Principles of metadata organization at the ENCODE data coordination center.

Eurie L Hong,Greg R Roe,Venkat S Malladi,Timothy R Dreszer,J Seth Strattan,Laurence D Rowe,Aditi K Narayanan,Nikhil R Podduturi,Benjamin C Hitz,Esther T Chan,Jean M Davidson,Marcus Ho,Cricket A Sloan,Brian T Lee,J Michael Cherry,Idan Gabdank,Jason A Hilton,Forrest Tanaka

doi:10.1093/database/baw001

Abstract

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center (DCC) is responsible for organizing, describing and providing access to the diverse data generated by the ENCODE project. The description of these data, known as metadata, includes the biological sample used as input, the protocols and assays performed on these samples, the data files generated from the results and the computational methods used to analyze the data. Here, we outline the principles and philosophy used to define the ENCODE metadata in order to create a metadata standard that can be applied to diverse assays and multiple genomic projects. In addition, we present how the data are validated and used by the ENCODE DCC in creating the ENCODE Portal (https://www.encodeproject.org/).Database URL: www.encodeproject.org

Highlights

The goal of the Encyclopedia of DNA Elements (ENCODE) project is to annotate functional regions in the human and mouse genomes
The project has surveyed the landscape of the human genome using over 35 high-throughput experimental methods in > 250 different cell and tissue types, resulting in over 4000 experiments [1, 3]
These datasets are submitted to a Data Coordinating Center (DCC), whose role is to describe, organize and provide access to these diverse datasets [4]

Summary

Introduction

The goal of the Encyclopedia of DNA Elements (ENCODE) project is to annotate functional regions in the human and mouse genomes. We describe how metadata are organized at the ENCODE DCC and define the metadata standard that is used to describe the experimental assays and computational analyses generated by the ENCODE project.

Results

Conclusion