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

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

doi:10.1093/nar/gkz1062

Abstract

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.

Keywords

BiologyENCODEEncyclopediaComputational biologyDNAGeneticsLibrary scienceGeneComputer science

Affiliated Institutions

Stanford University US

Related Publications

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Federico Abascal , Reyes Acosta , Nicholas J. Addleman +97 more

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate t...

2020 Nature 2295 citations

ENCODE whole-genome data in the UCSC Genome Browser: update 2012

Kate R. Rosenbloom , Timothy R. Dreszer , Jeffrey C. Long +24 more

The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year of production-level effort generating high-quality whole-genome functional annotations of the human...

2011 Nucleic Acids Research 254 citations

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

The ENCODE Project Consortium

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to under...

2011 PLoS Biology 1557 citations

PDBe-KB: a community-driven resource for structural and functional annotations

Mihály Váradi , John M. Berrisford , Mandar Deshpande +52 more

Abstract The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and...

2019 Nucleic Acids Research 127 citations

An integrated encyclopedia of DNA elements in the human genome

Sylvain Foissac

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) pro...

2012 Nature 18617 citations

Publication Info

Year: 2019
Type: article
Volume: 48
Issue: D1
Pages: D882-D889
Citations: 1000
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

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

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

1000

OpenAlex

Cite This

APA Style

                            
                                
                                    Yunhai Luo, 
                                
                                    Benjamin C. Hitz, 
                                
                                    Idan Gabdank
                                
                                et al.
                            
                            (2019). 
                            New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. 
                            Nucleic Acids Research
                            , 48
                            (D1)
                            , D882-D889.
                            https://doi.org/10.1093/nar/gkz1062
                        

Identifiers

DOI: 10.1093/nar/gkz1062