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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 Manager; Anne Eagle, Technical Manager; and Yvonne Bradford, Project Manager; and the rest of the ZFIN Database Team.
Advisory board:
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Shawn Burgess – NIH
Elisabeth Busch-Nentwich – Queen Mary University of London
Mike Cherry – Stanford University
Jeff De Pons – Medical College of Wisconsin
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Anna Hutenlocher – University of Wisconsin – Madison
Kristen Kwan – University of Utah
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Adam Miller – University of Oregon
Sierra Moxon – Lawrence Berkeley National Laboratory
Robyn Tanguay – Oregon State University
Ajay Pillai - Program Officer, NHGRI, NIH
Publications:
RuzickaBradford, LY.M., HoweVan Slyke, DC.GE., RamachandranRuzicka, SL., Toro, S., Van Slyke, C.E., Bradford, Y.MSinger, A., Eagle, A., Fashena, D., FrazerHowe, K., Kalita, PD.G., ManiFrazer, PK., Martin, R., Moxon, S.T., Paddock, H., Pich, C., SchaperRamachandran, KS., ShaoWesterfield, X., Singer, A., Westerfield, M. (2018) The M. (2022) 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-D873the knowledgebase for Danio rerio research. Genetics. 220(4):.
Ruzicka, L., Howe, D.G., BlakeRamachandran, J.AS., Toro, S., Van Slyke, C.E., Bradford, Y.M., BultEagle, C.JA., CalviFashena, B.RD., EngelFrazer, S.RK., KadinKalita, J.AP., KaufmanMani, T.CP., KishoreMartin, R., LaulederkindMoxon, S.J.FT., LewisPaddock, SH.E., MoxonPich, S.A.T., Richardson, J.E., Smith, C. (2018) Model organism data evolving in support of translational medicine. Lab animal. 47(10):277-289C., 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. (2018) A statistical approach to identify, monitor, and manage incomplete curated data sets. BMC Bioinformatics. 19:110Van Slyke, C.E., Blake, J.A., Bradford, Y.M., HoweBult, DC.GJ., FashenaCalvi, DB.SR., RamachandranEngel, S.R., RuzickaKadin, LJ.A., ZFIN Staff* (2018) Using ZFIN: Data Types, Organization, and Retrieval. Methods in molecular biology (Clifton, N.J.). 1757:307-347Bradford, Y.M., Toro, S., Ramachandran, S., Ruzicka, L., , 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. , 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(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., 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., 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. (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-D768Howe, D.G., Bradford, Y.M., Eagle, A., Fashena, D., Frazer, 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. (2016) A scientist's guide for submitting data to ZFIN. Methods in cell biology. 135:451-812017) 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) The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. Nucleic acids research. 45(D1):D758-D768A scientist's guide for submitting data to ZFIN. Methods in cell biology. 135:451-81
Howe DG, D.G., Bradford YM, Y.M., 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.
Howe, D.G., A.E., Fashena, D., Frazer, K., FashenaKnight, DJ., RuzickaMani, LP., BradfordMartin, YR., RamachandranMoxon, S.A., RuefPaddock, B.JH., Van SlykePich, C., SingerRamachandran, AS., and Westerfield, M. (2011) Data extraction, transformation, and dissemination through ZFIN. Methods in cell biology. 104:311-325.Ramachandran, S., RuefRuef, B.J., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Sprunger, B., PichVan Slyke, C.E., and SpragueWesterfield, JM. (20102013) Exploring zebrafish genomic, functional and phenotypic data using ZFIN. Current protocols in bioinformatics. Chapter 1:Unit 1.18Sprague, J., Bayraktaroglu, L., 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., Haendel, M., Howe, D.G., Knight, J., Mani, P., Martin, R., Moxon, S.A., Paddock, H., Pich, C., Ramachandran, S, S., Ruef, B.J., Ruzicka, L., Bauer Schaper, KH., SegerdellSchaper, EK., Shao, X., Singer, A., SongSprague, PJ., Sprunger, B., Van Slyke, C.E., and Westerfield, M. (2008) The Zebrafish Information Network: 2011). ZFIN: enhancements and updates to the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic acids research. 36:D768-772.Sprague, J., Bayraktaroglu, L., ClementsAcids Res. 39(suppl 1):D822-D829.
Howe, D.G., Frazer, K., Fashena, D., ConlinRuzicka, TL., FashenaBradford, DY., FrazerRamachandran, KS., HaendelRuef, MB.J., Howe, D.GVan Slyke, C., ManiSinger, PA., Ramachandranand Westerfield, SM. (2011) Data extraction, Schaper, K., Segerdell, E., Song, P., Sprungertransformation, and dissemination through ZFIN. Methods in cell biology. 104:311-325.
Ramachandran, S., Ruef, B., Taylor, S., Van SlykePich, C.E., and WesterfieldSprague, MJ. (2006). The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res. Jan 1;34(Database issue):D581-5.2010) Exploring zebrafish genomic, functional and phenotypic data using ZFIN. Current protocols in bioinformatics. Chapter 1:Unit 1.18
Sprague, J., Bayraktaroglu, L., ClementsBradford, DY., Conlin, T., Dunn, N., 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 research. 34:D581-585.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), 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 . Nucleic Acids Res. Jan 1;31(1):241-3provides expanded support for genotypes and phenotypes. Nucleic acids research. 36:D768-772.
Sprague, J., Bayraktaroglu, L., Clements, D., Conlin, T., EdwardsFashena, PD., Frazer, K., Haendel, M., Howe, D.G., Mani, P., Ramachandran, S., Schaper, K., Segerdell, E., Song, P., Sprunger, B, B., Taylor, S., Van Slyke, C.E., and Westerfield, M. (20032006). The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic acids research. 31(1):241-243 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 Res. Jan 1;acids research. 31(1):241-3243.
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