Implementation of Zebrafish Ontologies for Toxicology Screening.

Autor:	Thessen AE; Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, United States., Marvel S; Department of Biological Sciences, Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States., Achenbach JC; Aquatic and Crop Resource Development Research Center, National Research Council of Canada, Halifax, NS, Canada., Fischer S; aQuaTox-Solutions Ltd, Wallisellen, Switzerland., Haendel MA; Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, United States., Hayward K; Department of Environmental and Molecular Toxicology and the Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States., Klüver N; Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany., Könemann S; Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland., Legradi J; Environment & Health, Vrije Universiteit Amsterdam, Amsterdam, Netherlands., Lein P; Department of Molecular Biosciences, University of California, Davis, Davis, CA, United States., Leong C; Department of Environmental and Molecular Toxicology and the Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States., Mylroie JE; Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, United States., Padilla S; Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States., Perone D; Department of Environmental and Molecular Toxicology and the Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States., Planchart A; Center for Human Health and the Environment, and Center for Environmental and Health Effects of PFAS, Biological Sciences, NC State University, Raleigh, NC, United States., Prieto RM; ZeClinics SL, Badalona, Spain., Muriana A; Biobide USA, Cambridge, MA, United States., Quevedo C; Biobide, Donostia-San Sebastian, Spain., Reif D; Department of Biological Sciences, Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States., Ryan K; Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Durham, NC, United States., Stinckens E; Zebrafishlab, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium., Truong L; Department of Environmental and Molecular Toxicology and the Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States., Vergauwen L; Zebrafishlab, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium., Vom Berg C; Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland., Wilbanks M; Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, United States., Yaghoobi B; Department of Molecular Biosciences, University of California, Davis, Davis, CA, United States., Hamm J; Integrated Laboratory Systems, LLC, Contractor supporting the National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, Durham, NC, United States.
Jazyk:	angličtina
Zdroj:	Frontiers in toxicology [Front Toxicol] 2022 Mar 11; Vol. 4, pp. 817999. Date of Electronic Publication: 2022 Mar 11 (Print Publication: 2022).
DOI:	10.3389/ftox.2022.817999
Abstrakt:	Toxicological evaluation of chemicals using early-life stage zebrafish ( Danio rerio ) involves the observation and recording of altered phenotypes. Substantial variability has been observed among researchers in phenotypes reported from similar studies, as well as a lack of consistent data annotation, indicating a need for both terminological and data harmonization. When examined from a data science perspective, many of these apparent differences can be parsed into the same or similar endpoints whose measurements differ only in time, methodology, or nomenclature. Ontological knowledge structures can be leveraged to integrate diverse data sets across terminologies, scales, and modalities. Building on this premise, the National Toxicology Program's Systematic Evaluation of the Application of Zebrafish in Toxicology undertook a collaborative exercise to evaluate how the application of standardized phenotype terminology improved data consistency. To accomplish this, zebrafish researchers were asked to assess images of zebrafish larvae for morphological malformations in two surveys. In the first survey, researchers were asked to annotate observed malformations using their own terminology. In the second survey, researchers were asked to annotate the images from a list of terms and definitions from the Zebrafish Phenotype Ontology. Analysis of the results suggested that the use of ontology terms increased consistency and decreased ambiguity, but a larger study is needed to confirm. We conclude that utilizing a common data standard will not only reduce the heterogeneity of reported terms but increases agreement and repeatability between different laboratories. Thus, we advocate for the development of a zebrafish phenotype atlas to help laboratories create interoperable, computable data. Competing Interests: Author SF is employed by aQuaTox-Solutions Ltd. Author AM is employed by Biobide. Author CQ is employed by Viralgen Vector Core. Author JH is employed by Integrated Laboratory Systems, LLC. Author RP is employed by ZeClinics SL. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2022 Thessen, Marvel, Achenbach, Fischer, Haendel, Hayward, Klüver, Könemann, Legradi, Lein, Leong, Mylroie, Padilla, Perone, Planchart, Prieto, Muriana, Quevedo, Reif, Ryan, Stinckens, Truong, Vergauwen, Vom Berg, Wilbanks, Yaghoobi and Hamm.)
Databáze:	MEDLINE
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