term
showPathsToTerm: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns paths to the specified term from ontology's root term
showPathsToTermById: signature(object = "Ontology", id = "character"): Returns paths to the specified term from ontology's root term
getOntologyRelationNames: signature(object = "Ontology"): Returns list of relations used in ontology
getTermRelationNames: signature(object1 = "Ontology", object2 = "OntologyTerm"): Returns list of relations that term has
getTermRelationNamesById: signature(object1 = "Ontology", id = "character"): Returns list of relations that term under given accession has
getTermRelations: signature(object1 = "Ontology", object2 = "OntologyTerm", relation = "character"): Returns list of terms that are in defined relation with term of interest
getTermRelations: signature(object = "Ontology", id = "character", relation = "character"): Returns list of terms that are in defined relation with term of interest

This package ships with the EFO OWL file, version released at the time of the package build. Provided EFO OWL file can be loaded as any other OWL or OBO file by using getOntology function.

Another option is to load the latest EFO version on the fly by using getEFO function.

Natalja Kurbatova

Adamusiak T, Burdett T, van der Velde K J, Abeygunawardena N, Antonakaki D, Parkinson H and Swertz M: OntoCAT – a simpler way to access ontology resources. Available from Nature Precedings http://dx.doi.org/10.1038/npre.2010.4666.1 (2010)

Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H: Modeling Sample Variables with an Experimental Factor Ontology. Bioinformatics 2010, 26(8):1112–1118

Experimental Factor Ontology http://www.ebi.ac.uk/efo

Ontology Common API Tasks java library http://www.ontocat.org

Java sources and javadocs: http://sourceforge.net/projects/ontocat/files/

getOntology,getEFO and OntologyTerm

    ontology <- getEFO()
    getEFOBranchRootIds(ontology)
    term <- getTermById(ontology,"EFO_0001221")
    getTermParents(ontology,term)
    searchTermPrefix(ontology,"leuk")
    getTermAndAllChildrenById(ontology,"EFO_0000318")
    searchTerm(ontology,"thymus")
    file <- system.file("extdata", "cell.obo", package="ontoCAT")
    ontology <- getOntology(file)
    getAllTermIds(ontology)