Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts

TLDR

The Drug‑Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that compiles drug‑gene interactions and druggable genes from publications, databases, and other web‑based sources. This update aims to integrate crowdsourced contributions by leveraging the Drug Target Commons for community‑contributed interaction data, using Wikidata for term normalization, and exporting drug‑gene interaction networks to NDEx. The database normalizes and merges drug, gene, and interaction data into conceptual groups, provides access via a search interface, API, and TSV downloads, and incorporates the crowdsourced integration, Wikidata normalization, and NDEx export. DGIdb 4.0, the latest major release, adds seven new sources (total 41), updates 15 existing sources, refines drug normalization and grouping, and introduces a more sophisticated query score, updated interaction score, interaction directionality, and enhanced search features, data releases, licensing documentation, and application framework.

Abstract

The Drug-Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that provides information on drug-gene interactions and druggable genes from publications, databases, and other web-based sources. Drug, gene, and interaction data are normalized and merged into conceptual groups. The information contained in this resource is available to users through a straightforward search interface, an application programming interface (API), and TSV data downloads. DGIdb 4.0 is the latest major version release of this database. A primary focus of this update was integration with crowdsourced efforts, leveraging the Drug Target Commons for community-contributed interaction data, Wikidata to facilitate term normalization, and export to NDEx for drug-gene interaction network representations. Seven new sources have been added since the last major version release, bringing the total number of sources included to 41. Of the previously aggregated sources, 15 have been updated. DGIdb 4.0 also includes improvements to the process of drug normalization and grouping of imported sources. Other notable updates include the introduction of a more sophisticated Query Score for interaction search results, an updated Interaction Score, the inclusion of interaction directionality, and several additional improvements to search features, data releases, licensing documentation and the application framework.