ontology-class {ontoTools} | R Documentation

## Class "ontology" wraps a rooted DAG with some ontology metadata

### Description

instances of class ontology are used to represent things like Gene Ontology

### Objects from the Class

Objects can be created by calls of the form `new("ontology", ...)`. This simply possesses information on name and version of ontology.

### Slots

`name`:
  Object of class `"character"` name of ontology
`version`:
  Object of class `"character"` version tag
`rDAG`:
  Object of class `"rootedDAG"` the rooted DAG representing the terminlogy hierarchy

### Methods

accessMat
  `signature(object = "ontology")`: returns square matrix with 1 in element r,c if term corresponding to r can be reached from term corresponding to c
name
  `signature(x = "ontology")`: access name
OVersion
  `signature(x = "ontology")`: access version
rDAG
  `signature(x = "ontology")`: access the rooted DAG
show
  `signature(object = "ontology")`: concise report

### Note

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.

### Author(s)

~~who you are~~

### Examples

    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))

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