ontology-class {ontoTools} | R Documentation |
instances of class ontology are used to represent things like Gene Ontology
Objects can be created by calls of the form new("ontology", ...)
.
This simply possesses information on name and version of ontology.
name
:"character"
name of ontology version
:"character"
version tag rDAG
:"rootedDAG"
the rooted
DAG representing the terminlogy hierarchy signature(object = "ontology")
: returns
square matrix with 1 in element r,c if term corresponding
to r can be reached from term corresponding to csignature(x = "ontology")
: access name signature(x = "ontology")
: access versionsignature(x = "ontology")
: access the rooted DAG signature(object = "ontology")
: concise report This class was written to deal with ontologies that are representable as rooted DAGs. It is not clear that this is a good use of the term 'ontology', which has broader implications. However this does work for Gene Ontology.
~~who you are~~
data(litOnto) print(litOnto) g1 <- new("rootedDAG", DAG=litOnto, root="A") o1 <- new("ontology", name="demo", version="0.1", rDAG=g1) # can also use o1b <- makeOntology( name="demo", version="0.1", graph=litOnto, root="A") show(o1) print(accessMat(o1)) print(OVersion(o1))