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ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

Douglas G. Howe, Yvonne M. Bradford, Tom Conlin, Anne E. Eagle, David Fashena, Ken Frazer, Jonathan Knight, Prita Mani, Ryan Martin, Sierra A. Taylor Moxon, Holly Paddock, Christian Pich (+9 others)
2012 Nucleic Acids Research  
ZFIN, the Zebrafish Model Organism Database (http://zfin.org), is the central resource for zebrafish genetic, genomic, phenotypic and developmental data.  ...  Among the vertebrate model organisms, zebrafish are uniquely well suited for rapid and targeted generation of mutant lines.  ...  MUTANT AND TRANSGENIC DATA Zebrafish have become one of the pre-eminent model organisms for studies of gene function aimed at understanding human development and disease.  ... 
doi:10.1093/nar/gks938 pmid:23074187 pmcid:PMC3531097 fatcat:uzddasd6qrhjvmphh7z4qtp3ay

ZFIN, The zebrafish model organism database: Updates and new directions

Leyla Ruzicka, Yvonne M. Bradford, Ken Frazer, Douglas G. Howe, Holly Paddock, Sridhar Ramachandran, Amy Singer, Sabrina Toro, Ceri E. Van Slyke, Anne E. Eagle, David Fashena, Patrick Kalita (+8 others)
2015 Genesis  
The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for genetic and genomic data from zebrafish (Danio rerio) research.  ...  The use of zebrafish as a model for human disease is increasing.  ...  Acknowledgments Grant Support: This work was supported by the National Human Genome Research Institute (HG002659, and HG004834) of the National Institutes of Health.  ... 
doi:10.1002/dvg.22868 pmid:26097180 pmcid:PMC4545674 fatcat:tba5jdejl5grxavmzhzgzjfcpa

ZFIN: enhancements and updates to the zebrafish model organism database

Y. Bradford, T. Conlin, N. Dunn, D. Fashena, K. Frazer, D. G. Howe, J. Knight, P. Mani, R. Martin, S. A. T. Moxon, H. Paddock, C. Pich (+11 others)
2010 Nucleic Acids Research  
ZFIN, the Zebrafish Model Organism Database, http://zfin.org, serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data.  ...  ZFIN manually curates comprehensive data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications.  ...  forms combined with Java/JSP, GWT, JavaScript, Perl and CGI scripts provide access to the database.  ... 
doi:10.1093/nar/gkq1077 pmid:21036866 pmcid:PMC3013679 fatcat:w23trxqicjdifkyqkbpeqepale

The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes

J. Sprague, L. Bayraktaroglu, Y. Bradford, T. Conlin, N. Dunn, D. Fashena, K. Frazer, M. Haendel, D. G. Howe, J. Knight, P. Mani, S. A.T. Moxon (+10 others)
2007 Nucleic Acids Research  
The Zebrafish Information Network (ZFIN, http:// zfin.org), the model organism database for zebrafish, provides the central location for curated zebrafish genetic, genomic and developmental data.  ...  ZFIN is the definitive source for zebrafish gene and allele nomenclature, the zebrafish anatomical ontology (AO) and for zebrafish gene ontology (GO) annotations.  ...  ACKNOWLEDGEMENTS Funds for the development of the Zebrafish Information Network are provided by the NIH HG002659.  ... 
doi:10.1093/nar/gkm956 pmid:17991680 pmcid:PMC2238839 fatcat:3jookkeqbfbifhku6ymfqsns7q

The Zebrafish Information Network: the zebrafish model organism database

J. Sprague
2006 Nucleic Acids Research  
10 The Zebrafish Information Network (ZFIN; http://zfin. org) is a web based community resource that implements the curation of zebrafish genetic, genomic and developmental data.  ...  Recent enhancements to ZFIN include (i) comprehensive curation of gene expression data from the literature and from directly sub-20 mitted data, (ii) increased support and annotation of the genome sequence  ...  ACKNOWLEDGEMENTS 5 Funds for the development of the Zebrafish Information Network are provided by the NIH HG002659.  ... 
doi:10.1093/nar/gkj086 pmid:16381936 pmcid:PMC1347449 fatcat:hn2czv6dkbg2rjpedqetwwym5i

The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching

Douglas G. Howe, Yvonne M. Bradford, Anne Eagle, David Fashena, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin, Sierra Taylor Moxon, Holly Paddock, Christian Pich, Sridhar Ramachandran (+7 others)
2016 Nucleic Acids Research  
The Zebrafish Model Organism Database (ZFIN; http: //zfin.org) is the central resource for zebrafish (Danio rerio) genetic, genomic, phenotypic and developmental data.  ...  Here, we describe recent enhancements to ZFIN including use of the zebrafish experimental conditions ontology, 'Fish' records in the ZFIN database, support for gene expression phenotypes, models of human  ...  INTRODUCTION The Zebrafish Model Organism Database (ZFIN; http:// zfin.org) is the community resource for genetic and genomic data involving zebrafish (Danio rerio).  ... 
doi:10.1093/nar/gkw1116 pmid:27899582 pmcid:PMC5210580 fatcat:nrztsq4p3jas5fpea43lanrauq

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information

Michelle N Knowlton, Tongbin Li, Yongliang Ren, Brent R Bill, Lynda BM Ellis, Stephen C Ekker
2008 BMC Bioinformatics  
The zebrafish is a powerful model vertebrate amenable to high throughput in vivo genetic analyses.  ...  MODB also serves as a template for future sequencebased functional genetic screen databases, and it is currently being used as a model for the creation of a mutagenic insertional transposon database.  ...  Eric Klee and Kyong Jin Shim. Funding for this project was obtained from the NIH to SCE (GM63904 and CA65493). This work was supported in part by the University of Minnesota Supercomputing Institute.  ... 
doi:10.1186/1471-2105-9-7 pmid:18179718 pmcid:PMC2221974 fatcat:6jsytilfcbcvtijgow3vl2jivu

Model organism databases are in jeopardy

Hugo J. Bellen, E. J. A. Hubbard, Ruth Lehmann, Hiten D. Madhani, Lila Solnica-Krezel, E. Michelle Southard-Smith
2021 Development  
They provide open access, searchable and well-curated information about the diverse biological properties of each organism, such as their respective genes, mutant and transgenic alleles, gene and protein  ...  /all/2016/07/14/a-look-attrends-in-nihs-model-organism-research-support/).  ...  Competing interests The authors declare no competing or financial interests.  ... 
doi:10.1242/dev.200193 pmid:35231122 fatcat:zl7eztg4ibagvfgjp6o236fy2i

Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis

Yoel Bogoch, Allison Jamieson-Lucy, Charles E. Vejnar, Karine Levy, Antonio J. Giraldez, Mary C. Mullins, Yaniv M. Elkouby
2022 Frontiers in Cell and Developmental Biology  
We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish.  ...  Our analysis provides the first molecular description for oogenesis in zebrafish, which we deposit online as a resource for the community.  ...  We thank Albert Pan and Rene Ketting for the Tg(ub:zebrabow) and Tg(vasa:GFP) fish lines, respectively.  ... 
doi:10.3389/fcell.2022.826892 pmid:35733854 pmcid:PMC9207522 fatcat:wjdoedw425aytbshbefq4xyzci

PhenoDigm: analyzing curated annotations to associate animal models with human diseases

D. Smedley, A. Oellrich, S. Kohler, B. Ruef, M. Westerfield, P. Robinson, S. Lewis, C. Mungall
2013 Database: The Journal of Biological Databases and Curation  
C.M. and S.L. provided the OWLSim source code, guidance and support and how to apply OWLSim to the input data.  ...  S.K. and P.R. generated the pre-composed version of zebrafish annotations (ZP), that was then curated and corrected by B.R. and M.W.  ...  As for the mouse, recent advances allow high-throughput generation of mutants and transgenics and their phenotype characterization.  ... 
doi:10.1093/database/bat025 pmid:23660285 pmcid:PMC3649640 fatcat:5c5jjafnbzbrrdsodzw4xe2ghq

Zebrafish Models of Human Disease: Gaining Insight into Human Disease at ZFIN

Yvonne M. Bradford, Sabrina Toro, Sridhar Ramachandran, Leyla Ruzicka, Douglas G. Howe, Anne Eagle, Patrick Kalita, Ryan Martin, Sierra A. Taylor Moxon, Kevin Schaper, Monte Westerfield
2017 ILAR journal  
The Zebrafish Model Organism Database (ZFIN; https://zfin.org) is the central resource for genetic, genomic, and phenotypic data for zebrafish (Danio rerio) research.  ...  To facilitate disease-related research, ZFIN developed support to provide human disease information as well as annotation of zebrafish models of human disease.  ...  Acknowledgments The authors want to thank the entire ZFIN curatorial and software development team for their help in implementing this project and ongoing data curation.  ... 
doi:10.1093/ilar/ilw040 pmid:28838067 pmcid:PMC5886338 fatcat:erm6yxw66bfbvanekywrd7twme

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, Prita Mani, Ryan Martin (+7 others)
2018 Nucleic Acids Research  
The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio).  ...  New features at ZFIN include increased support for genomic regions and for non-coding genes, and support for more expressive Gene Ontology annotations.  ...  ZFIN collects, organizes, and makes available a wide range of data on zebrafish, including genes, gene function, sequences, mutants, transgenic lines, human disease models, expression, phenotype, orthology  ... 
doi:10.1093/nar/gky1090 pmid:30407545 pmcid:PMC6323962 fatcat:dhrucy7vmve75jckjuofnine2e

The Zebrafish Information Network: major gene page and home page updates

Douglas G Howe, Sridhar Ramachandran, Yvonne M Bradford, David Fashena, Sabrina Toro, Anne Eagle, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin, Sierra Taylor Moxon, Holly Paddock (+7 others)
2020 Nucleic Acids Research  
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  ...  ZFIN collects, organizes and makes available a wide range of data on zebrafish, including genes, gene function, sequences, mutants, transgenic lines, human disease models, expression, phenotype, orthology  ... 
doi:10.1093/nar/gkaa1010 pmid:33170210 pmcid:PMC7778988 fatcat:sofsxiaecncnnkvkeh3y5nwem4

The Molecular Biology Database Collection: 2002 update

A. D. Baxevanis
2002 Nucleic Acids Research  
Short, searchable summaries and updates for each of the databases included in the Collection are available through the Nucleic Acids Research Web site at http:// nar.oupjournals.org.  ...  The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community.  ...  The most eagerly-anticipated model organism map is that of the mouse.  ... 
doi:10.1093/nar/30.1.1 pmid:11752241 pmcid:PMC99169 fatcat:n46iu5l6oreapd5yxswe7pmg5m

The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio

Ceri E Van Slyke, Yvonne M Bradford, Monte Westerfield, Melissa A Haendel
2014 Journal of Biomedical Semantics  
The zebrafish model organism database (ZFIN) uses the ZFA and ZFS to annotate phenotype and gene expression data from the primary literature and from contributed data sets.  ...  Conclusions: The ZFA describes zebrafish anatomy and development semantically for the purposes of annotating gene expression and anatomical phenotypes.  ...  We acknowledge Christian Pich for extensive technical help in updating the load of the ZFA into ZFIN, Perian Song for providing technical support for integrating CL terms into ZFA, Brock Sprunger for data  ... 
doi:10.1186/2041-1480-5-12 pmid:24568621 pmcid:PMC3944782 fatcat:bmhhm3n4dzfuba3tkwnkfzoee4
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