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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


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