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ZFIN updates to support zebrafish environmental exposure data

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Bibliographic Details
Title: ZFIN updates to support zebrafish environmental exposure data
Authors: 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, Leyla Ruzicka, Amy Singer, Ryan Taylor, Monte Westerfield
Source: Genetics
Publisher Information: Oxford University Press (OUP), 2025.
Publication Year: 2025
Subject Terms: Phenotype, Databases, Genetic, Animals, Humans, Knowledgebase and Database Resources, Environmental Exposure, Zebrafish
Description: 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.
Document Type: Article
Other literature type
Language: English
ISSN: 1943-2631
DOI: 10.1093/genetics/iyaf021
Access URL: https://pubmed.ncbi.nlm.nih.gov/39903545
Rights: CC BY
URL: http://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Accession Number: edsair.doi.dedup.....a94d1290eb3b974641a92b098b01f57a
Database: OpenAIRE
Description
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.
ISSN:19432631
DOI:10.1093/genetics/iyaf021