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ChEMBL 28 Released!

 We are pleased to announce the release of ChEMBL_28. This version of the database, prepared on 15/01/2021 contains:

* 2,680,904 compound records
* 2,086,898 compounds (of which 2,066,376 have mol files)
* 17,276,334 activities
* 1,358,549 assays
* 14,347 targets
* 80,480 documents

Data can be downloaded from the ChEMBL FTP site:  https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_28.

Please see ChEMBL_26 release notes for full details of all changes in this release: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_28/chembl_28_release_notes.txt

DATA CHANGES SINCE THE LAST RELEASE

This release includes several new deposited data sets:

Donated Chemical Probes data from SGC Frankfurt (src_id = 54)
SARS-CoV-2 screening data from the Fraunhofer Institute (src_id = 52)
Antimicrobial screening data sets from CO-ADD (src_id = 40)
Plasmodium screening data from the UCSD Winzeler lab (src_id = 51)
MMV pathogen box screening data (src_id = 34)

Curated data sets:

Drug safety warning information:
Safety-related information for approved drugs has been curated to include the assignment of toxicity classes (e.g., Cardiotoxicity, Hepatotoxicity Teratogenicity etc), based on their withdrawn status and/or black box warning information described on medicinal product labels. Two new tables have been included in ChEMBL to hold this information: DRUG_WARNING and WARNING_REFS and a new web service endpoint is also available: https://www.ebi.ac.uk/chembl/api/data/drug_warning. For more information about this data set and the methods used, please see: https://doi.org/10.1021/acs.chemrestox.0c00296
This information can be seen on the Compound Report Card for the relevant drugs e.g., https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL118/


Metabolism Pathways:
Further metabolic pathways have been curated from the Journal of Drug Metabolism and Disposition and are included in the METABOLISM table. This dataset comprises more than 900 additional reactions in pathways for 98 distinct drugs/compounds. Where available, this information is displayed on the Compound Report Card e.g., https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1370/



Prodrug active ingredients (src_id = 53):
Compound records have now been included for active ingredients that are formed through metabolic activation of prodrugs. These active ingredients have also been updated in the molecule_hierarchy (as the ACTIVE_MOLREGNO) to link them to the corresponding prodrug (PARENT_MOLREGNO).

The following data sources have also been updated:

Scientific Literature, Patent Bioactivity Data, USP Dictionary of USAN and International Drug Names, Clinical Candidates, WHO Anatomical Therapeutic Chemical Classification, Orange Book, Manually Added Drugs

OTHER CHANGES TO THE WEB INTERFACE:

  • Advanced search with a list of molecule or target ChEMBL IDs is now available (see separate blog post for more details):
  • Assay parameters and activity properties included on Browse Activities view (these columns are hidden initially and need to be added with the 'Show/hide columns' button). Since there can be multiple parameters/properties for an assay/activity, these columns show a concatenated list.
  • Variant sequences information included on Assay Report Card and Browse Activities view e.g., https://www.ebi.ac.uk/chembl/assay_report_card/CHEMBL1937980/
  • Obsolete or downgraded ChEMBL IDs now resolve to a message page that indicates the status of each entity. For example, https://www.ebi.ac.uk/chembl/id_lookup/CHEMBL101033  indicates that the compound has been permanently removed from the database and https://www.ebi.ac.uk/chembl/id_lookup/CHEMBL102436 indicates that the compound is currently downgraded in ChEMBL_28. If a user is not sure what type of entity a given ChEMBL ID corresponds to, they can now use a single URL with any type of ChEMBL ID (compound/target/assay/document/cell/tissue) and it will resolve to the correct Report Card page e.g., https://www.ebi.ac.uk/chembl/entity/CHEMBL25 or https://www.ebi.ac.uk/chembl/entity/CHEMBL2971. Furthermore, if the wrong report card URL is used for a valid ChEMBL ID, it will be redirected to the correct Report Card page (e.g., https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL25/ will redirect to https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL25/, since CHEMBL25 is a compound).

DATABASE CHANGES SINCE THE LAST RELEASE

Columns Added:

DRUG_MECHANISM
COLUMN_NAME DATA_TYPE COMMENT
VARIANT_ID NUMBER(9,0) Foreign key to VARIANT_SEQUENCES table, indicating that the drug targets a specific variant form of the protein.

Columns Removed:

MOLECULE_DICTIONARY
The following columns are deprecated (replaced by the new tables below) and will be removed in a future release:
WITHDRAWN_YEAR
WITHDRAWN_COUNTRY
WITHDRAWN_REASON
WITHDRAWN_CLASS

Tables Added:

DRUG_WARNING
COLUMN_NAME DATA_TYPE COMMENT
WARNING_ID NUMBER(9,0 Primary key for the drug warning
RECORD_ID NUMBER(9,0) Foreign key to the compound_records table
MOLREGNO NUMBER(9,0) Foreign key to molecule_dictionary table
WARNING_TYPE VARCHAR2(20 BYTE) Description of the drug warning type (e.g., withdrawn vs black box warning)
WARNING_CLASS VARCHAR2(100 BYTE) High-level class of the drug warning
WARNING_DESCRIPTION VARCHAR2(4000 BYTE) Description of the drug warning
WARNING_COUNTRY VARCHAR2(1000 BYTE) List of countries/regions associated with the drug warning
WARNING_YEAR NUMBER(4,0) Year the drug was first shown the warning

WARNING_REFS
COLUMN_NAME DATA_TYPE COMMENT
WARNREF_ID NUMBER(9,0) Primary key for the warning reference
WARNING_ID NUMBER(9,0) Foreign key to the drug_warning table
REF_TYPE VARCHAR2(50 BYTE) Type/source of reference
REF_ID VARCHAR2(4000 BYTE) Identifier for the reference in the source
REF_URL VARCHAR2(4000 BYTE) Full URL linking to the reference

CHANGES TO WEB SERVICES AND DOWNLOADS

The following changes have been made to web services:
Assay, Activity and Mechanism endpoints now include variant sequence information

Download formats:
Please note, from ChEMBL_29 onward, we will no longer be able to provide Oracle 10g/11g/12c dumps. Only Oracle 19c dumps will be provided (in addition to the usual PostgreSQL/MySQL/SQLite dumps).

Funding acknowledgements:

Work contributing to ChEMBL28 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
# For details of upcoming webinars, please see: http://chembl.blogspot.com/search/label/Webinar

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