ChEMBL
Encyclopedia
ChEMBL or ChEMBLdb is a manually curated chemical database
of bioactive molecules with drug-like properties.
It is maintained by the European Bioinformatics Institute
(EBI), based on the Wellcome Trust Genome Campus
, Hinxton, UK. The database, originally known as StARlite, was developed by a biotechnology company, Inpharmatica Ltd. latterly acquired by Galapagos NV
. The data was acquired for EMBL in 2008 with an award from The Wellcome Trust
, resulting in the creation of the ChEMBL chemogenomics
group at EBI, led by John Overington.
measurements covering 622,824 compounds, including 24,000 natural products. This was obtained from curating over 34,000 publications across twelve medicinal chemistry
journals. ChEMBL's coverage of available bioactivity data has grown to become "the most comprehensive ever seen in a public database.". In October 2010 ChEMBL version 8 (ChEMBL_08) was launched, with over 2.97 million bioassay measurements covering 636,269 compounds.
ChEMBL_10 saw the addition of the PubChem
confirmatory assays, in order to integrate data that is comparable to the type and class of data contained within ChEMBL.
ChEMBLdb can be accessed via a web interface or downloaded by File Transfer Protocol
. It is formated in a manner amenable to computerized data mining
, and attempts to standardize activities between different publications, to enable comparative analysis. ChEMBL is also integrated into other large-scale chemistry resources, including PubChem
and the ChemSpider
system of the Royal Society of Chemistry
.
. GPCR SARfari is a similar workbench focussed on GPCRs and ChEMBL-Neglected Tropical Diseases (ChEMBL-NTD) is a repository for Open Access primary screening and medicinal chemistry data directed at endemic tropical diseases of the developing regions of the Africa, Asia, and the Americas. The primary purpose of ChEMBL-NTD is to provide a freely accessible and permanent archive and distribution centre for deposited data.
Chemical database
A chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data.- Chemical structures :...
of bioactive molecules with drug-like properties.
It is maintained by the European Bioinformatics Institute
European Bioinformatics Institute
The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
(EBI), based on the Wellcome Trust Genome Campus
Wellcome Trust Genome Campus
The Wellcome Trust Genome Campus is a scientific research campus built in the grounds of Hinxton Hall, located in the village of Hinxton, Cambridgeshire....
, Hinxton, UK. The database, originally known as StARlite, was developed by a biotechnology company, Inpharmatica Ltd. latterly acquired by Galapagos NV
Galapagos NV
Galapagos is a mid-size biotechnology company specialized in the discovery and development of small molecule and antibody therapies with novel modes-of-action. The Company is progressing one of the largest pipelines in biotech, with seven clinical and over 50 small molecule discovery/pre-clinical...
. The data was acquired for EMBL in 2008 with an award from The Wellcome Trust
Wellcome Trust
The Wellcome Trust was established in 1936 as an independent charity funding research to improve human and animal health. With an endowment of around £13.9 billion, it is the United Kingdom's largest non-governmental source of funds for biomedical research...
, resulting in the creation of the ChEMBL chemogenomics
Chemogenomics
Chemogenomics is the study of genomic responses to chemical compounds. The goal is the rapid identification of novel drugs and drug targets, embracing multiple early phase drug discovery technologies ranging from target identification and validation, through compound design and chemical synthesis,...
group at EBI, led by John Overington.
Scope and access
ChEMBL version 2 (ChEMBL_02) was launched in January 2010, including 2.4 million bioassayBioassay
Bioassay , or biological standardization is a type of scientific experiment. Bioassays are typically conducted to measure the effects of a substance on a living organism and are essential in the development of new drugs and in monitoring environmental pollutants...
measurements covering 622,824 compounds, including 24,000 natural products. This was obtained from curating over 34,000 publications across twelve medicinal chemistry
Medicinal chemistry
Medicinal chemistry and pharmaceutical chemistry are disciplines at the intersection of chemistry, especially synthetic organic chemistry, and pharmacology and various other biological specialties, where it is involved with design, chemical synthesis and development for market of pharmaceutical...
journals. ChEMBL's coverage of available bioactivity data has grown to become "the most comprehensive ever seen in a public database.". In October 2010 ChEMBL version 8 (ChEMBL_08) was launched, with over 2.97 million bioassay measurements covering 636,269 compounds.
ChEMBL_10 saw the addition of the PubChem
PubChem
PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information , a component of the National Library of Medicine, which is part of the United States National Institutes of Health . PubChem can...
confirmatory assays, in order to integrate data that is comparable to the type and class of data contained within ChEMBL.
ChEMBLdb can be accessed via a web interface or downloaded by File Transfer Protocol
File Transfer Protocol
File Transfer Protocol is a standard network protocol used to transfer files from one host to another host over a TCP-based network, such as the Internet. FTP is built on a client-server architecture and utilizes separate control and data connections between the client and server...
. It is formated in a manner amenable to computerized data mining
Data mining
Data mining , a relatively young and interdisciplinary field of computer science is the process of discovering new patterns from large data sets involving methods at the intersection of artificial intelligence, machine learning, statistics and database systems...
, and attempts to standardize activities between different publications, to enable comparative analysis. ChEMBL is also integrated into other large-scale chemistry resources, including PubChem
PubChem
PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information , a component of the National Library of Medicine, which is part of the United States National Institutes of Health . PubChem can...
and the ChemSpider
ChemSpider
ChemsSpider is a free chemical database, owned by the Royal Society of Chemistry.-Database:The database contains more than 26 million unique molecules from over 400 data sources including those listed below.* A-L: EPA DSSTox, U.S...
system of the Royal Society of Chemistry
Royal Society of Chemistry
The Royal Society of Chemistry is a learned society in the United Kingdom with the goal of "advancing the chemical sciences." It was formed in 1980 from the merger of the Chemical Society, the Royal Institute of Chemistry, the Faraday Society and the Society for Analytical Chemistry with a new...
.
Associated resources
In addition to the database, the ChEMBL group have developed tools and resources for data mining. These include Kinase SARfari, an integrated chemogenomics workbench focussed on kinases. The system incorporates and links sequence, structure, compounds and screening dataScreening (medicine)
Screening, in medicine, is a strategy used in a population to detect a disease in individuals without signs or symptoms of that disease. Unlike what generally happens in medicine, screening tests are performed on persons without any clinical sign of disease....
. GPCR SARfari is a similar workbench focussed on GPCRs and ChEMBL-Neglected Tropical Diseases (ChEMBL-NTD) is a repository for Open Access primary screening and medicinal chemistry data directed at endemic tropical diseases of the developing regions of the Africa, Asia, and the Americas. The primary purpose of ChEMBL-NTD is to provide a freely accessible and permanent archive and distribution centre for deposited data.
External links
- ChEMBLdb
- Kinase SARfari
- ChEMBL-Neglected Tropical Disease Archive
- GPCR SARfari
- The ChEMBL-og Open data and drug discovery blog run by the ChEMBL team.