ChEMBL is medicinal chemistry database by the team of dr. J. Overington at the EBI.
It is detailed in this paper (doi:10.1093/nar/gkt1031):
This project develops, releases, and hosts a RDF version of ChEMBL, independent from the ChEMBL team who make their own RDF version.
The main SPARQL end point is available from Uppsala University at:
Or as SNORQL at:
Additionally, the data is available as Linked Data via LinkedChemistry.info:
If you use this (3rd party) RDF version of ChEMBL, please cite this paper. It is currently under review:
E.L. Willighagen, A. Waagmeester, O. Spjuth, P. Ansell, A.J. Williams, V. Tkachenko, J. Hastings, B. Chen, D.J. Wild, The ChEMBL database as Linked Open Data, 2013, J. Cheminformatics, 2013, 5:23 doi:10.1186/1758-2946-5-23, http://www.jcheminf.com/content/5/1/23/abstract
Alternatively, you can download the full set of triples as n3 or n-triples from www.dataverse.nl:
Copyright / License
The ChEMBL database is copyrighted by John Overington et al., and licensed CC-BY-SA:
as explained on:
The ChEMBL FAQ explains how you can fullfil the attribution part of the license:
If you use this RDF version of ChEMBL, you should cite the above mentioned JChemInf paper.
Authors that contributed to the RDF structure (see also the Git commit history) are:
Egon Willighagen, Peter Ansell
These scripts were tested against version 13 of ChEMBL, as downloaded from:
ChEMBL 13, OpenRDF (aka Sesame), SLF4J, and the MySQL JDBC plugin.
For PHP the MySQL server user and password are configured in a file called like mysqli.ini, for example on Debian:
The scripts expect a script only readble by the server software called vars.properties, with content like:
<?php $version = '13'; $rooturi = 'http://data.kasabi.com/dataset/chembl-rdf/' . $version . '/'; $db = 'chembl_' . $version; $user = 'user'; $pwd = 'secret'; // use the next line to limit the output // $limit = ' LIMIT 5'; $limit = ''; ?>
to access the MySQL database with the ChEMBL content.