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

Liu, Yi, Elsworth, Benjamin, Erola, Pau, Haberland, Valeriia, Hemani, Gibran, Lyon, Matt, Zheng, Jie, Lloyd, Oliver, Vabistsevits, Marina and Gaunt, Tom R. (2021) EpiGraphDB: a database and data mining platform for health data science. Bioinformatics, 37 (9). 1304–1311. ISSN 1367-4803

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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.

Item Type: Article
Additional Information: An erratum can be found at: https://doi.org/10.1093/bioinformatics/btab104 "Upon the original publication of this article, there was an error in the source code syntax under sub-section “2.2 Integration of epidemiological evidence” in the “Materials and methods” section. The source code syntax should read: “(e.g. (Gwas {trait: ‘Body mass index’})-[MR {beta, se, pval}]->(Gwas {trait: ‘Coronary heart disease’}))” instead of “ (e.g. [Gwas (trait: ‘Body mass index’)]-[MR {beta, se, pval}]->(Gwas {trait: ‘Coronary heart disease’})))”. This error has now been corrected. The Publisher apologizes for the error."
Uncontrolled Keywords: statistics and probability,biochemistry,molecular biology,computer science applications,computational theory and mathematics,computational mathematics,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/2600/2613
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
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Depositing User: LivePure Connector
Date Deposited: 03 Nov 2020 01:06
Last Modified: 30 Sep 2021 15:49
URI: https://ueaeprints.uea.ac.uk/id/eprint/77497
DOI: 10.1093/bioinformatics/btaa961

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