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Zebrafish Information Network

Background:

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

Goals:

ZFIN serves as the zebrafish model organism database. 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:

Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, Knight J, Mani P, Martin R, Moxon SA, Paddock H, Pich C, Ramachandran S, Ruef BJ, Ruzicka L, Schaper K, Shao X, Singer A, Sprunger B, Van Slyke CE, Westerfield M. (2013).  ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Res. Jan;41(Database issue):D854-60.

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:

Shawn Burgess, National Human Genome Research Center, National Institutes of Health; Jim Kadin, The Jackson Laboratory; Teresa Nicolson, Howard Hughes Medical Institute Oregon Hearing and Research Center and Vollum Institute, Oregon Health & Science University; Derek Stemple, Vertebrate Development and Genetics (Team 31) Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton

Publications:

Ruzicka, L., Bradford, Y.M., Frazer, K., Howe, D.G., Paddock, H., Ramachandran, S., Singer, A., Toro, S., Van Slyke, C.E., Eagle, A.E., Fashena, D., Kalita, P., Knight, J., Mani, P., Martin, R., Moxon, S.A., Pich, C., Schaper, K., Shao, X., Westerfield, M. (2015) ZFIN, the Zebrafish Model Organism Database: Updates and new directions. Genesis (New York, N.Y. : 2000). 53(8):498-509

Lyne, R., Sullivan, J., Butano, D., Contrino, S., Heimbach, J., Hu, F., Kalderimis, A., Lyne, M., Smith, R.N., Štěpán, R., Balakrishnan, R., Binkley, G., Harris, T., Karra, K., Moxon, S.A., Motenko, H., Neuhauser, S., Ruzicka, L., Cherry, M., Richardson, J., Stein, L., Westerfield, M., Worthey, E., Micklem, G. (2015) Cross-Organism Analysis Using InterMine. Genesis (New York, N.Y. : 2000). 53(8):547-60

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

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) 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

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 DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, Knight J, Mani P, Martin R, Moxon SA, Paddock H, Pich C, Ramachandran S, Ruef BJ, Ruzicka L, Schaper K, Shao X, Singer A, Sprunger B, Van Slyke CE, Westerfield M. (2013).  ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Res. Jan;41(Database issue):D854-60.

Sullivan, J., Karra, K., Moxon, S.A.T., Vallejos, A., Motenko, H., Wong, J.D., Aleksic, J., Balakrishnan, R., Binkley, G., Harris, T., Hitz, B., Jayaraman, P., Lyne, R., Neuhauser, S., Pich, C., Smith, R.N., Trinh, Q., Cherry, J.M., Richardson, J., Stein, L., Twigger, S., Westerfield, M., Worthey, E., and Micklem, G. (2013) InterMOD: integrated data and tools for the unification of model organism research. Scientific Reports. 3:1802

Köhler, S., Doelken, S.C., Ruef, B.J., Bauer, S., Washington, N., Westerfield, M., Gkoutos, G., Schofield, P., Smedley, D., Lewis, S.E., Robinson, P.N., and Mungall, C.J. (2013) Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000 Research. 2:30

Dahdul, W.M., Balhoff, J.P., Blackburn, D.C., Diehl, A.D., Haendel, M.A., Hall, B.K., Lapp, H., Lundberg, J.G., Mungall, C.J., Ringwald, M., Segerdell, E., Van Slyke, C.E., Vickaryous, M.K., Westerfield, M., and Mabee, P.M. (2012) A unified anatomy ontology of the vertebrate skeletal system. PLoS One. 7(12):e51070

Howe DG, Frazer K, Fashena D, Ruzicka L, Bradford Y, Ramachandran S, Ruef BJ, Van Slyke C, Singer A, Westerfield M. (2011).  Data extraction, transformation, and dissemination through ZFIN. Methods Cell Biol.104:311-25.

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.

Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., and Mabee, P.M. (2010) The teleost anatomy ontology: anatomical representation for the genomics age. Systematic biology. 59(4):369-383

Ramachandran S, Ruef B, Pich C, Sprague J. (2010). Exploring zebrafish genomic, functional and phenotypic data using ZFIN. Curr. Protoc. Bioinformatics. Chapter 1:Unit 1.18.

Washington, N.L., Haendel, M.A., Mungall, C.J., Ashburner, M., Westerfield, M., and Lewis, S.E. (2009) Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation. PLoS Biology. 7(11):e1000247

Toro, S., Wegner, J., Muller, M., Westerfield, M., and Varga, Z.M. (2009) Identification of differentially expressed genes in the zebrafish hypothalamic-pituitary axis. Gene Expression Patterns. 9(4):200-208

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.

Mabee, P.M., Ashburner, M., Cronk, Q., Gkoutos, G.V., Haendel, M., Segerdell, E., Mungall, C., and Westerfield, M. (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology & Evolution. 22(7):345-350

Mabee, P.M., Arratia, G., Coburn, M., Haendel, M., Hilton, E.J., Lundberg, J.G., Mayden, R.L., Rios, N., and Westerfield, M. (2007) Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. Journal of experimental zoology. Part B, Molecular and developmental evolution. 308(5):655-668

Henrich, T., Ramialison, M., Segerdell, E., Westerfield, M., Furutani-Seiki, M., Wittbrodt, J., Kondoh, H. (2004) GSD: a genetic screen database. Mechanisms of Development. 121(7-8):959-963

Sprague J, Clements D, Conlin T, Edwards P, Frazer K, Schaper K, Segerdell E, Song P, Sprunger B, Westerfield M. (2003) The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res. Jan 1;31(1):241-3.

Yan, Y.-L., Miller, C.T., Nissen, R.M., Singer, A., Liu, D., Kirn, A., Draper, B., Willoughby, J., Morcos, P.A., Amsterdam, A., Chung, B.-C., Westerfield, M., Haffter, P., Hopkins, N., Kimmel, C., and Postlethwait, J.H. (2002) A zebrafish sox9 gene required for cartilage morphogenesis. Development (Cambridge, England). 129(21):5065-5079

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.

 Sprague J, Clements D, Conlin T, Edwards P, Frazer K, Schaper K, Segerdell E, Song P, Sprunger B, Westerfield M. (2003) The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res. Jan 1;31(1):241-3.

Fashena, D. and Westerfield, M. (1999) Secondary motoneuron axons localize DM-GRASP on their fasciculated segments. The Journal of comparative neurology. 406(3):415-424

 Westerfield, M., Doerry, E., and Douglas, S. (1999). Zebrafish in the net. Trends Genet. 15(6):248-249. This manuscript describes the history of the ZFIN database project.

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

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. This report describes our design process.

Eckehard Doerry, Sarah A. Douglas, Arthur E. Kirkpatrick, Monte Westerfield. (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 Dept., University of Oregon. This paper describes the design methodology used to create the ZFIN system, and the hybrid, web-accessible interface developed to satisfy stringent usability requirements.

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. This paper briefly examines the special challenges of applying the user-centered design methodology to widely-distributed scientific communities.

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. The Zebrafish Database contents and use are described with examples written for both biologists and computer scientists.

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. This short paper introduces the notion of using a representation of known user tasks to provide navigational feedback during multi-step transactions with a web-accessible database.

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