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ZFIN: enhancements and updates to the zebrafish model organism database
2010
Nucleic Acids Research
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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
2015
Genesis
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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
2012
Nucleic Acids Research
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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
2001
Nucleic Acids Research
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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
2007
Nucleic Acids Research
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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
2006
Nucleic Acids Research
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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
2018
Nucleic Acids Research
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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
2016
Nucleic Acids Research
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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
2020
Nucleic Acids Research
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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
2014
Database: The Journal of Biological Databases and Curation
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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
2014
Journal of Biomedical Semantics
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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
2008
BMC Bioinformatics
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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
2008
Journal of Integrative Bioinformatics
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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
2015
Nucleic Acids Research
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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
2015
Genomics, Proteomics & Bioinformatics
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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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