General Questions
What is the ChEMBLID?
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 Assay Type?
- 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?
The publications used to cite ChEMBL are:
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.
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.We have a dedicated email address for data queries, error reporting or help requests. This is: [email protected]
- 2.
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.
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 Oracle or MySQL.
Is there a ChEMBL RDF?
Yes, there is a ChEMBL RDF. It is stored on the FTP site.
Why do Assays and Documents both have ChEMBLIDs?
ChEMBLIDs are assigned to targets, assays, documents, tissues, cell types and compounds in ChEMBL and they are used as the unique identifiers for each.
What is the difference between the different releases of ChEMBLdb, 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.
Where can I find more details on the target prediction?
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.
Where can I find more details on the assay classification?
How do you use the Web Services?
Useful Links
Links to webinar slides and PDFs:
Last modified 1yr ago
Copy link
Contents
What is the ChEMBLID?
What is the Assay Type?
The publications used to cite ChEMBL are:
How do I report errors or make suggestions for the interface?
What is the difference between Molregno and ChEMBLID?
What is the best way to access large amounts of data in ChEMBL?
Is there a ChEMBL RDF?
Why do Assays and Documents both have ChEMBLIDs?
What is the difference between the different releases of ChEMBLdb, e.g. ChEMBL_14 and ChEMBL_15?
Where can I find more details on the target prediction?
Where can I find more details on the assay classification?
How do you use the Web Services?
Useful Links