Discovering the functions of the tens of thousands of genes in the human genome is a required step for understanding human biology and disease. Genetic model organisms, including zebrafish, play a critical role in this discovery process, because genetic analysis can connect gene sequence and function. Model organism databases, like ZFIN, provide tools required to make this connection. Zebrafish has emerged as a premiere model organism because powerful techniques allow efficient generation and recovery of zebrafish mutations affecting genes that regulate developmental patterning, organogenesis, physiology and behavior. Recent advances make it easy to study gene function in transgenic zebrafish and with antisense oligonucleotides. The functions of many of these genes are conserved among vertebrate groups. Thus, analysis of zebrafish mutations provides insights into gene functions in other vertebrates, including humans. The long term goals for ZFIN are a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology and f) to serve the needs of the research community. This project will expand curation of zebrafish phenotypes, implement Gene Ontology annotation of ZFIN gene records and incorporate the assembled zebrafish whole genome sequence into ZFIN. This work will provide a powerful means for researchers to associate gene sequence and function, thus facilitating cross-species analyses of genome organization and evolution as well as studies of vertebrate gene function and disease.
| Ruzicka, Leyla; Howe, Douglas G; Ramachandran, Sridhar et al. (2018) The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources. Nucleic Acids Res : |
| Lovering, Ruth C; Roncaglia, Paola; Howe, Douglas G et al. (2018) Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology. Circ Genom Precis Med 11:e001813 |
| Van Slyke, Ceri E; Bradford, Yvonne M; Howe, Douglas G et al. (2018) Using ZFIN: Data Types, Organization, and Retrieval. Methods Mol Biol 1757:307-347 |
| Bradford, Yvonne M; Toro, Sabrina; Ramachandran, Sridhar et al. (2017) Zebrafish Models of Human Disease: Gaining Insight into Human Disease at ZFIN. ILAR J 58:4-16 |
| Huntley, Rachael P; Sitnikov, Dmitry; Orlic-Milacic, Marija et al. (2016) Guidelines for the functional annotation of microRNAs using the Gene Ontology. RNA 22:667-76 |
| Edmunds, Richard C; Su, Baofeng; Balhoff, James P et al. (2016) Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. Mol Biol Evol 33:13-24 |
| Howe, D G; Bradford, Y M; Eagle, A et al. (2016) A scientist's guide for submitting data to ZFIN. Methods Cell Biol 135:451-81 |
| Diehl, Alexander D; Meehan, Terrence F; Bradford, Yvonne M et al. (2016) The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics 7:44 |
| Ruzicka, Leyla; Bradford, Yvonne M; Frazer, Ken et al. (2015) ZFIN, The zebrafish model organism database: Updates and new directions. Genesis 53:498-509 |
| Van Slyke, Ceri E; Bradford, Yvonne M; Westerfield, Monte et al. (2014) The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomed Semantics 5:12 |
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