Skip to main content

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 synthesize at least 100 high-quality, open-access chemical probes and to develop infrastructure, technologies and platforms. Screening data generated during this 5 year project will be deposited in ChEMBL. An initial data set of 16 probes/chemogenomic compounds targeting bromodomain proteins has been included in ChEMBL_29.

Donated Chemical Probes - SGC Frankfurt (src_id = 54, ChEMBL Document IDs CHEMBL4630901-CHEMBL4630909):
Data for 9 new chemical probes has been added, along with additional data for some existing probes.

Gates Library compound collection (src_id = 33, ChEMBL Document ID = CHEMBL3988442):
Data for an additional 33 assays screening the Gates Library/GHCDL (68K compounds) has been deposited by the University of Dundee. This includes screening data against a number of pathogenic organisms such as Mycobacterium tuberculosis, Leishmania infantum, Plasmodium falciparum, Schistosoma mansoni and Trypanosoma cruzi

Curated Data Sets

Drug mechanism of action information has been curated for more than 700 additional drugs and clinical candidates in this release.

Updated Data Sources

Scientific Literature
Donated Chemical Probes - SGC Frankfurt
Gates Library compound collection
USP Dictionary of USAN and International Drug Names
Clinical Candidates
WHO Anatomical Therapeutic Chemical Classification
Orange Book
Manually Added Drugs
Prodrug active ingredients

Database Changes

Columns Added:
CHEMBL_ID_LOOKUP
Column_name     Data_type     Comment
LAST_ACTIVE     NUMBER(3,0) Indicates the last ChEMBL version where the CHEMBL_ID was active

Web Interface

Drug Warning Browser:
A new Drug Warnings browser has been created (https://www.ebi.ac.uk/chembl/g/#browse/drug_warnings). This allows warning information (black box warnings and drug withdrawals) to be displayed and filtered across all drugs. It can also be accessed from the bubble chart on the home page, or from individual drug pages that have warning information. This browser also incorporates several new features that will be rolled out across other ChEMBL pages in due course, such as improved basic filtering capabilities (allowing text or range filters, depending on filter type) and custom filtering (allowing the user to more easily create sophisticated filters using Elastic search syntax).



Downgraded ChEMBL IDs:
In addition to the changes announced previously (see https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_28/chembl_28_release_notes.txt) regarding resolving of downgraded or deleted ChEMBL entries, an extra field showing the version of ChEMBL in which the entity was last active has now been added. Old versions of ChEMBL can be retrieved from our FTP site, if required.

Downloads

We are no longer be able to provide Oracle 10g/11g/12c dumps. In addition to the usual PostgreSQL/MySQL/SQLite dumps, an Oracle 19c data pump dump is available on request. Please contact us at chembl-help@ebi.ac.uk if you require this.

Funding acknowledgements:

Work contributing to ChEMBL29 was funded by the Wellcome Trust, EMBL Member States, Open Targets, National Institutes of Health (NIH), EU Innovative Medicines Initiative 2 (IMI2) and EU Horizon 2020 programmes. Please see https://chembl.gitbook.io/chembl-interface-documentation/acknowledgments for more details.

If you require further information about ChEMBL, please contact us: chembl-help@ebi.ac.uk

# To receive updates when new versions of ChEMBL are available, please sign up to our mailing list: http://listserver.ebi.ac.uk/mailman/listinfo/chembl-announce
# For general queries/feedback or to report any problems with data, please email: chembl-help@ebi.ac.uk


Comments

Popular posts from this blog

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

ChEMBL brings drug bioactivity data to the Protein Data Bank in Europe

In the quest to develop new drugs, understanding the 3D structure of molecules is crucial. Resources like the Protein Data Bank in Europe (PDBe) and the Cambridge Structural Database (CSD) provide these 3D blueprints for many biological molecules. However, researchers also need to know how these molecules interact with their biological target – their bioactivity. ChEMBL is a treasure trove of bioactivity data for countless drug-like molecules. It tells us how strongly a molecule binds to a target, how it affects a biological process, and even how it might be metabolized. But here's the catch: while ChEMBL provides extensive information on a molecule's activity and cross references to other data sources, it doesn't always tell us if a 3D structure is available for a specific drug-target complex. This can be a roadblock for researchers who need that structural information to design effective drugs. Therefore, connecting ChEMBL data with resources like PDBe and CSD is essen

Improved querying for SureChEMBL

    Dear SureChEMBL users, Earlier this year we ran a survey to identify what you, the users, would like to see next in SureChEMBL. Thank you for offering your feedback! This gave us the opportunity to have some interesting discussions both internally and externally. While we can't publicly reveal precisely our plans for the coming months (everything will be delivered at the right time), we can at least say that improving the compound structure extraction quality is a priority. Unfortunately, the change won't happen overnight as reprocessing 167 millions patents takes a while. However, the good news is that the new generation of optical chemical structure recognition shows good performance, even for patent images! We hope we can share our results with you soon. So in the meantime, what are we doing? You may have noticed a few changes on the SureChEMBL main page. No more "Beta" flag since we consider the system to be stable enough (it does not mean that you will never

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 vaccines). 71 out of the 882 newly added EMA drugs are only authorised by EMA, rather than from other regulatory bodies e.g.

New SureChEMBL announcement

(Generated with DALL-E 3 ∙ 30 October 2023 at 1:48 pm) We have some very exciting news to report: the new SureChEMBL is now available! Hooray! What is SureChEMBL, you may ask. Good question! In our portfolio of chemical biology services, alongside our established database of bioactivity data for drug-like molecules ChEMBL , our dictionary of annotated small molecule entities ChEBI , and our compound cross-referencing system UniChem , we also deliver a database of annotated patents! Almost 10 years ago , EMBL-EBI acquired the SureChem system of chemically annotated patents and made this freely accessible in the public domain as SureChEMBL. Since then, our team has continued to maintain and deliver SureChEMBL. However, this has become increasingly challenging due to the complexities of the underlying codebase. We were awarded a Wellcome Trust grant in 2021 to completely overhaul SureChEMBL, with a new UI, backend infrastructure, and new f