4 files

PharmacotherapyDB 1.0: the open catalog of drug therapies for disease

posted on 2016-03-15, 20:07 authored by Daniel HimmelsteinDaniel Himmelstein, Pouya Khankhanian, Christine S. Hessler, Ari J. Green, Sergio BaranziniSergio Baranzini
This is the initial release of the PharmacotherapyDB, a catalog of drug therapies for disease. The catalog contains physician curated medical indications.

This release contains 97 diseases and 601 drugs. Between these drug–disease pairs, there are 755 disease-modifying therapies, 390 symptomatic therapies, and 243 non-indications. To enable integrative analyses, drugs and diseases are coded using DrugBank and Disease Ontology identifiers.

Indications were classified by physician curators into three categories:

  • DM -- disease modifying
  • SYM -- symptomatic
  • NOT -- non-indication

This deposition contains the following files:
  • indications.tsv contains drug–disease pairs and their consensus category (DMSYM, or NOT). n_curators refers to how many of the three curators initially assigned the consensus classification. n_resources refers to how many of the four resources (MEDI-HPS, LabeledIn, EHRLink, PREDICT) included the indication.

  • diseases.tsv contains a list of diseases with indications. For each disease, the number of indications per category is provided.

  • drugs.tsv contains a list of drugs with indications. For each drug, the number of indications per category is provided.

  • catalog.xlsx is a spreadsheet with four sheets:

    1. indications — data from indications.tsv
    2. diseases — data from diseases.tsv
    3. drugs — data from drugs.tsv
    4. curation — the classifications from each of the three physician curators (AJGCSH, & PK).
The catalog is released as CC0 1.0. However, please consider that the catalog includes DrugBank and DIsease Ontology identifiers and reference their licenses when appropriate.


National Science Foundation Graduate Research Fellowship (#1144247) to DSH.