Skip to main content

ChEMBL 29 Released

By

 


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

Post a Comment

Popular posts from this blog

ChEMBL 34 is out!

By
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.
Post a Comment
Read more

New SureChEMBL announcement

By
(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
Post a Comment
Read more

Accessing SureChEMBL data in bulk

By
It is the peak of the summer (at least in this hemisphere) and many of our readers/users will be on holiday, perhaps on an island enjoying the sea. Luckily, for the rest of us there is still the 'sea' of SureChEMBL data that awaits to be enjoyed and explored for hidden 'treasures' (let me know if I pushed this analogy too far). See here and  here for a reminder of SureChEMBL is and what it does.  This wealth of (big) data can be accessed via the SureChEMBL interface , where users can submit quite sophisticated and granular queries by combining: i) Lucene fields against full-text and bibliographic metadata and ii) advanced structure query features against the annotated compound corpus. Examples of such queries will be the topic of a future post. Once the search results are back, users can browse through and export the chemistry from the patent(s) of interest. In addition to this functionality, we've been receiving user requests for  local (behind the
Post a Comment
Read more

A python client for accessing ChEMBL web services

By
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
1 comment
Read more

New Drug Approvals - Pt. XVII - Telavancin (Vibativ)

By jpo
The latest new drug approval, on 11th September 2009 was Telavancin - which was approved for the treatment of adults with complicated skin and skin structure infections (cSSSI) caused by susceptible Gram-positive bacteria , including Staphylococcus aureus , both methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) strains. Telavancin is also active against Streptococcus pyogenes , Streptococcus agalactiae , Streptococcus anginosus group (includes S. anginosus, S. intermedius and S. constellatus ) and Enterococcus faecalis (vancomycin susceptible isolates only). Telavancin is a semisynthetic derivative of Vancomycin. Vancomycin itself is a natural product drug, isolated originally from soil samples in Borneo, and is produced by controlled fermentation of Amycolatopsis orientalis - a member of the Actinobacteria . Telavancin has a dual mechanism of action, firstly it inhibits bacterial cell wall synthesis by interfering with the polymerization and cross-linking of peptid
Post a Comment
Read more