Epigenome switchboard

The epigenome switchboard is a web app that enables scientists to integrate large-scale epigenome data across databases via an API.

It is made up of a series 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.

Components that make up the epigenome switchboard

Project components

To build an epigenome switchboard requires 3 components:

1. A vocabulary server

The vocabulary server provides common terms so that distributed data sources can be integrated. There need only be a single vocabulary server for any number of instances of the other servers. It simply provides a permanent, static URL for common terms so that we can use json-ld to integrate data from multiple sources. Our vocabulary server buildes heavily on existing ontologies and vocabularies, including the Sequence Ontology for genomic sequence terms, Schema.org for generic data terms, and others.

2. One or more data providers

The data provider is a generic server that hosts actual epigenome data. The data is stored as regions (a.k.a. segments, or genomic intervals). This is a RESTful server that provides access to the raw data via the data provider API (which is still under development). There will be many data providers, and we aim to provide a packaged 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:

3. The hub, or query overlay server

The hub links together data providers. A hub provides 2 things: 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 could 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: