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Thursday, 28 March 2019

ChEMBL 25 and new web interface released

We are pleased to announce the release of ChEMBL 25 and our new web interface. This version of the database, prepared on 10/12/2018 contains:

  • 2,335,417 compound records
  • 1,879,206 compounds (of which 1,870,461 have mol files)
  • 15,504,603 activities
  • 1,125,387 assays
  • 12,482 targets
  • 72,271 documents


Data can be downloaded from the ChEMBL ftp site: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_25

Please see ChEMBL_25 release notes for full details of all changes in this release: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_25/chembl_25_release_notes.txt


DATA CHANGES SINCE THE LAST RELEASE

# Deposited Data Sets:

Kuster Lab Chemical Proteomics Drug Profiling (src_id = 48, Document ChEMBL_ID = CHEMBL3991601):
Data have been included from the publication: The target landscape of clinical kinase drugs. Klaeger S, Heinzlmeir S and Wilhelm M et al (2017), Science, 358-6367 (https://doi.org/10.1126/science.aan4368)

# In Vivo Assay Classification:

A classification scheme has been created for in vivo assays. This is stored in the ASSAY_CLASSIFICATION table in the database schema and consists of a three-level classification. Level 1 corresponds to the top-levels of the ATC classification i.e., anatomical system/therapeutic area (e.g., CARDIOVASCULAR SYSTEM, MUSCULO-SKELETAL SYSTEM, NERVOUS SYSTEM). Level 2 provides a more fine-grained classification of the phenotype or biological process being studied (e.g., Learning and Memory, Anti-Obesity Activity, Gastric Function). Level three represents the specific in vivo assay being performed (e.g., Laser Induced Thrombosis, Hypoxia Tolerance Test in Rats, Paw Edema Test) and is assigned a specific ASSAY_CLASS_ID. Individual in vivo assays in the ChEMBL ASSAYS table are mapped to reference in-vivo assays in the ASSAY_CLASSIFICATION table via the ASSAY_CLASS_MAP table. More information about the classification scheme is available in the following publication: https://doi.org/10.1038/sdata.2018.230. The assay classification is available via web services and will be included in the ChEMBL web interface in the near future.

# Updated Data Sets:
Scientific Literature
Patent Bioactivity Data
BindingDB Database (corrections to compound structures)


WEB INTERFACE/WEB SERVICE CHANGES SINCE THE LAST RELEASE

# Web Interface:

The new ChEMBL web interface is now live at https://www.ebi.ac.uk/chembl (this replaces the previous beta version). The old ChEMBL web interface will be retired before the ChEMBL_26 release, but is available on the following URL until then: https://www.ebi.ac.uk/chembl/old. The new interface provides richer search and filtering capabilities. Documentation regarding this new functionality and frequently asked questions are available on our help pages: https://chembl.gitbook.io/chembl-interface-documentation/

# Changes to Web Services:

The Assay web service has been updated to include both assay_parameters and the in vivo assay classification for an assay (where applicable):
https://www.ebi.ac.uk/chembl/api/data/assay

A separate endpoint has also been created for the in vivo assay classification:
https://www.ebi.ac.uk/chembl/api/data/assay_class

The Activity web service has been updated to include activity_properties. The 'published_type', 'published_relation', 'published_value' and 'published_units' fields have also been renamed to 'type', 'relation', 'value' and 'units':
https://www.ebi.ac.uk/chembl/api/data/activity

A new endpoint has been created to retrieve supplementary data associated with an activity measurement (or list of measurements):
https://www.ebi.ac.uk/chembl/api/data/activity_supplementary_data_by_activity


SCHEMA CHANGES SINCE THE LAST RELEASE

# Tables Added:

ASSAY_CLASSIFICATION:
Classification scheme for phenotypic assays e.g., by therapeutic area, phenotype/process and assay type. Can be used to find standard assays for a particular disease area or phenotype e.g., anti-obesity assays. Currently data are available only for in vivo efficacy assays

COLUMN_NAME DATA_TYPE COMMENT
ASSAY_CLASS_ID NUMBER(9,0) Primary key
L1 VARCHAR2(100) High level classification e.g., by anatomical/therapeutic area
L2 VARCHAR2(100) Mid-level classification e.g., by phenotype/biological process
L3 VARCHAR2(1000) Fine-grained classification e.g., by assay type
CLASS_TYPE VARCHAR2(50) The type of assay being classified e.g., in vivo efficacy
SOURCE VARCHAR2(50) Source from which the assay class was obtained

ASSAY_CLASS_MAP:
Mapping table linking assays to classes in the ASSAY_CLASSIFICATION table

COLUMN_NAME DATA_TYPE COMMENT
ASS_CLS_MAP_ID NUMBER Primary key.
ASSAY_ID NUMBER assay_id is the foreign key that maps to the 'assays' table
ASSAY_CLASS_ID NUMBER assay_class_id is the foreign key that maps to the 'assay_classification' table


# Columns Removed:

ACTIVITIES:
PUBLISHED_TYPE (DEPRECATED in ChEMBL_24, now removed, replaced by TYPE)
PUBLISHED_RELATION (DEPRECATED in ChEMBL_24, now removed, replaced by RELATION)
PUBLISHED_VALUE (DEPRECATED in ChEMBL_24, now removed, replaced by VALUE)
PUBLISHED_UNITS (DEPRECATED in ChEMBL_24, now removed, replaced by UNITS)


Funding Acknowledgements:
Work contributing to ChEMBL_25 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.

The ChEMBL Team