Research project

The EpiGraphDB platform integrates data from a range of biomedical and epidemiological sources into a Neo4j graph database and supports interactive and programmatic access using a variety of methods aimed at different needs. We provide a web user interface (UI) as a user-friendly entry point to the rich integrated resources that the platform offers, and users are able to programmatically query data via the application programming interface (API) web service or the client package in R. Finally, the Neo4j graph database can be directly queried in Cypher, which is supported as part of the API.

Maintainer(s): Yi Liu, Ben Elsworth, Tom Gaunt

contact: https://github.com/MRCIEU/epigraphdb/issues

Collaborator(s): Pau Erola, Valeriia Haberland, Gibran Hemani, Matt Lyon, Jie Zheng, Oliver Lloyd, Marina Vabistsevits

Publication: https://doi.org/10.1101/2020.08.01.230193

Software components

EpiGraphDB Graph Database

Neo4j graph database of the EpiGraphDB platform

Maintainer(s): Ben Elsworth

contact: ben.elsworth[at]bristol.ac.uk

Collaborator(s): Yi Liu, Tom Gaunt

Software URL: https://epigraphdb.org

Source code: https://github.com/MRCIEU/epigraphdb-graph

Open source license: GPLv3

Tags:

  • Active maintenance
  • Database
  • EpiGraphDB
  • GPLv3
  • Graph database
  • Neo4j
  • Python

Point of development: Active maintenance

Publication: https://doi.org/10.1101/2020.08.01.230193

EpiGraphDB API

API of the EpiGraphDB platform

Maintainer(s): Yi Liu

contact: yi6240.liu[at]bristol.ac.uk

Collaborator(s): Ben Elsworth, Tom Gaunt

Software URL: https://api.epigraphdb.org

Source code: https://github.com/MRCIEU/epigraphdb_api

Open source license: GPLv3

Tags:

  • Active maintenance
  • Application
  • EpiGraphDB
  • FastAPI
  • GPLv3
  • Python
  • Web service

Point of development: Active maintenance

Publication: https://doi.org/10.1101/2020.08.01.230193

EpiGraphDB WebUI

EpiGraphDB platform web application

Maintainer(s): Yi Liu

contact: yi6240.liu[at]bristol.ac.uk

Collaborator(s): Ben Elsworth, Tom Gaunt

Software URL: https://epigraphdb.org

Source code: https://github.com/MRCIEU/epigraphdb_web

Open source license: GPLv3

Tags:

  • Active maintenance
  • Application
  • Bootstrap-vue
  • EpiGraphDB
  • FastAPI
  • GPLv3
  • Python
  • Vue.js
  • Web app

Point of development: Active maintenance

Publication: https://doi.org/10.1101/2020.08.01.230193

EpiGraphDB R package

R package for EpiGraphDB

Maintainer(s): Yi Liu

contact: yi6240.liu[at]bristol.ac.uk

Collaborator(s): Marina Vabistsevits, Tom Gaunt

Software URL: https://mrcieu.github.io/epigraphdb-r

Source code: https://github.com/MRCIEU/epigraphdb-r

Open source license: GPLv3

Tags:

  • Active maintenance
  • EpiGraphDB
  • GPLv3
  • R
  • Software package
  • httr

Point of development: Active maintenance

Publication: https://doi.org/10.1101/2020.08.01.230193

epigraphdbpy

Python package for EpiGraphDB

Maintainer(s): Tom Gaunt

contact: tom.gaunt[at]bristol.ac.uk

Collaborator(s): Tom Gaunt

Software URL: https://github.com/MRCIEU/epigraphdbpy

Tags:

  • Active maintenance
  • EpiGraphDB
  • Python

Point of development: Active maintenance