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The Zebrafish Information Network (ZFIN): the zebrafish model organism database

J. Sprague
2003 Nucleic Acids Research  
The Zebrafish Information Network (ZFIN) is a web based community resource that serves as a centralized location for the curation and integration of zebrafish genetic, genomic and developmental data.  ...  ACKNOWLEDGEMENT Funds for the development of the Zebrafish Information Network are provided by the NIH (RR/HD 12546).  ...  INTRODUCTION The zebrafish has emerged as a model organism important for the identification and characterization of genes and pathways involved in development, organ function, behavior and disease.  ... 
doi:10.1093/nar/gkg027 pmid:12519991 pmcid:PMC165474 fatcat:5yyclbuwuzc5vhny2ueudbgrge

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.  ...  ZFIN provides an integrated representation of mutants, genes, genetic markers, 15 mapping panels, publications and community resources such as meeting announcements and contact information.  ...  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 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

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

The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research

J. Sprague
2001 Nucleic Acids Research  
The Zebrafish Information Network, ZFIN, is a WWW community resource of zebrafish genetic, genomic and developmental research information (http://zfin.org).  ...  The database, built on a relational, object-oriented model, provides integrated information about mutants, genes, genetic markers, mapping panels, publications and contact information for the zebrafish  ...  ACKNOWLEDGEMENTS The development of the Zebrafish Information Network is generously supported by the W.M. Keck Foundation. Funds are also provided by the NIH (RR/HD12546).  ... 
doi:10.1093/nar/29.1.87 pmid:11125057 pmcid:PMC29808 fatcat:hfkuvvjsebazjig7zdqamrc2ii

Zebrafish Information Network, the knowledgebase for Danio rerio research

Yvonne M Bradford, Ceri E Van Slyke, Leyla Ruzicka, Amy Singer, Anne Eagle, David Fashena, Douglas G Howe, Ken Frazer, Ryan Martin, Holly Paddock, Christian Pich, Sridhar Ramachandran (+1 others)
2022 Genetics  
The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for Danio rerio genetic and genomic data.  ...  Recently, ZFIN and six other model organism knowledgebases have collaborated to form the Alliance of Genome Resources, aiming to develop sustainable genome information resources that enable the use of  ...  Introduction The Zebrafish Information Network (ZFIN, zfin.org) is the knowledgebase for the model organism Danio rerio (zebrafish).  ... 
doi:10.1093/genetics/iyac016 pmid:35166825 pmcid:PMC8982015 fatcat:v737talhbvbqdn4edyablydogi

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).  ...  New features at ZFIN include major updates to the home page and the gene page, the two most used pages at ZFIN.  ...  INTRODUCTION The Zebrafish Information Network (ZFIN) (https://zfin. org/) is the central repository for zebrafish (Danio rerio) genetic and genomic data.  ... 
doi:10.1093/nar/gkaa1010 pmid:33170210 pmcid:PMC7778988 fatcat:sofsxiaecncnnkvkeh3y5nwem4

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).  ...  ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO).  ...  INTRODUCTION The Zebrafish Information Network (ZFIN) (https://zfin. org/) is the central repository for zebrafish (Danio rerio) genetic and genomic data.  ... 
doi:10.1093/nar/gky1090 pmid:30407545 pmcid:PMC6323962 fatcat:dhrucy7vmve75jckjuofnine2e

The Zebrafish Insertion Collection (ZInC): a web based, searchable collection of zebrafish mutations generated by DNA insertion

Gaurav K. Varshney, Haigen Huang, Suiyuan Zhang, Jing Lu, Derek E. Gildea, Zhongan Yang, Tyra G. Wolfsberg, Shuo Lin, Shawn M. Burgess
2012 Nucleic Acids Research  
Over the last two decades, the zebrafish has become a popular model organism for studying vertebrate development as well as for modeling human diseases.  ...  ZInC (Zebrafish Insertional Collection, http:// research.nhgri.nih.gov/ZInC/) is a web-searchable interface of insertional mutants in zebrafish.  ...  ACKNOWLEDGEMENTS We would like to thank Colin Huck for outstanding animal care, and Robert Blakesley, Alice Young and the NIH Intramural Sequencing Center (NISC) for providing sequence data.  ... 
doi:10.1093/nar/gks946 pmid:23180778 pmcid:PMC3531054 fatcat:cawbzo6fz5dpvb6pzj4j6viemy

Data integration for spatio-temporal patterns of gene expression of zebrafish development: the GEMS database

Mounia Belmamoune, Fons J Verbeek
2008 Journal of Integrative Bioinformatics  
The atlas contains 3D volume models of canonical stages of zebrafish development in which in each volume model element is annotated with an anatomical term.  ...  The GEMS operates in concert with a database containing a digital atlas of zebrafish embryo; this digital atlas of zebrafish development has been conceived prior to the expansion of the GEMS.  ...  Acknowledgments The authors would like to express gratitude to Dr. M.C. Welten, W. Spoor and A. Sels for their contributions by submitting experimental data to the system.  ... 
doi:10.2390/biecoll-jib-2008-92 pmid:20134060 fatcat:aeyoeaovafattonwa6hhestwb4

CRISPRz: a database of zebrafish validated sgRNAs

Gaurav K. Varshney, Suiyuan Zhang, Wuhong Pei, Ashrifia Adomako-Ankomah, Jacob Fohtung, Katherine Schaffer, Blake Carrington, Anoo Maskeri, Claire Slevin, Tyra Wolfsberg, Johan Ledin, Raman Sood (+1 others)
2015 Nucleic Acids Research  
CRISPRz can be searched using multiple inputs such as ZFIN IDs, accession number, UniGene ID, or gene symbols from zebrafish, human and mouse.  ...  Programmable RNA-guided CRISPR/Cas9 has recently emerged as a simple and efficient genome editing method in various cell types and organisms, including zebrafish.  ...  The database is also open for data submission from the research community. An effort is being made to cross-reference CRISPRz with the Zebrafish Information Network (ZFIN) database.  ... 
doi:10.1093/nar/gkv998 pmid:26438539 pmcid:PMC4702947 fatcat:xfmx7i4wsjf2dc6uiexv7sygde

Mapping of Zebrafish Research: A Global Outlook

Priyamvadah Kinth, Gopalakrishnan Mahesh, Yatish Panwar
2013 Zebrafish  
On the basis of analysis of 17,151 records on zebrafish identified from Zebrafish Information Network: the zebrafish model organism database and Web of Science, the research performance on this model organism  ...  The earliest research work on zebrafish as reflected in the databases goes back to 1951. After a rather slow growth till the 1980s, research on zebrafish gained momentum in the 1990s.  ...  Acknowledgment The authors thank the anonymous reviewers whose insightful comments enabled us to improve several sections of the article. Disclosure Statement No competing financial interests exist.  ... 
doi:10.1089/zeb.2012.0854 pmid:24131434 pmcid:PMC3842892 fatcat:rzlfborklffxhnjdurtd7b2g5q

Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish

Paula M. Mabee, Gloria Arratia, Miles Coburn, Melissa Haendel, Eric J. Hilton, John G. Lundberg, Richard L. Mayden, Nelson Rios, Monte Westerfield
2007 Journal of Experimental Zoology Part B: Molecular and Developmental Evolution  
http://www.bioontology.org/wiki/ index.php/PATO: Main_Page ZFIN-Zebrafish Information Network, the model organism database for zebrafish http://www.zfin.org/ P.  ...  We will utilize both existing and new ontologies to connect the evolutionary anatomy and image database that is being developed in the Cypriniformes Tree of Life project to the Zebrafish Information Network  ...  ACKNOWLEDGMENTS We thank the NSF National Evolutionary Synthesis Center (EF-0423641), NSF Cypriniformes Tree of Life (DEB-0431290), NIH HG002659 and HG004028 for support.  ... 
doi:10.1002/jez.b.21181 pmid:17599725 fatcat:g3zxqegl2jherodstnvyfo2kwm

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 is also cross-linked with ZFIN, allowing full searches between the two databases.  ...  Acknowledgements The authors would like to acknowledge the numerous collaborations that have contributed to the development of MODB such as the laboratories of Drs.  ... 
doi:10.1186/1471-2105-9-7 pmid:18179718 pmcid:PMC2221974 fatcat:6jsytilfcbcvtijgow3vl2jivu

Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database

Mounia Belmamoune, Fons J. Verbeek
2008 Journal of Integrative Bioinformatics  
The atlas contains 3D volume models of canonical stages of zebrafish development in which in each volume model element is annotated with an anatomical term.  ...  The GEMS operates in concert with a database containing a digital atlas of zebrafish embryo; this digital atlas of zebrafish development has been conceived prior to the expansion of the GEMS.  ...  Acknowledgments The authors would like to express gratitude to Dr. M.C. Welten, W. Spoor and A. Sels for their contributions by submitting experimental data to the system.  ... 
doi:10.1515/jib-2008-92 fatcat:ostxgnscnnfxrjehb6ehkfhu4m
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