The ChEMBL-og

We've just co-authored with a collaborator from GSK an editorial on Open Data available here .... %T Open data for drug discovery: learning from the biological community. %A A. Hersey %A S. Senger %A J.P. Overington %J Future Medicinal Chemistry %D 2012 %I 10 %V 4 %P 1865-1867 %O DOI:10.4155/fmc.12.159 The picture of the Fifty Shades of Grey dog I found on the internet somewhere...

I'm chairing a session at the ACS Spring meeting in New Orleans, in early April 2013 (the 7th thru 11th are the dates of the ACS meeting itself, but I'll probably be finished by the 9th) and am making a visit to Miami and Kentucky on the same trip. I can probably squeeze in two more lab visits if there is interest in a ChEMBL seminar (I would need to leave the US at the latest on Tuesday 16th April). I'll need to look into the practicalities of travel, and realistically they'll need to be in the South-East, but I'm pretty hardy in the air - I don't mind odd timed flights. So if there is any interest, let me know .

We're playing around with some visualisation techniques at the moment for ChEMBL, with one of our interests being the display of timelines. Here is a little standalone visualisation of the timeline of FDA drug approvals, annotated with ATC codes, loaded with some toy data (so don't rely on it for structures/publications/analysis!). Update : So the toolkit we use looks to be quite browser sensitive - we'll look into this, but by default, it looks like it doesn't render in Chrome.....

The world of data informatics is seeing a cultural change, from a world of databases, such as Chembl , to one where data is more self-descriptive and ad hoc queryable - an evolution into knowledge-bases : The data will be organized around controlled dictionaries and ontologies ( Semantic Web ), more exposed to programmatic and web service infrastructures, and more robustly linked to other repositories (for a current example of a large nascent network of coordinated data repositories, see the  ELIXIR  project). Brain  is a library created to achieve such linkage: It can handle and query large biomedical knowledge-bases. The Brain library can also serve as a framework for users interested in  Description Logic and Biology. Website of the library:  http://loopasam.github.com/Brain/ Documentation:  https://github.com/loopasam/Brain/wiki

Sometimes, when something great happens, you've just got to find out, or tell the world, straight away, just like those proud fellas in the picture above. So, would there be an interest in an RSS feed of selected ChEMBL content? The sort of thing that is probably useful would be to have alerts for new bioactivity for an already existing ChEMBL compound, or for an already existing ChEMBL target/assay. Any comments/mail gratefully received. If there is interest, we'll integrate this into our plans for next year.

ATC code: L01XE21 Wikipedia: Regorafenib On September 27th 2012 the FDA approved Stivarga (Regorafenib) for the treatment of metastatic colorectal cancer who have previously received chemotherapy, anti-EGFR or anti-VEGF therapy. Colorectal or bowl cancer is one of the most common cancers in the western world, is the third most common cancer in the United States and the second most common cause of cancer deaths in the United Kingdom (according to CRUK ). While Five-year survival rates of the primary cancer have been improving due to the availability of targeted therapy, they only extend to about 50%, however, the metastatic disease has poor prognosis. In clinical trials Regorafenib showed statistically significant improvement in survival of patients with metastatic disease as compared to the best standard care alone, with the median survival being extended from 5 to 6.4 months. Regorafenib (research code: BAY-73-4506; chembl id : CHEMBL1946170 is a monohydrate ...

Novartis have a position available in Cambridge MA.... ...for a highly motivated scientist in the in silico Lead Discovery group of the Center for Proteomic Chemistry platform. This is an exciting opportunity to perform cutting-edge computational research at their Cambridge USA site. The position will be responsible for the development of robust computational hypothesis with a variety of drug discovery project teams for the purposes of lead discovery, and will apply state of the art computational approaches to elucidate the biological profile of small molecules regarding their targets, off-targets and phenotypic outcome via an in-depth understanding of biological networks, systems biology, bioinformatics and cheminformatics. Further details are available here .