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Open Data for Neglected Tropical Disease Discovery, and Release of ChEMBL-04

It was clearly a slow news day in Swindon that day; but, in a way, wouldn't it be nice to live a place where this was big news. I for one, am glad the tortoise is OK (google with the headline and you'll get the full, detailed story).

Anyway, there are some significant publications in Nature this week on HTS screening and follow-up for Malaria screens (the papers are free content at the moment - Gamo et al, and Guiguemde et al. There are also some press releases for these papers and the public data release. We won't repeat the content of these formal things, but here provide some informal commentary...

The magic data pixies here at EMBL-EBI have been working hard and we have loaded all the data into the latest release of our SAR database - ChEMBL04. The data is now live in the web interface, and the ftp download of the whole database will be in the near future (we are still optimising our production processes, so sorry that the data is available in the front-end before the download files are fully ready and tested - but we took the view that people would probably not want us to hold back access where possible. However, the gap between loading into the front-end schema and the packaged export release will shorten.

We have also put together a 'microsite' called ChEMBL-NTD (NTD stands for Neglected Tropical Disease) accessible at http://www.ebi.ac.uk/chemblntd - this showcases and provides easy download of raw data from ChEMBL for this strategically important set of diseases, and also allows the addition of extra functionality for visualisation that isn't available in the ChEMBL front end. We have some exciting plans for community annotation of these data-sets, and more on this later. At the moment, there are download links, in a variety of common formats, for the GSK, St. Judes, and Novartis. Unfortunately we only had time to build some interactive query tools for the ChEMBL plasmodium and GSK datasets; but rest assured, were putting together some tools for cross datasets analysis and querying (given the scientific limits of analysis of large sets of single point screening data).


As you will probably guess, there are more data-sets in the pipeline for release, and we would be delighted if others with similar datasets would be interested in publicly archiving them here at the EMBL-EBI. As always, all the EMBL-EBI data is freely accessible, redistributable, etc>.

If you have any feedback on data formats, the interface, etc please let us know.

Chembl04 contains 680,293 compound records, 565,243 distinct compounds, and 2,705,136 assay data points.

Finally, a heartfelt thanks to many people who have helped us put this together, championed the release of data from their organisations, and acted as the social glue that is so important in getting these sort of things actually done. As the youth the world over now say - respect to Rick Keenan, Jose Garcia-Bustos, Frederic Bost, Pascal Fantauzzi, Richard Glynne, Thierry Diagana, Anang Shelat and Kip Guy!

%T Thousands of chemical starting points for antimalarial lead identification
%J Nature
%V 465
%P 305-310
%D 2010
%A F.-J. Gamo
%A L.M. Sanz
%A J. Vidal
%A C. de Cozar
%A E. Alvarez
%A J.-L. Lavandera
%A D.E. Vanderwall
%A D.V.S. Green
%A V. Kumar 
%A S. Hasan
%A J.R. Brown
%A C.E. Peishoff
%A L.R. Cardon
%A J.F. Garcia-Bustos

%T Chemical genetics of Plasmodium falciparum
%J Nature
%V 465
%P 311-315
%A W.A. Guiguemde 
%A A.A. Shelat
%A D. Bouck
%A S. Duffy
%A G.J. Crowther
%A P.H. Davis
%A D.C. Smithson
%A M. Connelly
%A J. Clark
%A F. Zhu
%A M.B. Jimnez-Dıaz
%A M.S. Martinez
%A E.B. Wilson
%A A.K. Tripathi 
%A J. Gut
%A E.R. Sharlow
%A I. Bathurst
%A F. El Mazouni1
%A J.W. Fowble 
%A I. Forquer
%A P.L. McGinley
%A S. Angulo-Barturen
%A S. Ferrer
%A P.J. Rosenthal
%A J.L. DeRisi
%A D.J. Sullivan Jr.
%A J.S. Lazo
%A D.S. Roos
%A M.K. Riscoe
%A M.A. Phillips
%A P.K. Rathod 
%A W.C. Van Voorhis
%A V.M. Avery 
%A R.K. Guy

Comments

Unknown said…
Can anyone tell me how to get these compounds and where i can get the available vendor list
jpo said…
Hi,

Some of the compounds are available commercially - it is pretty simple to do a search against ZINC to get a good starting point for sourcing the compounds. Let us know if you'd like us to look at this for you.

You could also try contacting either St. Judes, Novartis, or GSK (as appropriate and using the contact details in the papers) to get some samples. But they may not have sufficient sample left, and also I know have been inundated with request following the publications.

jpo

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