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

ChEMBL 34 is out!

We are delighted to announce the release of ChEMBL 34, which includes a full update to drug and clinical candidate drug data. This version of the database, prepared on 28/03/2024 contains: 2,431,025 compounds (of which 2,409,270 have mol files) 3,106,257 compound records (non-unique compounds) 20,772,701 activities 1,644,390 assays 15,598 targets 89,892 documents Data can be downloaded from the ChEMBL FTP site: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/ Please see ChEMBL_34 release notes for full details of all changes in this release: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/chembl_34_release_notes.txt New Data Sources European Medicines Agency (src_id = 66): European Medicines Agency's data correspond to EMA drugs prior to 20 January 2023 (excluding ...

SureChEMBL gets a facelift

Dear SureChEMBL users, Over the past year, we’ve introduced several updates to the SureChEMBL platform, focusing on improving functionality while maintaining a clean and intuitive design. Even small changes can have a big impact on your experience, and our goal remains the same: to provide high-quality patent annotation with a simple, effective way to find the data you need. What’s Changed? After careful consideration, we’ve redesigned the landing page to make your navigation smoother and more intuitive. From top to bottom: - Announcements Section: Stay up to date with the latest news and updates directly from this blog. Never miss any update! - Enhanced Search Bar: The main search bar is still your go-to for text searches, still with three pre-filter radio buttons to quickly narrow your results without hassle. - Improved Query Assistant: Our query assistant has been redesigned and upgraded to help you craft more precise queries. It now includes five operator options: E...

ChEMBL webinar @ School of Chemoinformatics in Latin America

Recently, the ChEMBL team participated in the " School of Chemoinformatics in Latin America " which was kindly organized by José Medina-Franco and Karina Martinez-Mayorga (both at the National Autonomous University of Mexico). The event was very well attended with 1,181 registrants from 79 different countries. 57% of the participants attended from Latin America, 23% from Asia, and around 8% from Africa and Europe, respectively. 52% of the participants were students (undergraduate and graduate students). Distribution by country Distribution by role Participants could learn a bou t the ChEMBL database and UniChem. We covered different topics to answer these questions: • What is ChEMBL and how is it structured ? • Which data does ChEMBL contain ? • How is data extracted from scientic articles ? • How is the data in ChEMBL curated ? • How is drug ...

Here's a nice Christmas gift - ChEMBL 35 is out!

Use your well-deserved Christmas holidays to spend time with your loved ones and explore the new release of ChEMBL 35! This fresh release comes with a wealth of new data sets and some new data sources as well. Examples include a total of 14 datasets deposited by by the ASAP ( AI-driven Structure-enabled Antiviral Platform) project, a new NTD data se t by Aberystwyth University on anti-schistosome activity, nine new chemical probe data sets, and seven new data sets for the Chemogenomic library of the EUbOPEN project. We also inlcuded a few new fields that do impr ove the provenance and FAIRness of the data we host in ChEMBL: 1) A CONTACT field has been added to the DOCs table which should contain a contact profile of someone willing to be contacted about details of the dataset (ideally an ORCID ID; up to 3 contacts can be provided). 2) In an effort to provide more detailed information about the source of a deposited dat...

Improvements in SureChEMBL's chemistry search and adoption of RDKit

Dear SureChEMBL users, If you frequently rely on our "chemistry search" feature, today brings great news! We’ve recently implemented a major update that makes your search experience faster than ever. What's New? Last week, we upgraded our structure search engine by aligning it with the core code base used in ChEMBL . This update allows SureChEMBL to leverage our FPSim2 Python package , returning results in approximately one second. The similarity search relies on 256-bit RDKit -calculated ECFP4 fingerprints, and a single instance requires approximately 1 GB of RAM to run. SureChEMBL’s FPSim2 file is not currently available for download, but we are considering generating it periodicaly and have created it once for you to try in Google Colab ! For substructure searches, we now also use an RDKit -based solution via SubstructLibrary , which returns results several times faster than our previous implementation. Additionally, structure search results are now sorted by...

The ChEMBL-og

Search This Blog