Skip to main content

ChEMBL_23 released


We are pleased to announce the release of ChEMBL_23. This release was prepared on 1st May 2017 and contains:

* 2,101,843 compound records
* 1,735,442 compounds (of which 1,727,112 have mol files)
* 14,675,320 activities
* 1,302,147 assays
* 11,538 targets
* 67,722 source documents

Data can be downloaded from the ChEMBL ftp site: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_23

Please see ChEMBL_23 release notes for full details of all changes in this release: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_23/chembl_23_release_notes.txt


DATA CHANGES SINCE THE LAST RELEASE

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

Patent Bioactivity Data
With funding from the NIH Illuminating the Druggable Genome project (https://commonfund.nih.gov/idg), we have extracted bioactivity data relating to understudied druggable targets from a number of patent documents and added this data to ChEMBL.  

Curated Drug Pharmacokinetic Data
We have manually extracted pharmacokinetic parameters for approved drugs from DailyMed drug labels. 

Drug information from British National Formulary and ATC classification
We have now included compound records for drugs that are in the WHO ATC classification or the British National Formulary (BNF). Currently only BNF drugs that already exist in ChEMBL have been assigned compound records. In future releases we will add new BNF drugs to ChEMBL.

Deposited Data Sets
CO-ADD, The Community for Open Antimicrobial Drug Discovery (http://www.co-add.org), is a global open-access screening initiative launched in February 2015 to uncover significant and rich chemical diversity held outside of corporate screening collections. CO-ADD provides unencumbered free antimicrobial screening for any interested academic researcher.  CO-ADD has been recognised as a novel approach in the fight against superbugs by the Wellcome Trust, who have provided funding through their Strategic Awards initiative. Open Source Malaria (OSM) is aimed at finding new medicines for malaria using open source drug discovery, where all data and ideas are freely shared, there are no barriers to participation, and no restriction by patents. The initial set of deposited data from the CO-ADD project consists of OSM compounds screened in CO-ADD assays (DOI = 10.6019/CHEMBL3832881).

Modelled on the Malaria Box, the MMV Pathogen Box contains 400 diverse, drug-like molecules active against neglected diseases of interest and is available free of charge (http://www.pathogenbox.org). The Pathogen Box compounds are supplied in 96-well plates, containing 10​uL of a 10mM dimethyl sulfoxide (DMSO) solution of each compound. Upon request, researchers around the world will receive a Pathogen Box of molecules to help catalyse neglected disease drug discovery. In return, researchers are asked to share any data generated in the public domain within 2 years, creating an open and collaborative forum for neglected diseases drug research. The initial set of assay data provided by MMV has now been included in ChEMBL (DOI = 10.6019/CHEMBL3832761).


FORTHCOMING CHANGES

Schema changes will be made in ChEMBL_24 to accommodate more complex data types. Details of these changes will be released soon. Please follow the ChEMBL blog or sign up to the ChEMBL announce mailing list for details (http://listserver.ebi.ac.uk/mailman/listinfo/chembl-announce)

Changes will also be made in ChEMBL_24 to the way some of the physicochemical properties are calculated. Details of these changes will be announced soon.


Funding acknowledgements:

Work contributing to ChEMBL_23 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


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 please email: chembl-help@ebi.ac.uk
# To report any problems with data content please email: chembl-data@ebi.ac.uk
# For details of upcoming webinars, please see: http://chembl.blogspot.com/search/label/Webinar

Comments

Popular posts from this blog

A python client for accessing ChEMBL web services

Motivation The CheMBL Web Services provide simple reliable programmatic access to the data stored in ChEMBL database. RESTful API approaches are quite easy to master in most languages but still require writing a few lines of code. Additionally, it can be a challenging task to write a nontrivial application using REST without any examples. These factors were the motivation for us to write a small client library for accessing web services from Python. Why Python? We choose this language because Python has become extremely popular (and still growing in use) in scientific applications; there are several Open Source chemical toolkits available in this language, and so the wealth of ChEMBL resources and functionality of those toolkits can be easily combined. Moreover, Python is a very web-friendly language and we wanted to show how easy complex resource acquisition can be expressed in Python. Reinventing the wheel? There are already some libraries providing access to ChEMBL d

ChEMBL 29 Released

  We are pleased to announce the release of ChEMBL 29. This version of the database, prepared on 01/07/2021 contains: 2,703,543 compound records 2,105,464 compounds (of which 2,084,724 have mol files) 18,635,916 activities 1,383,553 assays 14,554 targets 81,544 documents Data can be downloaded from the ChEMBL FTP site:   https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29 .  Please see ChEMBL_29 release notes for full details of all changes in this release: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29/chembl_29_release_notes.txt New Deposited Datasets EUbOPEN Chemogenomic Library (src_id = 55, ChEMBL Document IDs CHEMBL4649982-CHEMBL4649998): The EUbOPEN consortium is an Innovative Medicines Initiative (IMI) funded project to enable and unlock biology in the open. The aims of the project are to assemble an open access chemogenomic library comprising about 5,000 well annotated compounds covering roughly 1,000 different proteins, to synthesiz

Julia meets RDKit

Julia is a young programming language that is getting some traction in the scientific community. It is a dynamically typed, memory safe and high performance JIT compiled language that was designed to replace languages such as Matlab, R and Python. We've been keeping an an eye on it for a while but we were missing something... yes, RDKit! Fortunately, Greg very recently added the MinimalLib CFFI interface to the RDKit repertoire. This is nothing else than a C API that makes it very easy to call RDKit from almost any programming language. More information about the MinimalLib is available directly from the source . The existence of this MinimalLib CFFI interface meant that we no longer had an excuse to not give it a go! First, we added a BinaryBuilder recipe for building RDKit's MinimalLib into Julia's Yggdrasil repository (thanks Mosè for reviewing!). The recipe builds and automatically uploads the library to Julia's general package registry. The build currently targe

Identifying relevant compounds in patents

  As you may know, patents can be inherently noisy documents which can make it challenging to extract drug discovery information from them, such as the key targets or compounds being claimed. There are many reasons for this, ranging from deliberate obfuscation through to the long and detailed nature of the documents. For example, a typical small molecule patent may contain extensive background information relating to the target biology and disease area, chemical synthesis information, biological assay protocols and pharmacological measurements (which may refer to endogenous substances, existing therapies, reaction intermediates, reagents and reference compounds), in addition to description of the claimed compounds themselves.  The SureChEMBL system extracts this chemical information from patent documents through recognition of chemical names, conversion of images and extraction of attached files, and allows patents to be searched for chemical structures of interest. However, the curren

New Drug Warnings Browser

As mentioned in the announcement post of  ChEMBL 29 , a new Drug Warnings Browser has been created. This is an updated version of the entity browsers in ChEMBL ( Compounds , Targets , Activities , etc). It contains new features that will be tried out with the Drug Warnings and will be applied to the other entities gradually. The new features of the Drug Warnings Browser are described below. More visible buttons to link to other entities This functionality is already available in the old entity browsers, but the button to use it is not easily recognised. In the new version, the buttons are more visible. By using those buttons, users can see the related activities, compounds, drugs, mechanisms of action and drug indications to the drug warnings selected. The page will take users to the corresponding entity browser with the items related to the ones selected, or to all the items in the dataset if the user didn’t select any. Additionally, the process of creating the join query is no