#library(SPARQL)
#library(hash)
getLinks <- function(fromdb, todb, inference = FALSE, limit = 0, endpoint="http://www.genome.jp/sparql/linkdb/"){
limitC = ""
if (limit != 0)
if (is.numeric(limit) && ! is.null (grep ("/.",limit)))
limitC = paste( " limit " , limit)
else
warning ("limit should be an integer, limit omitted from the query")
sparql_base <- paste( "BASE <http://www.genome.jp/linkdb/> \n",
"SELECT ?fromlabel ?tolabel WHERE { \n",
"?from <equivalent> ?to . \n",
"?from <core/database> ?fromdb . \n",
"?to <core/database> ?todb . \n",
"?fromdb <core/dblabel> \"", fromdb, "\" . \n",
"?todb <core/dblabel> \"", todb, "\" . \n",
"?from rdfs:label ?fromlabel . \n",
"?to rdfs:label ?tolabel . \n",
"} ORDER BY ?fromlabel ?tolabel \n",
limitC , sep="")
# print (sparql_base)
if(inference) {
query <- paste( "DEFINE input:inference 'http://www.genome.jp/sparql/linkdb/' \n", sparql_base)
}
else {
query <- sparql_base
}
message("Performing query please wait...")
res <- tryCatch({
SPARQL(url=endpoint,query)
},
error = function(err){
message("an error occured when trying to query for linkdb ", err)
})#end tryCatch
#res<-SPARQL(url=endpoint,query)
return (res$results)
}
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