The ChEMBL-og

If you are a follower of this blog you will have seen some earlier posts ( here and here ) providing details on changes we are making to our Web Services. I recommend reviewing the previous posts, but in summary we have setup a temporary base URL to allow existing ChEMBL Web Service users to test the new ChEMBL API powered Web Services. The new temporary base URL is: https://www.ebi.ac.uk/chemblws2 As well as providing users with all existing functionality we have also added a couple of extra features, one of which is improved molecule rendering options. The current live Web Services provides the following REST call to allow you to get a molecule image:   https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image     You are able to provide a dimension argument (pixels) to change the size of the image: https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image?dimensions=200 The image quality has deteriorated, this is because the ima...

                                     We recently did some KNIME training for ChEMBL at a workshop, and it was very popular. It made us think a little about just how much was available within Knime for ChEMBL, and we thought we'd ask if there was interest in us running a specific, detailed course on ChEMBL/KNIME next year. So here's a poll. We'll keep this open for a month (i.e. closes 18th November 2013) and then decide what to do (if anything). The stoopid free poll server I sued doesn't like the browser safari - so I'll transfer across to another system over the weekend, and try and transfer votes. Thank you to those that have voted so far. Would you be interested in Knime ChEMBL training? Yes - I'd like a two day course at the EBI next year Yes - I'd like webinars Yes - I'd like you to visit our lab (charge involved) Yes - but not from you guys. No - Knime, what'...

Following the success of our ChEMBL Bot , there is now a new faithful bot out there which answers to the name  @MalariaSARLit and is looking for new followers. Its job is to tenaciously monitor PubMed for new malaria-related publications, score them according to our ChEMBL-likeness score and tweet a ChEMBL-like one daily at noon GMT. Followers of the bot will get a  free and reliable antimalarial SAR paper alert every day in their twitter feed.   George (NKOTB fan)

ATC code: not yet assigned Wikipedia: Riociguat On October 8, 2013, the FDA approved riociguat for the treatment of patients suffering from two forms of pulmonary hypertension - chronic thromboembolic pulmonary hypertension (CTEPH), and pulmonary arterial hypertension (PAH). Pulmonary hypertension (PH) is a disease characterized by abnormally high blood pressure in the lungs, which increases the workload for the right ventricle of the heart. Some of the symptoms of PH are dizziness, shortness of breath and water deposits in the legs and joints. PH progresses slowly and can lead to severe and often fatal circulatory and respiratory complications. CTEPH is a form of PH caused by blood clots obstructing the passage of blood through the vessels in the lung, often after a pulmonary embolism has occurred. PAH on the other hand is caused by a chronic tightening or constriction of blood vessels. Riociguat ( CHEMBL2107834 ) is a stimulator of soluble guanylate cyclase (sGC),...

Yesterday saw the release of the EMBL-EBI RDF Platform , the official announcement can be found here . The purpose of this new platform is to act as a central resource for all RDF and Semantic Technology focused work being carried out at the EMBL-EBI. The benefit to users of the RDF version of the ChEMBL database is that you now have access to documentation , a SPARQL endpoint , example SPARQL queries and a Linked Data browser . Other EMBL-EBI resources involved in this project include BioModels , BioSamples , Expression Atlas , Reactome and UniProt - we expect the number of resources offering RDF versions of their data to grow over the coming year. One of the very cool things the new platform offers users is the ability to run federated SPARQL queries across the separate resources listed above. Essentially this is removing the data integration burden, which would have previously been required in order to answer the questions asked by the federated queries. Example feder...

ATC Code: N06AX26 Wikipedia: Vortioxetine On September 30th 2013, FDA approved Vortioxetine (as the hydrobromide salt; tradename: Britellix ; research code: Lu AA21004 (Lu AA21004 (HBR) for the hydrobromide salt); ChEMBL: CHEMBL2104993 ), a multimodal antidepressant indicated for the treatment of major depressive disorder (MDD) . MDD is a mental disorder characterised by low mood and/or loss of pleasure in most activities, and by symptoms or signs such as increased fatigue, change in appetite or weight, insomnia or excessive sleeping and suicide attempts or thoughts of suicide. MDD is believed to arise from low levels of neurotransmitters (primarily serotonin (5-HT), norepinepherine (NE) and dopamine(DA)) in the synaptic cleft between neurons in the brain. Several antidepressants for the treatment of MDD are already available in the market and its choice depends on which symptoms need to be tackled. The most important classes of antidepressants include the Selective Serotonin ...

Here's a paper detailing some multi-method target prediction work as part of the GeMoA FP7 project. Proud, as ever, to publish Open Access. %A Martínez-Jiménez F %A Papadatos G %A Yang L %A Wallace IM %A Kumar V %A Pieper U %A Sali A %A Brown JR %A Overington JP %A Marti-Renom MA %D 2013 %T Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis %J PLoS. Comput. Biol. %V 9 %P e1003253 %O doi:10.1371/journal.pcbi.1003253 jpo