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Scripts to create RDF for ChEMBL.
PHP Groovy
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.gitignore
Makefile
README.markdown
TODO
activities.groovy
activities_qudt.groovy
assays.php
chembl-rdf-void.ttl
compounds.php
compounds_labels.groovy
compounds_ls_ebi.php
compounds_properties.php
createVoid.php
docs.php
docs_ls_crossref.php
docs_ls_pubmed.php
functions.php
jqudt.jar
mysql.jar
namespaces.php
openrdf-sesame-2.6.5-onejar.jar
ops.ttl
slf4j-api.jar
slf4j-simple.jar
targetOntology.php
targetOntology2.php
targetTypes.nt
targets.php
targets_ls_bio2rdf.php
targets_ls_uniprot.php
to.php
vars.properties.example
void.ttl

README.markdown

About

ChEMBL is medicinal chemistry database by the team of dr. J. Overington at the EBI.

http://www.ebi.ac.uk/chembl/

It is detailed in this paper (doi:10.1093/nar/gkt1031):

http://nar.oxfordjournals.org/content/42/D1/D1083

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:

http://rdf.farmbio.uu.se/chembl/sparql

Or as SNORQL at:

http://rdf.farmbio.uu.se/chembl/snorql

Additionally, the data is available as Linked Data via LinkedChemistry.info:

http://linkedchemistry.info

Citation

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

Download

Alternatively, you can download the full set of triples as n3 or n-triples from www.dataverse.nl:

http://hdl.handle.net/10411/10279

Copyright / License

The ChEMBL database is copyrighted by John Overington et al., and licensed CC-BY-SA:

http://creativecommons.org/licenses/by-sa/3.0/

as explained on:

http://www.ebi.ac.uk/chembldb/ ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_13/LICENSE

The ChEMBL FAQ explains how you can fullfil the attribution part of the license:

https://www.ebi.ac.uk/chembldb/index.php/faq#faq29

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:

ftp://ftp.ebi.ac.uk/pub/databases/chembl/releases/chembl_13/

Requirements

ChEMBL 13, OpenRDF (aka Sesame), SLF4J, and the MySQL JDBC plugin.

Installation

For PHP the MySQL server user and password are configured in a file called like mysqli.ini, for example on Debian:

/etc/php5/conf.d/20-mysqli.ini

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.

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