\name{ontology-class}
\docType{class}
\alias{ontology-class}
\alias{ontology}
\alias{name}
\alias{OVersion}
\alias{name,ontology-method}
\alias{OVersion,ontology-method}
\alias{show,ontology-method}
\alias{makeOntology}
\alias{rDAG,ontology-method}
\alias{accessMat,ontology-method}
\alias{rDAG}
\title{Class "ontology" wraps a rooted DAG with some
ontology metadata }
\description{  instances of class ontology are used to
represent things like Gene Ontology }
\section{Objects from the Class}{
Objects can be created by calls of the form \code{new("ontology", ...)}.
This simply possesses information on name and version of ontology.
}
\section{Slots}{
  \describe{
    \item{\code{name}:}{Object of class \code{"character"} name of ontology }
    \item{\code{version}:}{Object of class \code{"character"} version tag }
    \item{\code{rDAG}:}{Object of class \code{"rootedDAG"} the rooted
DAG representing the terminlogy hierarchy }
  }
}
\section{Methods}{
  \describe{
    \item{accessMat}{\code{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}
    \item{name}{\code{signature(x = "ontology")}: access name }
    \item{OVersion}{\code{signature(x = "ontology")}:  access version}
    \item{rDAG}{\code{signature(x = "ontology")}: access the rooted DAG }
    \item{show}{\code{signature(object = "ontology")}: concise report }
  }
}
%\references{ ~put references to the literature/web site here ~ }
\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.
}

% ~Make other sections like Warning with \section{Warning }{....} ~

%\seealso{
%  ~~objects to See Also as \code{\link{~~fun~~}}, ~~~
%  or \code{\link{CLASSNAME-class}} for links to other classes
%}
\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))
}
\keyword{classes}