ChEMBL Resources

Resources:
ChEMBL
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SureChEMBL
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ChEMBL-NTD
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ChEMBL-Malaria
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The SARfaris: GPCR, Kinase, ADME
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UniChem
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DrugEBIlity
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ECBD

Thursday, 29 September 2016

ChEMBL 22 Released


We are pleased to announce the release of ChEMBL 22. This version of the database, prepared on 8th August 2016 contains:

  • 2,043,051 compound records
  • 1,686,695 compounds (of which 1,678,393 have mol files)
  • 14,371,219 activities
  • 1,246,132 assays
  • 11,224 targets
  • 65,213 documents

Data can be downloaded from the ChEMBL ftpsite or viewed via the ChEMBL interface. Please see ChEMBL_22 release notes for full details of all changes in this release.

CHANGES SINCE THE LAST RELEASE

In addition to the regular updates to the Scientific Literature, PubChem, FDA Orange Book and USP Dictionary of USAN and INN Investigational Drug Names this release of ChEMBL also includes the following new data:

Deposited Data Sets:

Two new deposited data sets have been included in ChEMBL_22: the MMV Pathogen Box compound set (http://www.pathogenbox.org) and GSK Tres Cantos Follow-up TB Screening Data (http://dx.doi.org/10.1371/journal.pone.0142293).

Patent Data from BindingDB:

We have worked with the BindingDB team to integrate the bioactivity data that they have extracted from more than 1000 granted US patents published from 2013 onwards (https://www.bindingdb.org/bind/ByPatent.jsp) into ChEMBL. This data is incorporated into ChEMBL in the same way as literature-extracted bioactivity information, but with a new source (SRC_ID = 37, BindingDB Database) and a document type of 'PATENT'. In total this data set provides 99K bioactivity measurements for 68K compounds.

Withdrawn Drugs:

We have compiled a list of drugs that have been withdrawn in one or more countries due to safety or efficacy issues from multiple sources. Where available, the year of withdrawal, the applicable countries/areas and the reasons for the withdrawal are captured. Withdrawal information is shown on the Compound Report Card and a new icon has been added to the availability type section of the  Molecule Features image to denote drugs that have been withdrawn (e.g., https://www.ebi.ac.uk/chembl/compound/inspect/CHEMBL408).


Tissue Annotation:

We have identified tissues used in assays (e.g., tissues in which measurements were made after in-vivo dosing, isolated tissues on which assays were performed, or tissues from which sub-cellular fractions were prepared) using the Uberon ontology (http://uberon.github.io). A TISSUE_DICTIONARY table has been created, which stores a list of the identified tissues, their corresponding ChEMBL_IDs, names and Uberon IDs. Mappings are also provided to the Experimental Factor Ontology (http://www.ebi.ac.uk/ols/ontologies/efo), Brenda Tissue Ontology (http://www.ebi.ac.uk/ols/ontologies/bto) and CALOHA Ontology (ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo). Tissue Report Cards have been created (e.g., https://www.ebi.ac.uk/chembl/tissue/inspect/CHEMBL3638244), providing a mechanism to view all of the assay data associated with a particular tissue. The keyword search now also allows searching by tissue name, Uberon ID, EFO ID, Brenda Tissue ID or CALOHA tissue ID.



Indications for Clinical Candidates:

Indication information has now been extended to cover clinical candidates. This information has been extracted from ClinicalTrials.gov and is included in the 'Browse Drug Indications' view and on Compound Report Cards.

Drug Metabolism Viewer:

An additional section has been added to Compound Report Cards to display drug metabolism schemes (e.g., https://www.ebi.ac.uk/chembl/compound/inspect/CHEMBL1064). These schemes can be opened in an expanded view by clicking the link above the image. Where known, enzyme information is shown on edges and clicking on an edge of interest will provide additional information about the reaction, including references. Clicking on the nodes allows linking to Compound Report Cards for the metabolites.


Variant Sequences:

For cases where assay data has been measured against a variant protein (e.g., site-directed mutagenesis or drug-resistance studies) we have created a VARIANT_SEQUENCES table to store the variant protein sequence used in the assay (the target for the assay will still be the wild-type protein). Since the exact protein sequence used in an assay is rarely reported in the medicinal chemistry literature, these sequences have been re-created by introducing the specified point mutation into the current UniProt sequence for the target. The resulting sequence is not therefore guaranteed to be the exact sequence used in the assay but provides a more robust way to document the relevant mutation(s) than the current use of residue name and position in most publications and ChEMBL assay descriptions (which quickly becomes obsolete when sequences change). In cases where the reported residue positions could not be reconciled with any UniProt sequence, variant sequence information has not been included in ChEMBL. Further sequences (requiring more curation) will be added in future releases. Assays with variant sequence information available are linked to the VARIANT_SEQUENCES table via the VARIANT_ID column. Please note, this information is not yet displayed on the ChEMBL interface.

We recommend you review the ChEMBL_22 release notes for a comprehensive overview of all updates and changes in ChEMBL 22, including schema changes, and as always, we greatly appreciate the reporting of any omissions or errors.

Keep an eye on the ChEMBL twitter and blog accounts for news and updates.

The ChEMBL Team

Monday, 19 September 2016

ChEMBL_22 is coming soon....

ChEMBL_22 will be released in the next week or two. For those of you who want to plan ahead, here is a preview of the new schema (full documentation here)

We would also like to inform users that we plan to discontinue the Oracle 9i download format after this release. Please contact us as soon as possible if you rely on this version.