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Scripts to create RDF for ChEMBL.
PHP Groovy
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.gitignore Fixes: output the title as Literal, and add the type of the creation … Dec 7, 2012
Makefile Properties now generated with make too Nov 13, 2012
README.markdown Updated the data download link. Mar 4, 2014
TODO Updated the TODO Mar 17, 2011
activities.groovy Added VoID stuff for the Target subset Jan 8, 2013
activities_qudt.groovy Remove redundant spaces, fixing normalizing 'IC50 '/uM activities May 10, 2013
assays.php The assay data generation now also creates VoID Dec 13, 2012
chembl-rdf-void.ttl Updated the data Sep 27, 2012
compounds.php The compound data generation now also creates VoID Dec 13, 2012
compounds_labels.groovy Fixed output of synonyms Nov 13, 2012
compounds_ls_ebi.php The compound data generation now also creates VoID Dec 13, 2012
compounds_properties.php Properties now generated with make too Nov 13, 2012
createVoid.php Complete Open PHACTS compatible data set VoID Dec 8, 2012
docs.php The docs data generation now also creates VoID Jan 8, 2013
docs_ls_crossref.php Added VoID output Dec 9, 2012
docs_ls_pubmed.php OK, getting the hang of it: VoID headers for the remaining LS sets Dec 9, 2012
functions.php Type all literals as xsd:string by default Oct 25, 2012
jqudt.jar Factored out creating of QUDT-formatted activities Sep 27, 2012
mysql.jar Names and synonyms are now generated using Groovy / Open RDF Apr 13, 2012
namespaces.php Ironed out the last issues Dec 9, 2012
openrdf-sesame-2.6.5-onejar.jar Names and synonyms are now generated using Groovy / Open RDF Apr 13, 2012
ops.ttl Added a few more units Mar 10, 2013
slf4j-api.jar Names and synonyms are now generated using Groovy / Open RDF Apr 13, 2012
slf4j-simple.jar Names and synonyms are now generated using Groovy / Open RDF Apr 13, 2012
targetOntology.php Upgraded the password handling, closing #30. Nov 13, 2012
targetOntology2.php Updated for the to.php changes: key is now a code, and the label is a… Sep 27, 2012
targetTypes.nt Added skos:Concept's for the other target types Sep 27, 2012
targets.php The targets data generation now also creates VoID Dec 13, 2012
targets_ls_bio2rdf.php The targets data generation now also creates VoID Dec 13, 2012
targets_ls_uniprot.php The targets data generation now also creates VoID Dec 13, 2012
to.php Added the level and classification info from ChEMBL Sep 27, 2012
vars.properties.example Complete Open PHACTS compatible data set VoID Dec 8, 2012
void.ttl Complete Open PHACTS compatible data set VoID Dec 8, 2012

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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