ChEMBL PostgreSQL

With the aim of providing more options to access the ChEMBL database, a PostgreSQL version of the most recent ChEMBL release is now available on the ChEMBL FTP site, (thanks to the Ora2Pg project for making the conversion process relatively painless).

The main goal of this project is make it easier for users to integrate the chemical data in the ChEMBL database with freely available chemical cartridges, such as the excellent RDKit and Bingo. Now that we have the PostgreSQL version of the database available, we are in the process of benchmarking the aforementioned chemical cartridges - we will report back soon the results of the benchmarking exercises we are undertaking. We are also looking to build and release a virtual machine, which will come preloaded with ChEMBL, PostgreSQL, RDKit and/or Bingo. When we have more details on this we will let you know.

Right now everyone has the opportunity to download and install the PostgreSQL version of the ChEMBL database and optionally install a chemical cartridge. We hope this will help as many projects as possible and any comments or feedback will be very much appreciated. Enjoy it :)

(You can download the ChEMBL_14 PostgreSQL here, the tarball also comes with some basic install instructions, but does assume you have a PostgreSQL instance up and running).

Comments

greg landrum said…

Nice!

Let me know if there's anything I can do to help with the benchmarking.

13 August 2012 at 04:32

Unknown said…

oh yes, you'll hear from us soon
:)

15 August 2012 at 12:30

greg landrum said…

Any chance you would be willing/able to share logs of substructures that people have executed against ChEMBL?

That kind of real-world (and public) data would be very helpful for optimizing SSS fingerprints.

15 August 2012 at 15:52

jpo said…

Greg - we've been asked this a lot of times, and quite simply it's against our terms of use of the resources here at the EBI. The queries are confidential, and we have written the application, so anything that may be considered confidential is cleared from any caches as soon as is practicable, consistent with reasonable performance, or is only stored client side.

In summary, we don't store the queries.

There have been a few apocryphal cases where in the field of drug discovery, people have gone and mined or shared the queries of their web resources, and it is quite a sad tale......

26 August 2012 at 09:36

Kyle Kinney said…

Awesome, this is almost exactly what I needed - I was not looking forward to trying to convert this into postgresql myself. There's only one little issue - I'm running postgresql 9.0, and this is for postgresql 9.1. Any idea what kinds of compatibility issues am I likely to run into? The only noticeable failure I saw on loading was the failure of the CREATE EXTENSION plpgsql, and I may or may not be able to substitute CREATE LANGUAGE there. Not sure how much plpgsql has changed between versions, other than being an extension now.
Push comes to shove, I can migrate, but if it's a matter of changing a couple lines at the top, I'd rather avoid it.

9 September 2012 at 03:17

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