@@ -360,11 +360,12 @@ specificOntologyResult <- function(object, ontology) {

 comparisonBetweenTwoLists <- function(go1,go2,ontology,direction) {

+	ontData <- semData('org.Hs.eg.db', ont=ontology)

 	finalmat <- NULL

 	for (i in 1:nrow(go1)) {

 		mat <- NULL

 		for (j in 1:nrow(go2)) {

-			sim <- goSim(go1[i, 1], go2[j, 1], measure="Wang")

+			sim <- goSim(go1[i, 1], go2[j, 1], semData=ontData, measure="Wang")

 			mat <- rbind(mat, c(go1[i, 1],go1[i, 2],go2[j, 1],go2[j, 2],sim))	

 		}