Basics

The idea behind DeepBlue is to provide a central access hub for large collections of epigenomic data and organize this data using controlled vocabularies. The data are kept in a central server, where they can be accessed, operated, and transfered as needed.

The DeepBlue Epigenomic Data Server has three main parts:

• The Data - Experiments and Annotations. Experiments data are the data from epigenomics experiments, e.g. the methylation data of a given sample, while the annotations data are auxiliary data, e.g. genes positions.
• We organize the genomes, projects, epigenetic marks, biosources, and techniques into controlled vocabularies. The BioSources controlled vocabulary contains terms imported from the CL, EFO, and UBERON ontologies.
• Operations - It is possible to refine the data search parameters, aggregate the data, filter it by overlap region, and retrieve it in a user selected format.

The Epigenomic Data contains the experimental data from the ENCODE, Roadmap Epigenomic Mapping Consortium, BLUEPRINT, and (soon) DEEP projects.

This manual explains DeepBlue's usage fully. From Accessing DeepbBlue, Creating a user account, and understanding the different Data Types used by DeepBlue, to Exploring the data, Inserting new data, and Working with the data. All the examples were tested in Python 2.7, but can easily be adapted to others programming language. Along with this manual, we provide links to the DeepBlue API Reference Guide command specification.