Epigenome switchboard

The epigenome switchboard is a web app that integrates large-scale epigenome data across databases.

It is made up of data providers and data hubs that together provide fast web and API access to data from many different public data sources. Via a subscription interface, users can add new public or private data providers into their switchboards, enabling them to easily integrate their own data with other curated data resources via the hub.

Prerequisite: A controlled vocabulary

Components that make up the epigenome switchboard

In order to be integrated, the distributed data must use a controlled vocabulary. We are implementing an epigenome-specific controlled vocabulary called bioterms that builds on existing work from the Sequence Ontology and schema.org.

The epigenome switchboard is made up of 2 components:

1. One or more data providers

A data provider is a generic server that hosts actual epigenome data. The data is stored as regions (a.k.a. genomic intervals). This is a RESTful server that provides access to the raw data via the data provider API. We provide a containerized system so that a third party with either public or private data could fit that data into a data provider instance that would integrate with the epigenome switchboard.

Our protoype data provider is housed here:

2. The hub, or query overlay server

The hub links together data providers, and then provides access that data for users. A hub can be accessed in 2 ways: a web interface for user-friendly data queries, and a documented hub API for programmatic access to integrated data. A hub connects any number of public or private data providers. Furthermore, there can be several hubs, each one connecting a different set of data providers. For example, a given hub may focus on private data, or a certain species or data type, etc.

Our protoype hub is housed here: