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ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics
Open accessAbstract
ZFIN, the Zebrafish Model Organism Database (http://zfin.org), is the central resource for zebrafish genetic, genomic, phenotypic and developmental data. ZFIN curators manually curate and integrate comprehensive data involving zebrafish genes, mutants, transgenics, phenotypes, genotypes, gene expressions, morpholinos, antibodies, anatomical structures and publications. Integrated views of these data, as well as data gathered through collaborations and data exchanges, are provided through a wide selection of web-based search forms. Among the vertebrate model organisms, zebrafish are uniquely well suited for rapid and targeted generation of mutant lines. The recent rapid production of mutants and transgenic zebrafish is making management of data associated with these resources particularly important to the research community. Here, we describe recent enhancements to ZFIN aimed at improving our support for mutant and transgenic lines, including (i) enhanced mutant/transgenic search functionality; (ii) more expressive phenotype curation methods; (iii) new downloads files and archival data access; (iv) incorporation of new data loads from laboratories undertaking large-scale generation of mutant or transgenic lines and (v) new GBrowse tracks for transgenic insertions, genes with antibodies and morpholinos.
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Cited by
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Aken, B. L., Achuthan, P., Akanni, W., Amode, M. R., Bernsdorff, F., Bhai, J., Billis, K., Carvalho-Silva, D., Cummins, C., Clapham, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1104 · Cited by 512
“We collaborate with other informatics resources and tools including the Genome Reference Consortium (GRC) (15), the UCSC Genome Browser (16), UniProt (17), model organism databases (18,19) and relevant resources at the NCBI (20) to coordinate data presentation and standards.”
MethodHunt, S. E., McLaren, W., Gil, L., Thormann, A., Schuilenburg, H., Sheppard, D., Parton, A., Armean, I. M., Trevanion, S. J., Flicek, P., et al. (2018) · Database · doi:10.1093/database/bay119 · Cited by 452
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Kaufman, C. K., Mosimann, C., Fan, Z. P., Yang, S., Thomas, A. J., Ablain, J., Tan, J. L., Fogley, R. D., van Rooijen, E., Hagedorn, E. J., et al. (2016) · Science · doi:10.1126/science.aad2197 · Cited by 398
Metadata
- Authors
- Howe, D. G., Bradford, Y. M., Conlin, T., Eagle, A. E., Fashena, D., Frazer, K., Knight, J., Mani, P., Martin, R., Moxon, S. A. T., Paddock, H., Pich, C., Ramachandran, S., Ruef, B. J., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Sprunger, B., Van Slyke, C. E., & Westerfield, M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-10-15
- Volume
- 41
- Issue
- D1
- Pages
- D854-D860
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2055961987
- Cited by
- 250
- References
- 0
- FWCI
- 5.24
- Type
- journal article
- Language
- en
- Open access
- gold
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- Howe, D. G., Bradford, Y. M., Conlin, T., Eagle, A. E., Fashena, D., Frazer, K., Knight, J., Mani, P., Martin, R., Moxon, S. A. T., Paddock, H., Pich, C., Ramachandran, S., Ruef, B. J., Ruzicka, L., Schaper, K., Shao, X., Singer, A., Sprunger, B., . . . Westerfield, M. (2012). ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Research. https://doi.org/10.1093/nar/gks938
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
