DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.
paper
Cited
Public
- Authors
- Cotto, Kelsy C; Wagner, Alex H; Feng, Yang-Yang; Kiwala, Susanna; Coffman, Adam C; Spies, Gregory; Wollam, Alex; Spies, Nicholas C; Griffith, Obi L; Griffith, Malachi
- Year
- 2018
- Journal
- Nucleic acids research
- PMID
- 29156001
- DOI
- 10.1093/nar/gkx1143
- PMCID
- PMC5888642
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 30 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 24 sources were updated. Six new resources were added, bringing the total number of sources to 30. 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 anti-neoplastic 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, interaction type and other interaction metadata.
DGIdb 3.0 content by source. The number of drugβgene interaction claims (first panel) and druggable gene categories (second panel) are separated into three categories: sources that existed in the DGIdb previously, sources that existed in the DGIdb previously but have been updated for 3.0 or sources that are entirely new to the DGIdb. Abbreviations: CF: Clearity Foundation; CGI = Cancer genome interpreter, CKB = JAX-Clinical Knowledgebase, CMI = Caris Molecular Intelligence, FO = Foundation One, GTP = Guide to pharmacology, MCG = My cancer genome, OncoKB = Precision Oncology Knowledge Base, TALC = Targeted agents in lung cancer, TTD = Therapeutic Target Database, TEND = Trends in the exploration of novel drug targets, GO = Gene Ontology and MSK = Memorial Sloan Kettering.
Comparison of the DGIdb 2.0 and 3.0 response time by search and result size. The left panel summarizes observed response times (n = 100) for searches of various sizes (1, 2, 3, 4, 5, 10, 15, 20 and 25) of randomly selected genes. The right panel summarizes observed response times for the corresponding interaction search result sizes.
The DGIdb interaction search interface. (A) A search field accepts drug or gene identifiers, depending on which tab is selected and provides auto-completion suggestions for search terms. (B) Preset options are provided to filter search results based on the attributes of mapped interactors. (C) Advanced filters allow the user to further filter based on source database, gene category or interaction type. (D) The interaction search results (Unique Matches) view shows results for search terms that were matched within the DGIdb. (E) The interaction search results (Ambiguous or Unmatched) view shows search terms that were either ambiguously matched or unmatched within the DGIdb. (F) Additional side panels provide a brief summary of unmatched and ambiguously matched terms.
| # | Section | Preview |
|---|---|---|
| 20 | AVAILABILITY | DGIdb is an open access database and web interface (www.dgidb.org) with open source code available⦠|
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