Evidence map›Paper›PMID 29126249›Full record

ArticleNucleic acids research2018

The Encyclopedia of DNA elements (ENCODE): data portal update.

Carrie A Davis, Benjamin C Hitz, Cricket A Sloan, Esther T Chan, Jean M Davidson, Idan Gabdank, Jason A Hilton, Kriti Jain, Ulugbek K Baymuradov, Aditi K Narayanan and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,043 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
1,043citing papers in PubMed, 1 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

1,043 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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983 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

18 authors.

Carrie A DavisDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Benjamin C HitzDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Cricket A SloanDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Esther T ChanDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Jean M DavidsonDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Idan GabdankDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Jason A HiltonDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Kriti JainDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Ulugbek K BaymuradovDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Aditi K NarayananDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Kathrina C OnateDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Keenan GrahamDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Stuart R MiyasatoDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Timothy R DreszerDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
J Seth StrattanDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Otto JolankiDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Forrest Y TanakaDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
J Michael CherryDepartment of Genetics, Stanford University, Stanford, CA 94305-5120, USA.

Funding

A Data Coordinating Center for ENCODEU24HG009397 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2017 to 2023
$26.0M
A Data Coordinating Center for ENCODEU41HG006992 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2012 to 2016
$16.6M
NHGRI NIH HHS U24 HG009397NHGRI NIH HHS U41 HG006992
6 · The paper itself

Abstract

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/.

Indexed as

Databases, GeneticGene ComponentsGenomicsHigh-Throughput Nucleotide SequencingMetadataAnimalsCaenorhabditis elegansData DisplayDatasets as TopicDNADrosophila melanogasterForecastingGenome, HumanHumansMiceUser-Computer InterfaceDNA

Identifiers

PMID29126249
PMCPMC5753278

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.