DGIdb 3.0: a redesign and expansion of the drug–gene interaction database

By Kelsy C. Cotto, A. Wagner, Yang-Yang Feng, Susanna Kiwala, Adam C. Coffman, Gregory C. Spies, Alexander T. Wollam, Nick Spies, Obi L. Griffith, Malachi Griffith. bioRxiv, 2017

790 citations recorded by the source corpus.

The Drug-Gene Interaction Database (DGIdb, www.dgidb.org) consolidates, organizes, and presents drug-gene interactions and gene druggability information from papers, databases, and web resources. DGIdb normalizes content from more than thirty disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (API), and public cloud-based server image. DGIdb v3.0 represents a major update of the database. Nine of the previously included twenty-eight sources were updated. Six new resources were added, bringing the total number of sources to thirty-three. These updates and additions of sources have cumulatively resulted in 56,309 interaction claims. This has also substantially expanded the comprehensive catalogue of druggable genes and antineoplastic drug-gene interactions included in the DGIdb. Along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times, and upgrading the underlying web application framework. In addition, the expanded API features new endpoints which allow users to extract more detailed information about queried drugs, genes, and drug-gene interactions, including listings of PubMed IDs (PMIDs), interaction type, and other interaction metadata.

Subfields: Computational Theory and Mathematics, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/47c27885c80ded97209f39e257ff6c4ab1eb34d6

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Citations in the corpus

Proteogenomic characterization reveals therapeutic vulnerabilities in lung adenocarcinoma (2020, background): “Furthermore, we identified 27 putatively druggable kinases with known but as yet non-FDA approved inhibitors (Cotto et al., 2018).”
Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts (2020, background): “0 (3) (in 2018) included improvements to the user interface and search response times, the addition of an 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.”
Machine learning approaches and databases for prediction of drug–target interaction: a survey paper (2020, methodology): “The latest update of DGIdb was in 2017 and in total 30 data sources are included in the 3.0 version [254].”