Skip to main content

ChEMBL 24 Released!

By

We are pleased to announce the release of ChEMBL 24. This version of the database, prepared on 23/04/2018 contains:

    2,275,906 compound records
    1,828,820 compounds (of which 1,820,035 have mol files)
    15,207,914 activities
    1,060,283 assays
    12,091 targets
    69,861 documents

Data can be downloaded from the ChEMBL ftp site: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_24_1

Please see ChEMBL_24 release notes for full details of all changes in this release: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_24_1/chembl_24_1_release_notes.txt

Change in data model and addition of activity properties and supplementary data:

A new data submission format and database loader has been implemented. The new deposition system allows more advanced functionality, including the ability to update previously deposited data sets, and the ability to deposit activity data against existing ChEMBL compound or assay collections. This means that in future releases, it will be possible for the SRC_ID for data in the ACTIVITIES table to be different from the SRC_ID in the COMPOUND_RECORDS and/or ASSAYS tables to which the measurements relate.

We have now added an ACTIVITY_PROPERTIES table to the database, to allow parameters such as compound dose or time points to be captured for individual activity measurements. The table can also be used to record key experimental measurements that are important in interpreting the values reported in the ACTIVITIES table (e.g., HILL_SLOPE for a dose-response curve).

The ACTIVITY_SUPP table has also been introduced to allow supplementary data for an activity measurement to be captured. For example, for in vivo toxicology data, the ACTIVITIES table may capture summary level data across a group of animals, while the ACTIVITY_SUPP table contains individual animal-level data.

As a result of these improvements, this release contains some schema changes (including changes to the existing ASSAY_PARAMETERS table). A number of existing data sets have also been reformatted to take advantage of these new tables. Please see the release notes (ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_24/chembl_24_release_notes.txt) and recent blog post (http://chembl.blogspot.co.uk/2018/04/schema-changes-coming-in-chembl24.html) for more details.


Other features in the new release include:

Several new deposited data sets:
#  K4DD Project - K4DD drug target binding kinetics data (src_id = 30, DOI = 10.6019/CHEMBL3885741)
#  MMV Pathogen Box - The Australian National University Dept Of Immunology (src_id = 34, DOI = 10.6019/CHEMBL3987221)
#  Published Kinase Inhibitor Set 2 - Northwick Park Institute for Medical Research (src_id = 43)(10.6019/CHEMBL3988181)
#  University of Dundee, Gates Library - Leishmania donovani Methionine tRNA synthetase screening (src_id = 33, DOI = 10.6019/CHEMBL3988442)

Withdrawn Class information:
Withdrawn drugs in ChEMBL (src_id = 36) have been annotated with a controlled vocabulary to describe the reasons for their withdrawal.

Change of InChI version:
The version of Standard InChI used in ChEMBL has now been updated from 1.02 to 1.05.

Compound properties are now calculated with RDKit:
We are now using RDKit to calculate the following compound properties:
MW_FREEBASE, ALOGP, HBA, HBD, PSA, RTB, QED_WEIGHTED, FULL_MWT, AROMATIC_RINGS, HEAVY_ATOMS, MW_MONOISOTOPIC, FULL_MOLFORMULA, HBA_LIPINSKI, HBD_LIPINSKI. ACDLabs properties are unaffected.

Updated data sets:
A number of existing data sets have been updated including:
#  Scientific Literature (src_id = 1)
#  Clinical Candidates (src_id = 8)
#  FDA Orange Book (src_id = 9)
#  Open TG-GATEs (src_id = 11)
#  Manually Added Drugs (src_id = 12)
#  USP Dictionary of USAN and International Drug Names (src_id = 13)
#  DrugMatrix (src_id = 15)
#  BindingDB (src_id = 37)
#  Patent Bioactivity Data (src_id = 38)
#  Curated Drug Pharmacokinetic Data (src_id = 39)
#  WHO Anatomical Therapeutic Chemical Classification (src_id = 41)

Oracle exports:
Oracle 12c exports are now available for download (ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/chembl_24/chembl_24_oracle12c.tar.gz)


Retirement of old ChEMBL web services:
Please note, the legacy ChEMBL web services, hosted at: https://www.ebi.ac.uk/chembl//ws/home_old will not be updated to ChEMBL_23 and will be retired at the end of June. If you have not already done so, please switch to our current web services: https://www.ebi.ac.uk/chembl/ws


Funding acknowledgements:
Work contributing to ChEMBL_24 was funded by the Wellcome Trust, EMBL Member States, Open Targets, National Institutes of Health (NIH) Common Fund, EU Innovative Medicines Initiative (IMI) and EU Framework 7 programmes. Please see https://www.ebi.ac.uk/chembl/funding 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 current users of the ChEMBL web interface, chembl-announce and chembl-help mailing lists, please see our Privacy Policy/Terms of Use at:
https://www.ebi.ac.uk/data-protection/privacy-notice/chembl-announce-mailing-list
https://www.ebi.ac.uk/data-protection/privacy-notice/chembl-helpdesk
https://www.ebi.ac.uk/about/terms-of-use
https://www.ebi.ac.uk/data-protection/privacy-notice/embl-ebi-public-website


Comments

Post a Comment

Popular posts from this blog

Here's a nice Christmas gift - ChEMBL 35 is out!

By
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...
Post a Comment
Read more

Improvements in SureChEMBL's chemistry search and adoption of RDKit

By Eloy
    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...
Post a Comment
Read more

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 ...
Post a Comment
Read more

Improved querying for SureChEMBL

By
    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 ...
Post a Comment
Read more

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

By
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...
Post a Comment
Read more