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Zebrafish Information Network

Background:

A group of us 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 researchersas 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.

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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:PMC6323962Bradford, Y.M., Van Slyke, C.E., Ruzicka, L., Singer, A., Eagle, A., Fashena, D., Howe, D.G., Frazer, K., Martin, R., Paddock, H., Pich, C., Ramachandran, S., Westerfield, M. (2022) Zebrafish Information Network, the knowledgebase for Danio rerio research. Genetics. 220(4).

PMID: 35166825  PMCID: PMC8982015  DOI: 10.1093/genetics/iyac016

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].

Data Curation Workflow

ZFIN's curation workflow is documented here

Versioning Information

ZFIN versioning information is documented here

Research staff:

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

Advisory board:

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Publications:

Ruzicka, L., Bradford, Y.M., FrazerVan Slyke, K., Howe, D.G., Paddock, H., Ramachandran, S., Singer, A., Toro, S., Van Slyke, C.E., Eagle, A.EC.E., Ruzicka, L., Singer, A., Eagle, A., Fashena, D., KalitaHowe, P., Knight, JD.G., ManiFrazer, PK., Martin, R., MoxonPaddock, S.AH., Pich, C., SchaperRamachandran, KS., Shao, X., WesterfieldWesterfield, M. (20152022) ZFIN, the Zebrafish Model Organism Database: Updates and new directions. Genesis (New York, N.Y. : 2000). 53(8):498-509Lyne, 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, KZebrafish Information Network, the knowledgebase for Danio rerio research. Genetics. 220(4):.

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.AT., MotenkoPaddock, H., NeuhauserPich, SC., RuzickaSchaper, LK., CherryShao, MX., RichardsonSinger, JA., Stein, L., Westerfield, M. , Worthey, E., Micklem, G. (2015) Cross-Organism Analysis Using InterMine. Genesis (New York, N.Y. : 2000). 53(8):547-60(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., EagleBult, AC.J., FashenaCalvi, DB.R., FrazerEngel, KS.R., KalitaKadin, PJ.A., ManiKaufman, PT.C., MartinKishore, R., MoxonLaulederkind, S.TJ.F., PaddockLewis, H., Pich, CS.E., RamachandranMoxon, S., Ruzicka, L., Schaper, KA.T., ShaoRichardson, X., Singer, A., Toro, S., Van Slyke, C., Westerfield, M. (2016) A scientist's guide for submitting data to ZFIN. Methods in cell biology. 135:451-81J.E., Smith, C. (2018) Model organism data evolving in support of translational medicine. Lab animal. 47(10):277-289

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(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., Schaper, K., Shao, X., Singer, A., ToroZFIN 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., Van SlykeRuzicka, CL., WesterfieldHowe, 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., 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., RuzickaVan Slyke, LC., 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):200-208Data 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., BradfordClements, YD., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Knight, J., Mani, P., MoxonRamachandran, S.A., Pich, C., Ramachandran, S., Schaper, K., Segerdell, E., Shao, X., Singer, A., Song, P., Sprunger, B., Taylor, S., Van Slyke, C.E., and Westerfield, M. (20082006). The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic acids research. 36:D768-772. Nucleic Acids Res. Jan 1;34(Database issue):D581-5.

Sprague, J., BayraktarogluClements, L., Clements, D., Conlin, T., FashenaEdwards, DP., 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. (20062003) . The Zebrafish Information Network (ZFIN): 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 DatabaseNucleic 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 Dept.Department, 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  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 communitiesthe 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 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  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.