{"id":17099226,"url":"https://github.com/dhimmel/drugbank","last_synced_at":"2026-02-03T05:03:29.839Z","repository":{"id":29025066,"uuid":"32552357","full_name":"dhimmel/drugbank","owner":"dhimmel","description":"User-friendly extensions of the DrugBank database","archived":false,"fork":false,"pushed_at":"2019-05-17T19:05:59.000Z","size":105373,"stargazers_count":188,"open_issues_count":6,"forks_count":73,"subscribers_count":10,"default_branch":"gh-pages","last_synced_at":"2025-06-27T15:03:09.634Z","etag":null,"topics":["compounds","drugbank","drugs","rephetio","terminology"],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dhimmel.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-03-19T23:51:02.000Z","updated_at":"2025-06-20T01:52:02.000Z","dependencies_parsed_at":"2022-07-26T04:02:27.376Z","dependency_job_id":null,"html_url":"https://github.com/dhimmel/drugbank","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/dhimmel/drugbank","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fdrugbank","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fdrugbank/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fdrugbank/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fdrugbank/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dhimmel","download_url":"https://codeload.github.com/dhimmel/drugbank/tar.gz/refs/heads/gh-pages","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fdrugbank/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29033716,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-03T02:28:16.591Z","status":"ssl_error","status_checked_at":"2026-02-03T02:27:48.904Z","response_time":96,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["compounds","drugbank","drugs","rephetio","terminology"],"created_at":"2024-10-14T15:09:23.180Z","updated_at":"2026-02-03T05:03:29.825Z","avatar_url":"https://github.com/dhimmel.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"## User-friendly extensions of the DrugBank database\n\n[![DOI 10.5281/zenodo.45579](https://zenodo.org/badge/doi/10.5281/zenodo.45579.svg)](https://doi.org/10.5281/zenodo.45579)\n\n[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.\n\nThis repository contains several code and data components:\n\n+ `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)).\n\n+ `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).\n\n+ `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)).\n\n+ `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).\n\n+ `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).\n\n+ `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.\n\n+ `predict-halflife.ipynb` -- builds supervised learning models to predict half-life based on structural properties of drugs.\n\n## License\n\nDrugBank 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\")\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fdrugbank","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdhimmel%2Fdrugbank","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fdrugbank/lists"}