Evidence map›Paper›PMID 31713622›Full record

ArticleNucleic acids research2020

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 Lam, Zachary Myers, Paul Sud, Jennifer Jou, Khine Lin and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 689 papers, 3 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
689citing papers in PubMed, 3 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

689 citing papers in PubMed, 3 syntheses or guidelines pooled it.

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629 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors.

Yunhai LuoDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Benjamin C HitzDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Idan GabdankDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Jason A HiltonDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Meenakshi S KagdaDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Bonita LamDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Zachary MyersDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Paul SudDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Jennifer JouDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Khine LinDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Ulugbek K BaymuradovDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Keenan GrahamDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Casey LittonDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Stuart R MiyasatoDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
J Seth StrattanDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Otto JolankiDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Jin-Wook LeeDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Forrest Y TanakaDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Philip AdenekanDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
Emma O'NeillDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.
J Michael CherryDepartment of Genetics, Stanford University, Stanford, CA 94305-5477, USA.

Funding

A Data Coordinating Center for ENCODEU24HG009397 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2017 to 2023
$26.0M
NHGRI NIH HHS U24 HG009397
6 · The paper itself

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.

Indexed as

Databases, GeneticGenome, HumanSoftwareAnimalsDNAGenomicsHumansMiceDNA

Identifiers

PMID31713622
PMCPMC7061942

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.