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Zebrafish Information Network

Background:

A group of zebrafish researchers were appointed at the 1994 Cold Spring Harbor meeting on zebrafish genetics and development, to establish an on-line database of information for zebrafish as a model organism.

The resulting database, The Zebrafish Information Network (ZFIN) (https://zfin.org/), is the database of genetic and genomic data for the zebrafish (Danio rerio) as a model organism. ZFIN provides a wide array of expertly curated, organized and cross-referenced zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, phenotypes, orthology, human disease models, nomenclature and reagents.

In 2016, ZFIN joined together with five other model organism databases (WormBase, FlyBase, Mouse Genome Database, Rat Genome Database, Saccharomyces Genome Database) and the Gene Ontology Consortium to form the Alliance of Genome Resources (The Alliance).  The primary mission of the Alliance is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease. This understanding is fundamental for advancing genome biology research and for translating human genome data into clinical utility.


Goals:

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.

ZIRC is the Zebrafish International Resource Center, an independent NIH-funded facility providing a wide range of zebrafish lines, probes and health services. ZFIN works closely with ZIRC to connect our genetic data with available probes and fish lines.


Citing ZFIN:

We recommend the following formats for citing ZFIN in publications:

1. For a general reference to the database:

Ruzicka L, Howe DG, Ramachandran S, Toro S, Van Slyke CE, Bradford YM, Eagle A, Fashena D, Frazer K, Kalita P, Mani P, Martin R, Moxon ST, Paddock H, Pich C, Schaper K, Shao X, Singer A, Westerfield M. (2019). The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources. Nucleic Acids Res. Jan 8;47(D1):D867-D873.

doi: 10.1093/nar/gky1090.      PubMed PMID:30407545      PubMed Central PMCID:PMC6323962

2. For citing a specific entry in ZFIN:

[Type of] data for this paper were retrieved from the Zebrafish Information Network (ZFIN), University of Oregon, Eugene, OR 97403-5274; URL: http://zfin.org/; [the date you retrieved the data cited].


Research staff:

Monte Westerfield, P.I.; Doug Howe, Data Curation Manager; Anne Eagle, Technical Manager; and the rest of the ZFIN Database Team.


Advisory board:

  • Carol Bult, The Jackson Laboratory Cancer Center
  • Shawn Burgess, National Human Genome Research Center, National Institutes of Health
  • Jeffrey De Pons, Medical College of Wisconsin
  • Richard Dorsky, Director of Neuroscience, University of Utah
  • John Postlethwait, University of Oregon
  • Paul Sternberg, Wormbase. 


Publications:

Ruzicka, L., Howe, D.G., Ramachandran, S., Toro, S., Van Slyke, C.E., Bradford, Y.M., Eagle, A., Fashena, D., Frazer, K., Kalita, P., Mani, P., Martin, R., Moxon, S.T., Paddock, H., Pich, C., Schaper, K., Shao, X., Singer, A., Westerfield, M. (2018) The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources. Nucleic acids research. 47(D1):D867-D873

Howe, D.G., Blake, J.A., Bradford, Y.M., Bult, C.J., Calvi, B.R., Engel, S.R., Kadin, J.A., Kaufman, T.C., Kishore, R., Laulederkind, S.J.F., Lewis, S.E., Moxon, S.A.T., Richardson, J.E., Smith, C. (2018) Model organism data evolving in support of translational medicine. Lab animal. 47(10):277-289

Howe, D.G. (2018) A statistical approach to identify, monitor, and manage incomplete curated data sets. BMC Bioinformatics. 19:110

Van Slyke, C.E., Bradford, Y.M., Howe, D.G., Fashena, D.S., Ramachandran, S., Ruzicka, L., ZFIN Staff* (2018) Using ZFIN: Data Types, Organization, and Retrieval. Methods in molecular biology (Clifton, N.J.). 1757:307-347

Bradford, Y.M., Toro, S., Ramachandran, S., Ruzicka, L., Howe, D.G., Eagle, A., Kalita, P., Martin, R., Taylor Moxon, S.A., Schaper, K., Westerfield, M. (2017) Zebrafish Models of Human Disease: Gaining Insight into Human Disease at ZFIN. ILAR journal. 58:4-16

Howe, D.G., Bradford, Y.M., Eagle, A., Fashena, D., Frazer, K., Kalita, P., Mani, P., Martin, R., Moxon, S.T., Paddock, H., Pich, C., Ramachandran, S., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Toro, S., Van Slyke, C., Westerfield, M. (2017) The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. Nucleic acids research. 45(D1):D758-D768

Howe, D.G., Bradford, Y.M., Eagle, A., Fashena, D., Frazer, K., Kalita, P., Mani, P., Martin, R., Moxon, S.T., Paddock, H., Pich, C., Ramachandran, S., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Toro, S., Van Slyke, C., Westerfield, M. (2016) A scientist's guide for submitting data to ZFIN. Methods in cell biology. 135:451-81

Van Slyke, C.E., Bradford, Y.M., Westerfield, M., Haendel, M.A. (2014) The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. Journal of biomedical semantics. 5:12

Howe, D.G., Bradford, Y.M., Conlin, T., Eagle, A.E., Fashena, D., Frazer, K., Knight, J., Mani, P., Martin, R., Moxon, S.A., Paddock, H., Pich, C., Ramachandran, S., Ruef, B.J., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Sprunger, B., Van Slyke, C.E., and Westerfield, M. (2013) ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic acids research. 41(D1):D854-860

Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Howe, D.G., Knight, J., Mani, P., Martin, R., Moxon, S.A., Paddock, H., Pich, C., Ramachandran, S., Ruef, B.J., Ruzicka, L., Bauer Schaper, H., Schaper, K., Shao, X., Singer, A., Sprague, J., Sprunger, B., Van Slyke, C., and Westerfield, M. (2011). ZFIN: enhancements and updates to the zebrafish model organism database. Nucleic Acids Res. 39(suppl 1):D822-D829.

Howe, D.G., Frazer, K., Fashena, D., Ruzicka, L., Bradford, Y., Ramachandran, S., Ruef, B.J., Van Slyke, C., Singer, A., and Westerfield, M. (2011) Data extraction, transformation, and dissemination through ZFIN. Methods in cell biology. 104:311-325.

Ramachandran, S., Ruef, B., Pich, C., and Sprague, J. (2010) Exploring zebrafish genomic, functional and phenotypic data using ZFIN. Current protocols in bioinformatics. Chapter 1:Unit 1.18

Sprague, J., Bayraktaroglu, L., Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Knight, J., Mani, P., Moxon, S.A., Pich, C., Ramachandran, S., Schaper, K., Segerdell, E., Shao, X., Singer, A., Song, P., Sprunger, B., Van Slyke, C.E., and Westerfield, M. (2008) The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic acids research. 36:D768-772.

Sprague, J., Bayraktaroglu, L., Clements, D., Conlin, T., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Mani, P., Ramachandran, S., Schaper, K., Segerdell, E., Song, P., Sprunger, B., Taylor, S., Van Slyke, C.E., and Westerfield, M. (2006). The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res. Jan 1;34(Database issue):D581-5.

Sprague, J., Clements, D., Conlin, T., Edwards, P., Frazer, K., Schaper, K., Segerdell, E., Song, P., Sprunger, B., and Westerfield, M. (2003) The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic acids research. 31(1):241-243.

Judy Sprague, Eckehard Doerry, Sarah Douglas and Monte Westerfield. (2001). The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research. Nucleic Acid Res. 29:87-90.

Westerfield, M., Doerry, E., and Douglas, S. (1999). Zebrafish in the net. Trends Genet. 15(6):248-249.

Monte Westerfield, Eckehard Doerry, Arthur E. Kirkpatrick and Sarah A. Douglas. (1999). Zebrafish informatics and the ZFIN database. Meth. Cell Biol. 60:339-355.

Edwards, P. (1999). Zebrafish Web Site Listings. In The Zebrafish: Genetics and Genomics, H.W. Detrich, III, M. Westerfield, and L.I. Zon, eds., San Diego: Academic Press, Meth. Cell Biol. 60:373-385.

Eckehard Doerry, Monte Westerfield, Sarah A. Douglas and Arthur E. Kirkpatrick. (1998). The zebrafish information network project. ACM Interactions 3:69.

Doerry, E., Douglas, S.A., Kirkpatrick, A.E., and Westerfield, M. (1998) The zebrafish information network project. Interactions. 3:69

Doerry, E., Kirkpatrick, A.E., Douglas, S.A., and Westerfield, M. (1997) Task-centered Navigation in a Web-accessible Data Space. AACE/WebNet97 conference on WWW, Internet, and Intranet, Toronto, Canada, Nov. 1,1997.

Westerfield, M., E. Doerry, A.E. Kirkpatrick, W. Driever, and S.A. Douglas (1997) An on-line database for zebrafish development and genetics research. Seminars in cell & developmental biology. 8:477-488

Doerry, E., Douglas, S.A., Kirkpatrick, A.E., and Westerfield, M. (1997) Participatory design for widely-distributed scientific communities. Proc. 3rd Conf. Human Factors and the Web.

Doerry, E., Douglas, S., Kirkpatrick, T., and Westerfield, M. (1997) Moving beyond html to create a multimedia database with user-centered design: a case study of a biological database. Tech. Report CIS-TR-97-02, Computer and Information Science Department, University of Oregon.

Eckehard Doerry, Sarah A. Douglas, Arthur E. Kirkpatrick, Monte Westerfield. (1997). Participatory Design for Widely-Distributed Scientific Communities. Proceedings of the 3rd Conference on Human Factors and the Web.

Westerfield, M., E. Doerry, A.E. Kirkpatrick, W. Driever and S.A. Douglas. (1997). An on-line database for zebrafish development and genetics research. Sem. Devel. Biol. 8:477-488.

Eckehard Doerry, Sarah A. Douglas, Ted Kirkpatrick, Monte Westerfield. (1997). Task-centered Navigation in Web-accessible Dataspaces. Position Paper submitted to the WebNet97 Conference, Oct. 31-Nov.5, 1997, Toronto, Canada.


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