Evidence map›Paper›PMID 39903545›Full record

ArticleGenetics2025

ZFIN updates to support zebrafish environmental exposure data.

Yvonne M Bradford, Ceri E Van Slyke, Jonathan B Muyskens, Wei-Chia Tseng, Douglas G Howe, David Fashena, Ryan Martin, Holly Paddock, Christian Pich, Sridhar Ramachandran and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
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

14 authors.

Yvonne M BradfordThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.ORCID 0000-0002-9900-7880
Ceri E Van SlykeThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.ORCID 0000-0002-2244-7917
Jonathan B MuyskensThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
Wei-Chia TsengThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
Douglas G HoweThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.ORCID 0000-0001-5831-7439
David FashenaThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
Ryan MartinThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
Holly PaddockThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
Christian PichThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
Sridhar RamachandranThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
Leyla RuzickaThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.ORCID 0000-0002-1009-339X
Amy SingerThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
Ryan TaylorThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.
Monte WesterfieldThe Institute of Neuroscience, University of Oregon, 5291 University of Oregon, Eugene, OR 97403-5291, USA.

Funding

Text mining in the CloudU24HG010859 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAROL J BULT, PAUL Warren STERNBERG · 2019 to 2026
$42.0M
ZFIN: The Zebrafish Model Organism DatabaseU41HG002659 · NHGRI · UNIVERSITY OF OREGON · PI HOWE, DOUGLAS GORDON · 2011 to 2020
$30.7M
ZFIN:THE ZEBRAFISH MODEL ORGANISM DATABASEP41HG002659 · NHGRI · UNIVERSITY OF OREGON · PI WESTERFIELD, MONTE · 2003 to 2010
$21.2M
ZFIN: The Zebrafish Model Organism DatabaseU24HG002659 · NHGRI · UNIVERSITY OF OREGON · PI WESTERFIELD, MONTE · 2021 to 2025
$10.8M
Alliance of Genome ResourcesNHGRI NIH HHS P41 HG002659NHGRI NIH HHS U24 HG002659NHGRI NIH HHS U24 HG010859NHGRI NIH HHS U41 HG002659NIH HHS U41 HG002659 (ZFIN) and U24 HG010859
6 · The paper itself

Abstract

The Zebrafish Information Network (ZFIN, zfin.org) is the database resource for genetic, genomic, and phenotypic data from research using zebrafish, Danio rerio. ZFIN curates information about genetic perturbations, gene expression, phenotype, gene function, and human disease models from zebrafish research publications and makes these data available to researchers worldwide. Over the past 20 years, zebrafish have increasingly been used to investigate the effects of environmental exposures, becoming an ideal model to study toxicity, phenotypic outcomes, and gene-chemical interactions. Despite this, database resources supporting zebrafish toxicology and environmental exposure research are limited. To fill this gap, ZFIN has expanded functionality to incorporate and convey toxicology data better. ZFIN annotations for gene expression, phenotype, and human disease models include information about genotypes and experimental conditions used. One type of experimental condition the database captures is the application of chemicals to zebrafish. ZFIN annotates chemicals using the Chemical Entities of Biological Interest Ontology (ChEBI) along with the Zebrafish Experimental Conditions Ontology (ZECO) to denote route of exposure and other experimental conditions. These features allow researchers to search phenotypes and human disease models linked to chemicals more efficiently. Here, we discuss how experimental conditions are displayed on ZFIN web pages, the data displayed on chemical term pages, and how to search and download data associated with chemical exposure experiments.

Indexed as

Databases, GeneticEnvironmental ExposureZebrafishAnimalsHumansPhenotypedanio rerioenvironmental exposureexpressionhuman disease modelmodel organism databasephenotypezebrafishZFIN

Identifiers

PMID39903545
PMCPMC11912870

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.