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## A repository dedicated to working with DrugBank | ||
## User-friendly extensions of the DrugBank database | ||
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[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](//thinklab.com/p/rephetio) [[2](https://doi.org/10.15363/thinklab.4)]. We are conducting this project openly on ThinkLab, and this README will reference ThinkLab discussions providing greater detail. | ||
[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. | ||
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This repository contains several code and data components: | ||
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+ `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](http://thinklab.com/d/70#192)). We also extract the [interacting proteins](data/proteins.tsv) for each drug, which include targets, enzymes, transporters, and carriers ([dicussion](//thinklab.com/d/65)). | ||
+ `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)). | ||
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+ `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). | ||
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+ `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)). | ||
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+ `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). | ||
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## License | ||
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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") |