New developments on the Encyclopedia of DNA Elements (ENCODE) data portal.

Philip Adenekan,Khine Lin,Jin-Wook Lee,Jennifer Jou,Casey Litton,Paul Sud,Otto Jolanki,Emma O’Neill,Zachary Myers,Yunhai Luo,Keenan Graham,Stuart R Miyasato ,Bonita R Lam ,Meenakshi S Kagda ,Ulugbek K Baymuradov ,Benjamin Hitz ,Forrest Tanaka ,J Seth Strattan ,Jason Hilton ,J Michael Cherry

doi:10.1093/nar/gkz1062

Philip Adenekan, Khine Lin + Show 18 more

Open Access

https://doi.org/10.1093/nar/gkz1062

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Journal: Nucleic acids research	Publication Date: Nov 12, 2019
Citations: 413	License type: CC BY 4.0

Affiliation: Stanford University

Abstract

The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation.

Highlights

Over 99% of the human genome was sequenced as a part of the Human Genome Project that was completed in April 2003 [1]
Raw data and analysis results generated by the Encyclopedia of DNA Elements (ENCODE) project are freely accessible to the scientific community on the ENCODE portal, developed and maintained by the ENCODE Data Coordinating Center (DCC) [3,4,5,6]
In addition to the data generated by the ENCODE consortium, the ENCODE portal hosts data from modENCODE [7], modERN [8], The NIH Roadmap Epigenomics Consortium [9] and Genomics of Gene Regulation projects as well as some datasets provided by other members of the scientific community

Summary

Introduction

Over 99% of the human genome was sequenced as a part of the Human Genome Project that was completed in April 2003 [1]. Raw data and analysis results generated by the ENCODE project are freely accessible to the scientific community on the ENCODE portal (https://www.encodeproject.org/), developed and maintained by the ENCODE Data Coordinating Center (DCC) [3,4,5,6]. The DCC processes the raw data using the ENCODE uniform processing pipelines and submits processed analysis files to the portal [3,4,6].

Results

Conclusion