EpiGraphDB: a database and data mining platform for health data science
Tom R Gaunt
Posted 04 Aug 2020
bioRxiv DOI: 10.1101/2020.08.01.230193 (published DOI: 10.1093/bioinformatics/btaa961)
Posted 04 Aug 2020
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 sup-port 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. Availability: The EpiGraphDB platform is openly available at https://epigraphdb.org. Code for repli-cating case study results is available at https://github.com/MRCIEU/epigraphdb as Jupyter notebooks using the API, and https://mrcieu.github.io/epigraphdb-r using the R package. ### Competing Interest Statement Tom Gaunt and Gibran Hemani receive research funding from GlaxoSmithKline and Biogen. Valeriia Haberland has previously been supported by funding from GlaxoSmithKline.
- Downloaded 236 times
- Download rankings, all-time:
- Site-wide: 99,442
- In bioinformatics: 8,566
- Year to date:
- Site-wide: 103,023
- Since beginning of last month:
- Site-wide: 118,437
Downloads over time
Distribution of downloads per paper, site-wide
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!