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

Sharon L Freshour,Obi L Griffith,Susanna Kiwala,Adam C Coffman,Alex H Wagner,Kelsy C Cotto,Joshua F Mcmichael,Malachi Griffith,Jonathan J Song

doi:10.1093/nar/gkaa1084

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.

Highlights

Released in 2013, the Drug–Gene Interaction database (DGIdb) [1] serves as a central aggregator of information on drug-gene interactions and druggability from multiple diverse sources
The subsequent major updates to DGIdb 2.0 [2] and 3.0 [3] included improvements to the user interface and search response times, the addition of an application programming interface (API), the introduction and improvement of gene and drug grouping methods, and the expansion of source content through the inclusion of new sources and updates of existing sources
DGIdb 4.0 focuses on numerous improvements of search results, including new and updated scores for interaction search results and improved drug normalization routines

Summary

Introduction

Released in 2013, the Drug–Gene Interaction database (DGIdb) [1] serves as a central aggregator of information on drug-gene interactions and druggability from multiple diverse sources. We have made an effort to integrate crowdsourced data and sources in several areas, including the addition of the crowdsourced Drug Target Commons [4] as a drug-gene interaction source, and the use of the open, community-curated Wikidata [5] resource for drug normalization.

Results

Conclusion