https://github.com/dhimmel/drugbank
User-friendly extensions of the DrugBank database
https://github.com/dhimmel/drugbank
compounds drugbank drugs rephetio terminology
Last synced: 4 months ago
JSON representation
User-friendly extensions of the DrugBank database
- Host: GitHub
- URL: https://github.com/dhimmel/drugbank
- Owner: dhimmel
- Created: 2015-03-19T23:51:02.000Z (over 10 years ago)
- Default Branch: gh-pages
- Last Pushed: 2019-05-17T19:05:59.000Z (over 6 years ago)
- Last Synced: 2025-06-27T15:03:09.634Z (4 months ago)
- Topics: compounds, drugbank, drugs, rephetio, terminology
- Language: HTML
- Homepage:
- Size: 100 MB
- Stars: 188
- Watchers: 10
- Forks: 73
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
## User-friendly extensions of the DrugBank database
[](https://doi.org/10.5281/zenodo.45579)
[DrugBank](http://www.drugbank.ca/) is a publicly-available resource of drug information [[1](https://doi.org/10.1093/nar/gkt1068)]. We rely on DrugBank for our [project to repurpose drugs](https://doi.org/10.15363/thinklab.4 "Thinklab: Repurposing drugs on a hetnet"). We are conducting this project openly on ThinkLab, and this README will reference Thinklab discussions providing greater detail.
This repository contains several code and data components:
+ `parse.ipynb` -- extracts information from the DrugBank xml download into a [tsv file](data/drugbank.tsv) where each row represents a drug. A [subset](data/drugbank-slim.tsv) referred to as slim contains only drugs that are approved, small molecules, and contain an InChI structure ([discussion](https://doi.org/10.15363/thinklab.d70#192)). We also extract the [interacting proteins](data/proteins.tsv) for each drug, which include targets, enzymes, transporters, and carriers ([dicussion](https://doi.org/10.15363/thinklab.d65)).
+ `similarity.ipynb` -- calculates chemical similarity between drugbank compounds using extended connectivity fingerprints ([dicussion](http://thinklab.com/d/70)). Similarities range from 0 to 1. The full similarity download is [available on figshare](https://doi.org/10.6084/m9.figshare.1418386). The subset of similarities for slim compounds is [on github](data/similarity-slim.tsv.gz).
+ `unichem-map.ipynb` -- maps DrugBank compounds to 30 other compound resources using [UniChem](http://www.ebi.ac.uk/unichem/info/widesearchInfo). The mapping is based on atomic connectivity and ignores differences in small molecular details. Mappings are available in a [bulk download](data/mapping.tsv.gz) or for [individual resources](data/mapping). Summary statistics are also [available](data/mapping-counts.tsv) ([discussion](http://thinklab.com/d/70)).
+ `pubchem-map.ipynb` -- DrugBank compounds were mapped to [PubChem](https://pubchem.ncbi.nlm.nih.gov/search/) based on exact InChi string matches. The mapping is available as a [tsv file](data/pubchem-mapping.tsv).
+ `parse-halflife.ipynb` -- extracts half-life and other structural information from the Drugbank xml download into a [tsv file](data/drugbank_halflife.tsv) where each row represents a drug. The half-life information was listed as free text in Drugbank. We manually extract the numeric value from free text into a [xlsx file](data/drugbank_halflife_curated.xlsx). All values were converted to hours. If the value was listed as time range (e.g. a ~ b) in DrugBank, average was calculated (e.g. (a + b)/2).
+ `extract-curated-halflife.ipynb` -- extracts subset of drugs with curated half-life into a [tsv file](data/drugbank_subset_halflife_curated.tsv) where each row represents a drug.
+ `predict-halflife.ipynb` -- builds supervised learning models to predict half-life based on structural properties of drugs.
## License
DrugBank content and derivates are licensed under [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/ "Creative Commons Attribution-NonCommercial 4.0 International"). Original content is released as [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/ "CC0 1.0 Universal: Public Domain Dedication")