The ChEMBL-og

Three of the group (Patricia Bento, Jon Chambers and I) are out at the ACS National in San Diego at the end of March. If you want to meet up and have a coffee, get in touch, if you'd like a talk on ChEMBL, I'm sure we could fit something in.

A paper on some of the toxicogenomics work we are involved in under the IMI eTox project. The paper is Open Access :) and downloadable here . %T Toxicogenomics Investigation Under the eTOX Project %A O. Taboureau %A A. Hersey %A K. Audouze %A L. Gautier %A U.P. Jacobsen %A R. Akhtar %A F. Atkinson %A J.P. Overington %A S. Brunak %O http://dx.doi.org/10.4172/2153-0645.S7-001 %J Pharmacogenomics & Pharmacoproteomics %V S7 %D 2012

For a long time now we have been keen to release a full and freely deployable version of the ChEMBL database with compound search capabilities built in. This has been possible in the past, but complicated by commercial licenses associated with either the databases or the chemical cartridges. There are now a number mature Open Source chemical toolkits available, such as the excellent CDK , and  RDKit. So with that brief bit of background there is now an opportunity for an intern to work in the ChEMBL group on the project for 2-3 months. The idea is will be to setup a process which: Creates a PostgreSQL version of the ChEMBL database (database required by RDKit). Install the RDKit chemical cartridge . Migrate this setup to Amazon Web Service public image . Migrate existing (or new) ChEMBL interface to run off new database and package this up into AWS image. Develop scripts to allow new releases of ChEMBL to be processed and uploaded as a new AWS image. Actually some wor...

We are pleased to announce that we have updated the ChEMBL RESTful Web Service API ( application programming interface ) with some more of the features that you - the ChEMBL users - have requested.  In particular, we have added support for the: Retrieval of compounds by Canonical SMILES string Retrieval of compounds containing a particular substructure, as given by a Canonical SMILES string Retrieval of a list of compounds similar, at a given cutoff percentage Tanimoto similarity, to one represented by a given Canonical SMILES string Retrieval of compound images, as given by a compound ChEMBLID Checking of the API's health status Inclusion of standard HTTP response codes in API responses Sample urls: Retrieve a compound image - https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image Retrieve a compound image sized to specific dimensions - https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image?dimensions=220 Retrieve a list of compounds containing ...

We have set up a schedule for the ChEMBL webinars for the first half of 2012. We strongly recommend that people developing against the ChEMBL schema, or performing data-mining attend the relevant webinars, since there are a few gotchas for the unwary, or those who don't like documentation ;) Times and subjects covered are as follows. Note all times are UK local times, and the dates span the application of Daylight Savings Times, so watch out! Secondly, details of how to participate in each meeting will be made available on the blog about a week before the scheduled webinar. 07-Mar-2012 3:30pm Interface and Searching 21-Mar-2012 3:30pm Schema and sql querying 04-Apr-2012 3:30pm structure based drugEBIlity  18-Apr-2012 3:30pm Interface and Searching 02-May-2012 3:30pm web services  16-May-2012 3:30pm Schema and sql querying  30-May-2012 9:00am Interface and Searching (Japanese language)  13-Jun-2012 3:30pm Interface and Searching  27-Jun-2012 3:30p...

Lee Harland , is a visitor in the ChEMBL group here at EMBL-EBI, and he is collaborating with us on semantic web data integration, text-mining, target ontologies and so forth.  I asked him to write a small piece for the ChEMBL-og on one of his personal projects - SciBites, and here is what he wrote...... "SciBite is a new biomedical alerting service tailored to pharmaceutically relevant questions and focused on targets, diseases and drugs. The premise is simple, right now if you're a scientist interested in say, Asthma, how can you stay on top of all the lastest developments? You can of course, set up pubmed searches, patent searches, google news searches (making sure you have remembered every possible synonym as these tools won't do that for you). What you'll get back is a stream of articles. Some relevant, many not, and you'll have to read them to actually find out. We thought there had to be a better way.. What we really wanted was a kind of Twitter for ...

We have assembled a large list of antibodies that are, or have been, in clinical development, and have full length sequences for a significant fraction of these. We have available an internship project over the summer to produce a library of structural models for this set of mAbs, and for selected cases to perform docking against their known antigen structures. Applicants should have prior experience of protein structure comparison and analysis, experience of comparative modelling (preferably with Modeller), and ideally experience of protein-protein docking. Additionally experience of antibody structure, CDRs, canonical residues, etc, would be fantastic.  If you are interested in a three to four month internship working on this on our Hinxton campus - please mail us  with a full cv.