Links

General Questions

How often do you update the data?

The data is updated regularly, with releases approximately 2-3 times a year.

What is the ChEMBLID and why do both Assays and Documents have ChEMBLIDs?

The ChEMBLID is a unique ID that has been assigned to compounds, targets, assays, documents, tissues and cell types in ChEMBL. It can be used to retrieve a Report Card page for these entities, or to search for them using the keyword search.

What is the difference between Molregno and ChEMBLID?

Molregno is our ChEMBL internal identification given to each compound. The ChEMBLID is the externally viewed identification for each compound.

How can I interconvert PubChem and ChEMBL_IDs?

1) UniChem can be used to map between 2 sets of identifiers.
The source mapping tables are on the FTP website and include a ChEMBL_ID to PubChem_ID mapping table (source mapping table for src1 to src22).
2) In the ChEMBL database, identifiers may be found in the compound_records table (as the compound_key).

What literature coverage is there in ChEMBL?

Data are routinely extracted from seven core journals:
However, we also have data from selected articles in more than 200 journals including Antimicrob Agents Chemother, Med Chem Res, J Agric Food Chem and Drug Metab Dispos. ChEMBL currently contains data from more than 86,000 journal articles, and we also now include data from selected patents.

How can I be informed of updates in ChEMBL?

You can sign up to our ChEMBL Announce mailing list (http://listserver.ebi.ac.uk/mailman/listinfo/chembl-announce), where you will be kept up to date with all new releases and changes to the database.

Do you show which compounds and/or bioactivity data has been changed or deleted with each release of ChEMBL?

As the data and the compounds are continually being curated, it is not possible to keep a track of these alterations or additions. The CHEMBL_ID_LOOKUP table stores a list of all active and inactive (obsolete) entities under the status field: ACTIVE OBS. It is also possible to download previous releases and identify changes through a comparison of the data.
If you need help, please contact us and we will be able to let you know what, if anything, has happened to the data you are interested in.

The publications used to cite ChEMBL are:

ChEMBL Database:
Mendez D, Gaulton A, Bento AP, Chambers J, De Veij M, Félix E, Magariños MP, Mosquera JF, Mutowo P, Nowotka M, Gordillo-Marañón M, Hunter F, Junco L, Mugumbate G, Rodriguez-Lopez M, Atkinson F, Bosc N, Radoux CJ, Segura-Cabrera A, Hersey A, Leach AR. (2019) 'ChEMBL: towards direct deposition of bioassay data.' Nucleic Acids Res., 47(D1) D930-D940.
ChEMBL Web Services:
Davies M, Nowotka M, Papadatos G, Dedman N, Gaulton A, Atkinson F, Bellis L, Overington JP. (2015) 'ChEMBL web services: streamlining access to drug discovery data and utilities.' Nucleic Acids Res., 43(W1) W612-W620.
ChEMBL RDF:
S. Jupp, J. Malone, J. Bolleman, M. Brandizi, M. Davies, L. Garcia, A. Gaulton, S. Gehant, C. Laibe, N. Redaschi, S.M Wimalaratne, M. Martin, N. Le Novère, H. Parkinson, E. Birney and A.M Jenkinson (2014) The EBI RDF Platform: Linked Open Data for the Life Sciences Bioinformatics 30 1338-1339

How do I report errors or make suggestions for the interface?

  1. 1.
    We have a dedicated email address for data queries, error reporting or help requests. This is: [email protected]
  2. 2.
    You can create an issue in our GitHub Repository to report issues with the interface only.

What is the best way to access large amounts of data in ChEMBL?

The best way to access large amounts of data is to install a database instance on your own computer using MySQL.

Is there a ChEMBL RDF?

Yes, there is a ChEMBL RDF. It is stored on the FTP site.

What is the difference between the different releases of ChEMBL, e.g. ChEMBL_14 and ChEMBL_15?

ChEMBL_14 is an earlier release of the data, with ChEMBL_15 being an updated version. Subsequent updates will have consecutive numbers, so the one with the highest number will be the most recent full version of the data.

What is the difference between ChEMBL and ChEMBL-NTD?

ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). We attempt to normalise the bioactivities into a uniform set of end-points and units where possible, and also to tag the links between a molecular target and a published assay with a set of varying confidence levels. The data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs.
ChEMBL-NTD is a repository for Open Access primary screening and medicinal chemistry data directed at neglected diseases - 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. ChEMBL-NTD is a subset of the data in the free medicinal chemistry and drug discovery database ChEMBLdb.

How do you use the Web Services?

Web Service documentation and example queries can be found at: https://www.ebi.ac.uk/chembl/ws

What data sources are stored in ChEMBL?

ChEMBL consists of data from a wide variety of data sources including scientific literature and patents, deposited data sets, PubChem BioAssay and BindingDB databases, toxicology data sets and drug/clinical candidate resources. The current list of sources is:
Source
Source ID
Scientific Literature
1
GSK Malaria Screening
2
Novartis Malaria Screening
3
St Jude Malaria Screening
4
Sanger Institute Genomics of Drug Sensitivity in Cancer
5
PDBe Ligands
6
PubChem BioAssays
7
Clinical Candidates
8
Orange Book
9
Guide to Receptors and Channels (DEPRECATED)
10
Open TG-GATEs
11
Manually Added Drugs
12
USP Dictionary of USAN and International Drug Names
13
Drugs for Neglected Diseases Initiative (DNDi)
14
DrugMatrix
15
GSK Published Kinase Inhibitor Set
16
MMV Malaria Box
17
TP-search Transporter Database
18
Harvard Malaria Screening
19
WHO-TDR Malaria Screening
20
Deposited Supplementary Bioactivity Data
21
GSK Tuberculosis Screening
22
Open Source Malaria Screening
23
Millipore Kinase Screening (DEPRECATED - MERGED WITH SRC_ID = 1
24
External Project Compounds
25
Gene Expression Atlas Compounds
26
AstraZeneca Deposited Data
27
FDA Approval Packages
28
GSK Kinetoplastid Screening
29
K4DD Project
30
Curated Drug Metabolism Pathways
31
St Jude Leishmania Screening
32
Gates Library compound collection
33
MMV Pathogen Box
34
HeCaToS Compounds
35
Withdrawn Drugs
36
BindingDB Database
37
Patent Bioactivity Data
38
Curated Drug Pharmacokinetic Data
39
CO-ADD antimicrobial screening data
40
WHO Anatomical Therapeutic Chemical Classification
41
British National Formulary
42
Published Kinase Inhibitor Set 2
43
Kuster lab chemical proteomics drug profiling
48
HESi
49
Winzeler Lab Plasmodium Screening Data
51
SARS-CoV-2 Screening Data 2020-21
52
Prodrug active ingredients
53
Donated Chemical Probes - SGC Frankfurt
54
EUbOPEN Chemogenomic Library
55
Salvensis and LSHTM Schistosomiasis screening data
56
IMI-CARE SARS-CoV-2 Data
57
Fraunhofer HDAC6
59
MMV Malaria HGL
60
International Nonproprietary Names
63
Links to webinar slides and PDFs: