What's Going On?

I’ve been asked a lot by mail recently ‘What’s Going On?’ Well, here is are some facts and some emotion.

So today is my last day at work here at EMBL-EBI. It’s been a fun and thrilling ride (for me at least), I’ve made lots of new friends, living life as an Open Data advocate and academic researcher, and most importantly having the privilege to lead the team here responsible for the ChEMBL database. It had been a long-term goal of mine to unlock large-scale bioactivity data from proprietary data silos and eye-wateringly expensive paywalls; so as US President George Bush famously said ‘Mission Accomplished!’. The impact of ChEMBL on academia, SMEs and large pharma has been great - and you can see the impact in new method development, but more importantly in potential new future drugs. My personal indebtedness to the Wellcome Trust for their support is immeasurable. An additional big shout out to Digital Science for their vision in donating the SureChEMBL platform to us.

I’ll be starting a new blog, covering my next adventure - artificial intelligence-enhanced drug discovery. I’ll tweet when this is up and running, but the first few weeks at a new job, as I’m sure you know, is spent sorting out pencils, working out where the best coffee is hidden and most importantly navigating the office politics of the milk in the fridge. When this blog starts up, I’ll tweet the url. For those of you interested in the ChEMBL groups activities, make sure you follow @ChEMBL and @SureChEMBL. If you want to see what I'm up to next, it's at @StratMed.

If any of you are ever in the West End of London (which to non-native Londoners actually means the centre) get in touch with me, and I’ll try to treat you to an orange mocha frappuccino.

Now for the bit you all actually care about….

Anne Hersey is taking over the ChEMBL Wellcome Trust Strategic Award grant for ChEMBL (which also covers SureChEMBL). Many of you will know Anne already, and know just what good news this is. Anne is also taking over the majority of our other grants and activities of the group, including our participation in IMI eTox, NIH IDG KMC, & GSK CTTV grants.
Jo McEntyre will be PI for EMBL-EBI on the IMI OpenPHACTS grant, although the majority of the work will be done by ChEMBL group staff. If you don’t know about the Open PHACTS platform, check out what they have done!
Ugis Sarkans will become PI for EMBL-EBI on the FP7 HeCaTos grant. The data content and modelling components will be done by ChEMBL group staff.

If you have general questions about ChEMBL or SureChEMBL first try the support email addresses chembl-help@ebi.ac.uk and surechembl-help@ebi.ac.uk.

Comments

Vladimir Chupakhin said…

you already the legend, how far you can get )

17 May 2015 at 18:37

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...

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...

A python client for accessing ChEMBL web services

Motivation The CheMBL Web Services provide simple reliable programmatic access to the data stored in ChEMBL database. RESTful API approaches are quite easy to master in most languages but still require writing a few lines of code. Additionally, it can be a challenging task to write a nontrivial application using REST without any examples. These factors were the motivation for us to write a small client library for accessing web services from Python. Why Python? We choose this language because Python has become extremely popular (and still growing in use) in scientific applications; there are several Open Source chemical toolkits available in this language, and so the wealth of ChEMBL resources and functionality of those toolkits can be easily combined. Moreover, Python is a very web-friendly language and we wanted to show how easy complex resource acquisition can be expressed in Python. Reinventing the wheel? There are already some libraries providing access to ChEM...

The ChEMBL-og

Search This Blog