https://github.com/dhimmel/sider2
Calculating compound similarities using side effects and indications extracted from drug labels
https://github.com/dhimmel/sider2
compound drug side-effect sider sider2
Last synced: about 2 months ago
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Calculating compound similarities using side effects and indications extracted from drug labels
- Host: GitHub
- URL: https://github.com/dhimmel/sider2
- Owner: dhimmel
- License: cc0-1.0
- Created: 2015-01-30T03:47:24.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2015-02-07T23:28:29.000Z (over 10 years ago)
- Last Synced: 2025-04-09T16:06:39.713Z (6 months ago)
- Topics: compound, drug, side-effect, sider, sider2
- Language: TeX
- Homepage: http://git.dhimmel.com/SIDER2/
- Size: 157 MB
- Stars: 3
- Watchers: 5
- Forks: 6
- Open Issues: 1
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Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# SIDER 2
This repository contains an analysis of the [SIDER 2](http://sideeffects.embl.de/) (**sid**e **e**ffect **r**esource) [data](http://sideeffects.embl.de/download/). This resource automatically extracted concepts from drug labels to create a database of drug side effects and indications.
This analysis provides the source for a [companion website](http://git.dhimmel.com/SIDER2/), which displays the analysis.
This project is divided into three parts and each part contains a single notebook:
1. `./parse` -- processing the SIDER 2 data in *R*
2. `./similarity` -- calculating compound-compound similarities in *R*
3. `./compounds` -- querying pubchem for compound attributes in *python*
The SIDER database was described in:
> Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P (2010) A side effect resource to capture phenotypic effects of drugs. *Molecular Systems Biology*. doi:[10.1038/msb.2009.98](http://dx.doi.org/10.1038/msb.2009.98)
To compute compound-compound similarity, we use an analysis similar to:
> Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P (2008). Drug Target Identification Using Side-Effect Similarity. *Science* doi:[10.1126/science.1158140](http://dx.doi.org/10.1126/science.1158140)