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ChEMBL 25 and new web interface released

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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

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