General Questions
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.
Binding (B) - Data measuring binding of compound to a molecular target, e.g. Ki, IC50, Kd.
Functional (F) - Data measuring the biological effect of a compound, e.g. %cell death in a cell line, rat weight.
ADMET (A) - ADME data e.g. t1/2, oral bioavailability.
Toxicity (T) - Data measuring toxicity of a compound, e.g., cytotoxicity.
Physicochemical (P) - Assays measuring physicochemical properties of the compounds in the absence of biological material e.g., chemical stability, solubility.
Unclassified (U) - A small proportion of assays cannot be classified into one of the above categories e.g., ratio of binding vs efficacy.
How can I cite ChEMBL in a publication?
ChEMBL Database:
Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrián-Uhalte E, Davies M, Dedman N, Karlsson A, Magariños MP, Overington JP, Papadatos G, Smit I, Leach AR. (2017) 'The ChEMBL database in 2017.' Nucleic Acids Res., 45(D1) D945-D954.
DOI: 10.1093/nar/gkw1074 PMC: PMC5210557
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.
DOI: 10.1093/nar/gkv352 PMC: PMC4489243
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
DOI: 10.1093/bioinformatics/btt765 PMID: 24413672
We have a dedicated email address for data queries, error reporting or help requests. This is: [email protected]
You can create an issue in our GitHub Repository.
Molregno is our ChEMBL internal identification given to each compound. The ChEMBLID is the externally viewed identification for each compound.
The best way to access large amounts of data is to install a database instance on your own computer using Oracle or MySQL.
Yes, there is a ChEMBL RDF. It is stored on the FTP site.
ChEMBLIDs are assigned to targets, assays, documents, tissues, cell types and compounds in ChEMBL and they are used as the unique identifiers for each.
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.
More details can be found in this Blog post. Target predictions can be found on the interface and predictions can be run using this Docker image.
More details can be found in this Blog post.
Web Service documentation and example queries can be found at: https://www.ebi.ac.uk/chembl/ws
Links to webinar slides and PDFs:
