"get.go.ontos" <-
function(ont="BP",organism="yeast")
  {
    if(!(ont %in% c("BP","MF","CC")))
      stop("Invalid ontology (must be one of 'BP','MF', or 'CC')")
    if(!(organism %in% c("yeast","human","mouse","rat")))
      stop("Invalid organism (must be one of 'yeast','human','mouse', or 'rat')")
    
    cat("Building GO graph...")
    expr <- paste("buildGOgraph(useenv=GO",ont,"PARENTS)",sep="")
    goGraph <- eval(parse(text=expr))
    cat("\n")
    goRDAG <- new("rootedDAG",root=get.go.root(ont),DAG=goGraph)
    goOnto <- new("ontology",name=ont,version="1.0",rDAG=goRDAG)

    cat("Computing accessibility matrix...")
    goAmat <- accessMat(goOnto)
    MAT.label <- paste("go",ont,"aMAT",sep="")
    expr <- paste(MAT.label," <- goAmat",sep="")
    eval(parse(text=expr))
    MAT.name <- paste("go",ont,"aMAT.RData",sep="")
    expr <- paste("save(",MAT.label,",file=\"",MAT.name,"\")",sep="")
    eval(parse(text=expr))

    cat("\nCreating probe-term map...")
    goMAP <- get.go.map(nodes(goGraph),organism)
    cat("\nMaking OOC...")
    goOOC <- makeOOC(goOnto,goMAP)
    ooc.label <- paste("go",ont,"ooc.",organism,sep="")
    expr <- paste(ooc.label," <- goOOC",sep="")
    eval(parse(text=expr))
    ooc.name <- paste("go",ont,"ooc.",organism,".RData",sep="")
    expr <- paste("save(",ooc.label,",file=\"",ooc.name,"\")",sep="")
    eval(parse(text=expr))
    
    cat("\nComputing concept probabilities...")
    goPC <- conceptProbs(goOOC,acc=goAmat)
    pc.label <- paste("go",ont,"pc.",organism,sep="")
    expr <- paste(pc.label," <- goPC",sep="")
    eval(parse(text=expr))
    pc.name <- paste("go",ont,"pc.",organism,".RData",sep="")
    expr <- paste("save(",pc.label,",file=\"",pc.name,"\")",sep="")
    eval(parse(text=expr))
  }