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Showing posts from October, 2013

EU-OPENSCREEN 3rd Stakeholder Meeting, Oslo, Norway

Dear future user, partner, collaborator or supporter!
The ESFRI project EU-OPENSCREEN is an academic infrastructure initiative in Chemical Biology to serve your research needs. We are currently preparing the implementation of this pan-European infrastructure of open screening platforms to support basic and applied research. EU-OPENSCREEN will offer access to a unique compound library representing the know-how of European chemists, to a broad range of cutting-edge screening technologies, to valuable tool compounds for research, and to the knowledge that emerges from validated output of hundreds of screens stored and made publically available in a central database.

We cordially invite you to join us in Oslo for an exciting science day where we inform about the progress of the project and the planned services with reports on the design of the joint European Compound Library, the screening services and the database. In particular, we would like to share with you your own experiences from ac…

Competition Time - Win a Raspberry Pi with ChEMBL - chempi

Here's a free to enter competition for a brand new, fully working raspberry pi running the brand new chempi implementation. It includes everything you need to get started at home with ChEMBL - a sort of in silicoBreaking Bad maybe (hopefully not, thinking about it). It includes everything you need, with the exception of a power supply and ethernet cable.

We have run out of our creative juices, and cannot think of a suitable poem to mark the release of chempi - so the competition is for you to finish a limerick for us, starting with the line.

There once was a hacker with chempi....

Entries must be posted in the comments section. Obscene or defamatory entries will be removed (all comments are moderated, so it may take a few hours for you entry to appear, so do not repost twenty times!). We haven't really decided how to pronounce chempi (with a hard 'k' start or a soft 'sh' start, just as with ChEMBL, both are used in the wild; and also does it rhyme with scampi, …

Tastypie & Chempi

One of the immediate consequences of refactoring our webservices using Django, Tastypie and related approaches (as described here) is that we can run them on almost any database backend. Django abstracts communication with database and using custom QueryManagers we were able to implement chemisty-specific opererations, such as substructure and similarity search in a database agnostic manner.

This means, that if we want, we can use only Open Source components (such as Postgres and RDKit), or elect to use optimised commercially sourced software as appropriate. However, what if we go one step further and try to use Open Hardware as well? This is exactly what we've just done! We managed to install full ChEMBL 17 on raspbery pi.

Some frequently asked questions (at lease those that have been asked internally) and technical details are below:

1. How much space does it take?

12 Gb, including OS, data and all relevant software. Unfortunately we a used 32 Gb SD card so this is size if you w…

Usan Watch: October 2013

The USANs for October 2013 have recently been published.

We have modified the sourcing of this data - using the new ChEMBL API to automatically parse the documents, extract and validate the mol files for the compounds. So in future, these reports should be more timely, complete and fun!

USAN Research Code InChIKey (Parent)Drug ClassTherapeutic classTargetalectinib
AF-802; CH-5424802

KDGFLJKFZUIJMX-UHFFFAOYSA-Nsynthetic small moleculetherapeuticALKapitolisib
GDC-0980.1, G-038390, G-038390.1, RG-7422

YOVVNQKCSKSHKT-HNNXBMFYSA-Nsynthetic small moleculetherapeuticMTOR,PI3Kcimaglermin-alfaGGF2, rhGGF2


n/aproteintherapeuticErbBdecernotinib
VX-509, VRT-831509

ASUGUQWIHMTFJL-QGZVFWFLSA-Nsynthetic small moleculetherapeuticJAK3elobixibat
A-3309; AZD-7806

XFLQIRAKKLNXRQ-UUWRZZSWSA-Nn/atherapeuticSLC10A2ipatasertib
GDC-0068; RG-7440

GRZXWCHAXNAUHY-NSISKUIASA-Nsynthetic small moleculetherapeuticAKTlixisenatide
AVE-0010

n/apeptidetherapeuticGLP1Rulocuplumab
MDX-1338, BMS-936564

n/amonoclonal antibodytherape…

New Drug Approvals 2013 - Pt. XVII - Macitentan (Opsumit ®)

ATC Code: C02KX(incomplete) Wikipedia:Macitentan ChEMBL: CHEMBL2103873
On October 13th the FDA approvedMacitentan (trade name Opsumit ®) for the treatment of pulmonary arterial hypertension (PAH). Macitentan is an endothelin receptor antagonist (with affinities to both Endothelin ET-A (ETA) and Endothelin ET-B (ETB) receptor subtypes, similar in mechanism of action to the previously licensed drug Bosentan, CHEMBLID957).
Target(s)
The Endothelin receptor ET-A (ETA, CHEMBLID252 ; Uniprot P25101) and Endothelin receptor ET-B (ETB, CHEMBLID1785 ; Uniprot P24530) receptors mediate a number of physiological effects via the natural peptide agonist Endothelin-1 (ET1 , CHEMBL437472 ; Uniprot P05305). In addition to normal roles in supporting homeostasis, these effects can include pathologies such as inflammation, vasoconstriction, fibrosis and hypertrophy.

Macitentan acts as an antagonist for both receptors with both a high affinity and long residence time in human pulmonary arterial smooth muscl…

ChEMBL Web Service Update 3: Image Rendering Changes

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 image returned is simply re-sized version of the first image. The new Ch…

ChEMBL KNIME training?

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's that

New Bot on the Blog

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)

New Drug Approvals 2013 - Pt. XVI - Riociguat (AdempasTM)

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), an ezyme that is acti…

EMBL-EBI RDF Platform

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 federated SPARQL queries …

New Drug Approvals 2013 - Pt. XV - Vortioxetine Hydrobromide (BrintellixTM)

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 Reuptake Inhi…

Paper: Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis

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

ChEMBL Web Service Update 2: JSONP Support

We posted earlier in the week about some behind the scenes changes we had made to our Web Services. Having read that post (if you missed the post and use our Web Services please take a look), you will know we setup a temporary base URL to allow users to test the new ChEMBL API powered services. The base URL is:

https://www.ebi.ac.uk/chemblws2
We have made it straightforward for users to test the new services as all current methods are available using the new base URL. As well as maintaining existing functionality, we have also been able to add a couple of new features, the first of which is JSONP support. Those familiar with web application development will be familiar with the issue of requesting data from a domain different from that of the domain the web application is running. This type of data requested is prevented by the web browser, due to the enforcement of the same-origin policy. This is an important security concept, but there are times when it being able pull data in from …

Compound Curation - The story so far...

As chemical curator for ChEMBL, I spend a lot of time processing, checking and standardising the compounds in the database. I use various pieces of software for this, but mostly it’s Pipeline Pilot. For those of you who don’t know, Pipeline Pilot is Accelrys’s graphical scientific workflow authoring application, that allows passing hundreds of thousands of compounds through various components to make sure they meet our standards to be loaded into ChEMBL.
However, it’s always incredibly useful to utilise other available software in a complementary manner to see if anything may have been missed, could be done in a different way or just to see what alternative results you can get. One such open source software package is Indigo, created by GGA Software Services. On of the web application developers was passing all of the ChEMBL compounds through the standard Indigo loader, via a Python script, during the course of his work, and found that there were about 9,000 compounds (0.7% of the curr…

Faculty positions for Bioinformatics and Computational Biology - The Crick Institute, London

An outstanding opportunity for computational research using approaches such as bioinformatics, genomics, systems biology, mathematical modelling, image analysis.
The Francis Crick Institutehttp://www.crick.ac.uk The Francis Crick Institute will open at St Pancras in central London in 2015. Its research will use interdisciplinary approaches to investigate the biology of human health and disease, supported by core funding from CRUK, the MRC, and the Wellcome Trust, and by grants from UK and international funding agencies.

The Crick is expanding Computational Biology research as a key component of its scientific strategy. The institute will offer an outstanding environment for computational research, with excellent opportunities for wet/dry collaborations across the range of biomedical and clinical research disciplines, supported by a strategic alliance with the Wellcome Trust Sanger Institute. The new Crick laboratories will feature excellent computational facilities including a state-of-t…

ChEMBL Web Service Update 1

Over the last the year we have be doing a lot work designing and building an API layer to the ChEMBL database. The reason for adding this programmatic interface is to simplify many of the daily tasks we carry out on the database. From a technical perspective the API is actually a series Object Relational Mapper (ORM) classes built on top of the ChEMBL database using the Python Django web framework. For many of our daily programmatic tasks we use the ORM directly, but we also expose the ORM as a RESTful Interface using Tastypie.

Some examples tools and processes currently using the new API include the ChEMBL twitter bot and the database migration process (creating PostgreSQL and MySQL versions of the ChEMBL Oracle database during the ChEMBL release cycle). We are now at the stage where we can start to think about updating some of the existing larger services to run off the new API and first of these to make the transition are the ChEMBL Web Services. So, what have we done? Essential…