ChEMBL, programmatically

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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). The data is abstracted and curated from the primary scientific literature, and covers a significant fraction of the SAR and discovery of modern drugs. 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. Additional data on clinical progress of compounds is being integrated into ChEMBL at the current time.

This webinar took place on 12th July 2017. It provides:

  • An overview of the ChEMBL API and its use, including how to execute API calls from the browser (0:23);
  • Where to find documentation (2:54);
  • How to user filtering and pagination (6:23);
  • Available output formats (17:13);
  • Scripting examples in Python, Bash and R (27:38).  

We also give examples of how the API can be used to create reusable web components and integrated into tools such as KNIME and Slack. The webinar assumes a degree of familiarity with the data in ChEMBL. If you are not famililar with ChEMBL we recommend watching our ChEMBL walkthrough: webinar first.

You can download the slides (including links to example scripts) here.

Have a look at the following links for help and documentation:

Or get in touch with the ChEMBL helpdesk [chembl-help[at]ebi.ac.uk].