I have updated the docs.n3 for the downloads I prepared, which can simply be loaded into your triples store. A typical change looks like, so loading the new triples will only add triples, and URIs of papers are not changed:
@@ -742,6 +802,7 @@ dc:isPartOf jrn:jaf567f18f5617b0fe77d704fe8f61a3e . res:r91 a bibo:Article ; bibo:doi "10.1016/S0960-894X(01)80794-0" ; + owl:sameAs <http://dx.doi.org/10.1016/S0960-894X(01)80794-0> ; dc:date "1991" ; bibo:volume "1" ; bibo:issue "3" ;
Info on the license (CC-SA-BY), and which two papers you are asked to cite if you use this data, can be found here. Oh, and have a peek at the series on database cheminformatics by John (part1, part2, part3)!