From cac6d7de6afbb12baf26844848eb539239bd1a31 Mon Sep 17 00:00:00 2001 From: Daniel Himmelstein Date: Thu, 4 Feb 2016 10:02:52 -0800 Subject: [PATCH] Add license and update more hrefs --- README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index ec32059..387451c 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ -## A repository dedicated to working with DrugBank +## User-friendly extensions of the DrugBank database -[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. 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](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)). + `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). @@ -12,3 +12,6 @@ This repository contains several code and data components: + `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). +## 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")