This repository contains basic examples for querying MR-EvE and literature data in EpiGraphDB. This code is made available alongside the analysis published in the article "Integrating Mendelian randomization and literature-mined evidence for breast cancer risk factors" on MedRxiv.
The main development repo of this project is https://github.com/mvab/epigraphdb-breast-cancer. The examples presented here may be helpful for understanding and/or replicating EpiGraphDB queries that were used in that project, or applying them to study your disease of interest.
The basic examples of querying EpiGraphDB with epigraphdb-r R package are provided in the "Getting started" guide.
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01_mr-eve_exposure_to_outcomes.ipynb- collect all risk factors for a disease outcome from MR-EvE -
02_query_mediators_between_traits.ipynb- identify potential mediators between exposure and outcome using MR-EvE -
03_extract_trait_literature_space.ipynb- extract literature-mined relationships related to a (GWAS) trait of interest