SIDER 2

This website documents parsing SIDER 2 (1), which is a database of indications and side effects extracted from drug labels. Using a similar method to an existing analysis (2), we compute similarity measures between compounds.

Components:

• Parse in R – reading, manipulating, and performing quality control on the raw SIDER 2 data
• Similarity in R – calculating pairwise similarities between compounds based on their side effect and indication profiles
• Compounds in python – querying PubChem for additional compound information

Downloads:

The project repository contains all files and code used for this project.

Several tab delimited text files are provided here for download:

• All side effects and indications, after processing. Each row represents an associated compound-concept pair.
• Pairwise compound similarities for the three different similarity methods (based on indications, side effects, and substructure). The subset of compound-pairs that had values for all three methods is also available.
• Compound information including canonical smiles and parents.

References

1. Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P (2010) A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol. doi:10.1038/msb.2009.98

2. Campillos M, Kuhn M, Gavin A-C, Jensen LJ, Bork P (2008) Drug Target Identification Using Side-Effect Similarity. Science. doi:10.1126/science.1158140

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To the extent possible under law, Daniel Himmelstein has waived all copyright and related or neighboring rights to SIDER 2. This work is published from: United States.