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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.  ...  Here, we describe recent additions to ZFIN including (i) enhanced access to images, (ii) genomic features, (iii) genome browser, (iv) transcripts, (v) antibodies and (vi) a community wiki for protocols  ...  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

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.  ...  Researchers can submit mutant, transgenic, expression, and phenotype data directly to ZFIN and use the ZFIN Community Wiki to share antibody and protocol information.  ...  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, 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

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

J. Sprague
2001 Nucleic Acids Research  
ZFIN provides an anatomical atlas and dictionary, developmental staging criteria, research methods, pathology information and a link to the ZFIN relational database (http://zfin.org/ZFIN/).  ...  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

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.  ...  Recent enhancements to ZFIN include (i) a new home page and navigation bar, (ii) expanded support for genotypes and phenotypes, (iii) comprehensive phenotype annotations based on anatomical, phenotypic  ...  Funds to ZFIN through the NCBO to further development of tools and curation of phenotype annotation are provided by the NIH HG004028.  ... 
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  
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  ...  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.  ...  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: 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).  ...  The ZFIN database was updated to record and display GO annotations with their annotation extensions, making zebrafish GO annotations more expressive.  ... 
doi:10.1093/nar/gky1090 pmid:30407545 pmcid:PMC6323962 fatcat:dhrucy7vmve75jckjuofnine2e

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

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.  ...  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 Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation

M. Singh, D. Bhartiya, J. Maini, M. Sharma, A. R. Singh, S. Kadarkaraisamy, R. Rana, A. Sabharwal, S. Nanda, A. Ramachandran, A. Mittal, S. Kapoor (+35 others)
2014 Database: The Journal of Biological Databases and Curation  
These authors contributed equally to this work. zAuthors are listed in the descending order based on their microattributions credits in the Zebrafish GenomeWiki database.  ...  §Authors provided technical assistance for creating and maintaining the database and related infrastructure.  ...  Acknowledgements The authors are grateful to the laboratory members for valuable inputs and encouragement. They thank the members of zebrafish community for freely sharing their data.  ... 
doi:10.1093/database/bau011 pmid:24578356 pmcid:PMC3936183 fatcat:lutnifz4ufc55jbbsk2qjqfkzu

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.  ...  The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular anatomy and development of the zebrafish  ...  John Lundberg for their anatomical expertise, and the entire ZFIN staff for their instrumental work on the expression and phenotype annotation system.  ... 
doi:10.1186/2041-1480-5-12 pmid:24568621 pmcid:PMC3944782 fatcat:bmhhm3n4dzfuba3tkwnkfzoee4

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.  ...  To improve the searchability of this database, we have incorporated a fixed-vocabulary defect ontology that allows for the organization of morpholino affects based on anatomical structure affected and  ...  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

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  
Our motivation to build this system was by the need to be able to organize and compare multiple patterns of gene expression at tissue level.  ...  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

MEPD: medaka expression pattern database, genes and more

Juan I. Alonso-Barba, Raza-Ur Rahman, Joachim Wittbrodt, Juan L. Mateo
2015 Nucleic Acids Research  
Based on this, we provide a link to the Zebrafish Model Organism Database (ZFIN) to allow researches to compare expression data between these two fish model organisms.  ...  As a second major improvement, we have modified the design of the database to enable it to host regulatory elements, promoters or enhancers, expression patterns in addition to gene expression.  ...  ACKNOWLEDGEMENT We want to thank all the members of the Wittbrodt lab and specially Thorsten Henrich and Mirana Ramialison for their comments and suggestions. FUNDING  ... 
doi:10.1093/nar/gkv1029 pmid:26450962 pmcid:PMC4702773 fatcat:uswqprth2fcnfplgmipic3ow6e

Web Resources for Model Organism Studies

Bixia Tang, Yanqing Wang, Junwei Zhu, Wenming Zhao
2015 Genomics, Proteomics & Bioinformatics  
Furthermore, all of the databases mentioned here update continually according to user feedback and with advancing technologies.  ...  In this paper, we review 13 databases of model organisms, most of which are reported by the National Institutes of Health of the United States (NIH; http://www.nih.gov/science/models/).  ...  Acknowledgements This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences of China (Grant No. XDB13040500).  ... 
doi:10.1016/j.gpb.2015.01.003 pmid:25707592 pmcid:PMC4411489 fatcat:s56qk3jnx5eq7baciz25exjsaq
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