EpiGraphDB: a database and data mining platform for health data science

Yi Liu, Benjamin Elsworth, Pau Erola, Valeriia Haberland, Gibran Hemani, Matt Lyon, Jie Zheng, Oliver Lloyd, Marina Vabistsevits, Tom R. Gaunt

Research output: Contribution to journalArticle

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Abstract

Motivation: The wealth of data resources on human phenotypes, risk factors, molecular traits and therapeutic interventions presents new opportunities for population health sciences. These opportunities are paralleled by a growing need for data integration, curation and mining to increase research efficiency, reduce mis-inference and ensure reproducible research. Results: We developed EpiGraphDB (https://epigraphdb.org/), a graph database containing an array of different biomedical and epidemiological relationships and an analytical platform to support their use in human population health data science. In addition, we present three case studies that illustrate the value of this platform. The first uses EpiGraphDB to evaluate potential pleiotropic relationships, addressing mis-inference in systematic causal analysis. In the second case study, we illustrate how protein-protein interaction data offer opportunities to identify new drug targets. The final case study integrates causal inference using Mendelian randomization with relationships mined from the biomedical literature to 'triangulate' evidence from different sources.

Original languageEnglish
Pages (from-to)1304–1311
Number of pages8
JournalBioinformatics
Volume37
Issue number9
Early online date9 Nov 2020
DOIs
Publication statusPublished - 1 May 2021

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