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Scripts to create RDF for ChEMBL.

branch: master
Octocat-spinner-32 .gitignore Fixes: output the title as Literal, and add the type of the creation … December 07, 2012
Octocat-spinner-32 Makefile Properties now generated with make too November 13, 2012
Octocat-spinner-32 README.markdown Updated the data download link. March 04, 2014
Octocat-spinner-32 TODO Updated the TODO March 17, 2011
Octocat-spinner-32 activities.groovy Added VoID stuff for the Target subset January 08, 2013
Octocat-spinner-32 activities_qudt.groovy Remove redundant spaces, fixing normalizing 'IC50 '/uM activities May 10, 2013
Octocat-spinner-32 assays.php The assay data generation now also creates VoID December 13, 2012
Octocat-spinner-32 chembl-rdf-void.ttl Updated the data September 27, 2012
Octocat-spinner-32 compounds.php The compound data generation now also creates VoID December 13, 2012
Octocat-spinner-32 compounds_labels.groovy Fixed output of synonyms November 13, 2012
Octocat-spinner-32 compounds_ls_ebi.php The compound data generation now also creates VoID December 13, 2012
Octocat-spinner-32 compounds_properties.php Properties now generated with make too November 13, 2012
Octocat-spinner-32 createVoid.php Complete Open PHACTS compatible data set VoID December 08, 2012
Octocat-spinner-32 docs.php The docs data generation now also creates VoID January 08, 2013
Octocat-spinner-32 docs_ls_crossref.php Added VoID output December 09, 2012
Octocat-spinner-32 docs_ls_pubmed.php OK, getting the hang of it: VoID headers for the remaining LS sets December 09, 2012
Octocat-spinner-32 functions.php Type all literals as xsd:string by default October 25, 2012
Octocat-spinner-32 jqudt.jar Factored out creating of QUDT-formatted activities September 27, 2012
Octocat-spinner-32 mysql.jar Names and synonyms are now generated using Groovy / Open RDF April 13, 2012
Octocat-spinner-32 namespaces.php Ironed out the last issues December 09, 2012
Octocat-spinner-32 openrdf-sesame-2.6.5-onejar.jar Names and synonyms are now generated using Groovy / Open RDF April 13, 2012
Octocat-spinner-32 ops.ttl Added a few more units March 10, 2013
Octocat-spinner-32 slf4j-api.jar Names and synonyms are now generated using Groovy / Open RDF April 13, 2012
Octocat-spinner-32 slf4j-simple.jar Names and synonyms are now generated using Groovy / Open RDF April 13, 2012
Octocat-spinner-32 targetOntology.php Upgraded the password handling, closing #30. November 13, 2012
Octocat-spinner-32 targetOntology2.php Updated for the to.php changes: key is now a code, and the label is a… September 27, 2012
Octocat-spinner-32 targetTypes.nt Added skos:Concept's for the other target types September 27, 2012
Octocat-spinner-32 targets.php The targets data generation now also creates VoID December 13, 2012
Octocat-spinner-32 targets_ls_bio2rdf.php The targets data generation now also creates VoID December 13, 2012
Octocat-spinner-32 targets_ls_uniprot.php The targets data generation now also creates VoID December 13, 2012
Octocat-spinner-32 to.php Added the level and classification info from ChEMBL September 27, 2012
Octocat-spinner-32 vars.properties.example Complete Open PHACTS compatible data set VoID December 08, 2012
Octocat-spinner-32 void.ttl Complete Open PHACTS compatible data set VoID December 08, 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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