Skip to main content

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

you already the legend, how far you can get )

Popular posts from this blog

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 ChEMBL d

ChEMBL 29 Released

  We are pleased to announce the release of ChEMBL 29. This version of the database, prepared on 01/07/2021 contains: 2,703,543 compound records 2,105,464 compounds (of which 2,084,724 have mol files) 18,635,916 activities 1,383,553 assays 14,554 targets 81,544 documents Data can be downloaded from the ChEMBL FTP site:   https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29 .  Please see ChEMBL_29 release notes for full details of all changes in this release: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29/chembl_29_release_notes.txt New Deposited Datasets EUbOPEN Chemogenomic Library (src_id = 55, ChEMBL Document IDs CHEMBL4649982-CHEMBL4649998): The EUbOPEN consortium is an Innovative Medicines Initiative (IMI) funded project to enable and unlock biology in the open. The aims of the project are to assemble an open access chemogenomic library comprising about 5,000 well annotated compounds covering roughly 1,000 different proteins, to synthesiz

Identifying relevant compounds in patents

  As you may know, patents can be inherently noisy documents which can make it challenging to extract drug discovery information from them, such as the key targets or compounds being claimed. There are many reasons for this, ranging from deliberate obfuscation through to the long and detailed nature of the documents. For example, a typical small molecule patent may contain extensive background information relating to the target biology and disease area, chemical synthesis information, biological assay protocols and pharmacological measurements (which may refer to endogenous substances, existing therapies, reaction intermediates, reagents and reference compounds), in addition to description of the claimed compounds themselves.  The SureChEMBL system extracts this chemical information from patent documents through recognition of chemical names, conversion of images and extraction of attached files, and allows patents to be searched for chemical structures of interest. However, the curren

Julia meets RDKit

Julia is a young programming language that is getting some traction in the scientific community. It is a dynamically typed, memory safe and high performance JIT compiled language that was designed to replace languages such as Matlab, R and Python. We've been keeping an an eye on it for a while but we were missing something... yes, RDKit! Fortunately, Greg very recently added the MinimalLib CFFI interface to the RDKit repertoire. This is nothing else than a C API that makes it very easy to call RDKit from almost any programming language. More information about the MinimalLib is available directly from the source . The existence of this MinimalLib CFFI interface meant that we no longer had an excuse to not give it a go! First, we added a BinaryBuilder recipe for building RDKit's MinimalLib into Julia's Yggdrasil repository (thanks Mosè for reviewing!). The recipe builds and automatically uploads the library to Julia's general package registry. The build currently targe

New Drug Warnings Browser

As mentioned in the announcement post of  ChEMBL 29 , a new Drug Warnings Browser has been created. This is an updated version of the entity browsers in ChEMBL ( Compounds , Targets , Activities , etc). It contains new features that will be tried out with the Drug Warnings and will be applied to the other entities gradually. The new features of the Drug Warnings Browser are described below. More visible buttons to link to other entities This functionality is already available in the old entity browsers, but the button to use it is not easily recognised. In the new version, the buttons are more visible. By using those buttons, users can see the related activities, compounds, drugs, mechanisms of action and drug indications to the drug warnings selected. The page will take users to the corresponding entity browser with the items related to the ones selected, or to all the items in the dataset if the user didn’t select any. Additionally, the process of creating the join query is no