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Case studies for the EpiGraphDB platform

We have created several case studies demonstrating the use of EpiGraphDB in research studies as Jupyter notebooks (using EpiGraphDB API) and as RMarkdown vignettes (using EpiGraphDB R package).

Jupyter notebooks

The Jupyter notebooks are available as part of the MRCIEU/epigraphdb repo on github.

Users can use Google Colab or Binder to play with these notebooks online, or clone the repo and set up a local Jupyter Lab environment.

Case studies for the EpiGraphDB paper
Case study 1: Distinguishing vertical and horizontal pleiotropy for SNP-protein associations Open In Colab Binder
Case study 2: Identification of potential drug targets Open In Colab Binder
Case study 3: Triangulating causal estimates with literature evidence Open In Colab Binder
General examples
Functionalities in getting metadata, entity search, and using Cypher queires Open In Colab Binder

RMarkdown vignettes

For users of the R package we have demonstrated how the above can be achieved in using the package in the vignettes.

Article
Using EpiGraphDB R package
Using EpiGraphDB API (from R and command line)
Meta functionalities of the EpiGraphDB platform
Case study 1: Distinguishing vertical and horizontal pleiotropy for SNP-protein associations
Case study 2: Identification of potential drug targets
Case study 3: Triangulating causal estimates with literature evidence