The ChEMBL-og

The latest ChEMBL database paper is now available online: http://nar.oxfordjournals.org/content/early/2016/11/28/nar.gkw1074.full This paper describes some of the additions to ChEMBL over the last few releases (ChEMBL_18 to ChEMBL_22) such as drug indications and clinical candidates, patent bioactivity data from BindingDB, drug metabolism information and richer assay annotation. A number of papers from our collaborators will also feature in the 2017 NAR database issue, so watch this space...

ChEMBL_22_1 data update: We would like to inform users that an update to ChEMBL_22 has been released.  The new version, ChEMBL_22_1, corrects an issue with the targets assigned to some BindingDB assays in ChEMBL (src_id = 37). If you are using the BindingDB data from ChEMBL, we recommend you download this update. This update also incorporates the mol file/canonical smiles correction announced previously. Updates have been made to BindingDB data in the ASSAYS, ACTIVITIES, CHEMBL_ID_LOOKUP, LIGAND_EFF and PREDICTED_BINDING_DOMAINS tables. Corrections have also been made to molfiles and canonical_smiles in the COMPOUND_STRUCTURES table. No changes have been made to other data sets or to other drug/compound/target tables in ChEMBL_22. The new release files can be downloaded from:  ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_22_1 A new version of the ChEMBL RDF is also available from: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChE...

The ChEMBL 22 release brings lots of new data. But we also released some new software so if you are interested in technical details please read on. 1. First of all, please note that ChEMBL 22 is the last release where we provide Oracle 9i dumps . Oracle 9i has been out of support now for at nearly a decade and shouldn't be in use anymore but please let us know if this is a problem. On the other hand, we will do our best to provide Oracle 12c dumps for the next release. 2. If you are using the python API client please upgrade it by running: [sudo] pip install -U chembl_webresource_client This will upgrade the client to the latest version which solves some minor bugs and adds an ability to search in document abstracts. It will also create a new cache so you will see new chembl data immediately. Otherwise, you will need to clear your cache manually. 3. New version ( 2.4.9 ) of the ChEMBL API has been released as well. This version includes:  - new endpoints: tissu...

We are pleased to announce the release of ChEMBL 22. This version of the database, prepared on 8th August 2016 contains: 2,043,051 compound records 1,686,695 compounds (of which 1,678,393 have mol files) 14,371,219 activities 1,246,132 assays 11,224 targets 65,213 documents Data can be downloaded from the ChEMBL ftpsite or viewed via the ChEMBL interface . Please see ChEMBL_22 release notes for full details of all changes in this release. CHANGES SINCE THE LAST RELEASE In addition to the regular updates to the Scientific Literature, PubChem, FDA Orange Book and USP Dictionary of USAN and INN Investigational Drug Names this release of ChEMBL also includes the following new data: Deposited Data Sets: Two new deposited data sets have been included in ChEMBL_22: the MMV Pathogen Box compound set ( http://www.pathogenbox.org ) and GSK Tres Cantos Follow-up TB Screening Data ( http://dx.doi.org/10.1371/journal.pone.0142293 ). Patent Data from BindingDB: We have wo...

ChEMBL_22 will be released in the next week or two. For those of you who want to plan ahead, here is a preview of the new schema (full documentation here ) We would also like to inform users that we plan to discontinue the Oracle 9i download format after this release. Please  contact us  as soon as possible if you rely on this version.

We are currently seeking multiple talented individuals to join the Chemogenomics team here at EMBL-EBI, both to work on our group resources (ChEMBL, SureChEMBL) and support external projects (FP7 HeCaToS and NIH Illuminating the Druggable Genome). If you are interested in applying for these positions (or for more information) please follow the links below. The closing date for all positions is 12th June. Java Back End Developer: https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj&id=54993&aid=15470 Web Developer: https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj&id=54992&aid=15470 Scientific Programmer: https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj&id=54991&aid=15470 Data Mining and Analysis Scientist: https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj&id=54990&aid=15470 Biological Data Curator: https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj&id=54985&aid=15470

In case you have been too busy to notice, ChEMBL_21 has arrived with the usual additions, improvements and enhancements both on the data/annotation side, as well as on the interface/services. To complement this, we have also updated the target prediction models , which can be downloaded from our ftp  here .  The good news is that, besides the increase in terms of training data (compounds and targets), the new models were built using the latest stable versions of RDKit ( 2015.09.2) and scikit-learn (0.17). The latter was upgraded from the much older 0.14 version, which was causing incompatibility issues (see  MultiLabelBinarizer ) to several of you while trying to use the models. We've also put together a quick Jupyter Notebook demo on how to get predictions from the models here:  https://github.com/madgpap/notebooks/blob/master/target_pred_21_demo.ipynb The new models will also be available on myChEMBL 21 along with a more detai...