Evidence map›Paper›PMID 30407545›Full record

ArticleNucleic acids research2019

The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources.

Leyla Ruzicka, Douglas G Howe, Sridhar Ramachandran, Sabrina Toro, Ceri E Van Slyke, Yvonne M Bradford, Anne Eagle, David Fashena, Ken Frazer, Patrick Kalita and 9 more

Abstract read
In one paragraph

Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.

0numbers the graph read from it
0cells of the map it votes in
83citing papers in PubMed
–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

83 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Article
  6. Review
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Article
  14. Review
  15. genomepy: genes and genomes at your fingertips.Bioinformatics (Oxford, England) · 2023
    Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Review

23 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

19 authors.

Leyla RuzickaThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Douglas G HoweThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Sridhar RamachandranThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Sabrina ToroThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Ceri E Van SlykeThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Yvonne M BradfordThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Anne EagleThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
David FashenaThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Ken FrazerThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Patrick KalitaThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Prita ManiThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Ryan MartinThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Sierra Taylor MoxonThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Holly PaddockThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Christian PichThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Kevin SchaperThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Xiang ShaoThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Amy SingerThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.
Monte WesterfieldThe Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA.

Funding

Text mining in the CloudU24HG010859 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAROL J BULT, PAUL Warren STERNBERG · 2019 to 2026
$42.0M
Resource ProjectU41HG002273 · NHGRI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI CHERRY, J. MICHAEL, MUNGALL, CHRISTOPHER J · 2012 to 2021
$34.7M
ZFIN: The Zebrafish Model Organism DatabaseU41HG002659 · NHGRI · UNIVERSITY OF OREGON · PI WESTERFIELD, MONTE · 2011 to 2020
$30.7M
ZFIN:THE ZEBRAFISH MODEL ORGANISM DATABASEP41HG002659 · NHGRI · UNIVERSITY OF OREGON · PI WESTERFIELD, MONTE · 2003 to 2010
$21.2M
NHGRI NIH HHS P41 HG002659NHGRI NIH HHS U24 HG010859NHGRI NIH HHS U41 HG002273NHGRI NIH HHS U41 HG002659
6 · The paper itself

Abstract

The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, nomenclature and reagents. New features at ZFIN include increased support for genomic regions and for non-coding genes, and support for more expressive Gene Ontology annotations. ZFIN has recently taken over maintenance of the zebrafish reference genome sequence as part of the Genome Reference Consortium. ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO). The recently launched Alliance portal (https://alliancegenome.org) provides a unified, comparative view of MOD, GO, and human data, and facilitates foundational and translational biomedical research.

Indexed as

Databases, GeneticGenomicsAnimalsGene ExpressionGene OntologyGenomeHumansMolecular Sequence AnnotationMutationPhenotypeZebrafish

Identifiers

PMID30407545
PMCPMC6323962

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.