A scientist's guide for submitting data to ZFIN
- 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.
- Methods in cell biology 135: 451-81 (Chapter)
- Registered Authors
- Bradford, Yvonne, Eagle, Anne, Fashena, David, Frazer, K., Howe, Doug, Kalita, Patrick, Mani, Prita, Martin, Ryan, Moxon, Sierra (fka Taylor), Paddock, Holly, Pich, Christian, Ramachandran, Sridhar, Ruzicka, Leyla, Schaper, Kevin, Shao, Xiang, Singer, Amy, Toro, Sabrina, Van Slyke, Ceri E., Westerfield, Monte
- Direct data submission, Gene expression, Model organism database, Mutant, Phenotype, Transgenic
- MeSH Terms
- Animals, Genetically Modified
- Databases, Genetic*
- 27443940 Full text @ Meth. Cell. Biol.
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.
The Zebrafish Model Organism Database (ZFIN; zfin.org) serves as the central repository for genetic and genomic data produced using zebrafish (Danio rerio). Data in ZFIN are either manually curated from peer-reviewed publications or submitted directly to ZFIN from various data repositories. Data types currently supported include mutants, transgenic lines, DNA constructs, gene expression, phenotypes, antibodies, morpholinos, TALENs, CRISPRs, disease models, movies, and images. The rapidly changing methods of genomic science have increased the production of data that cannot readily be represented in standard journal publications. These large data sets require web-based presentation. As the central repository for zebrafish research data, it has become increasingly important for ZFIN to provide the zebrafish research community with support for their data sets and guidance on what is required to submit these data to ZFIN. Regardless of their volume, all data that are submitted for inclusion in ZFIN must include a minimum set of information that describes the data. The aim of this chapter is to identify data types that fit into the current ZFIN database and explain how to provide those data in the optimal format for integration. We identify the required and optional data elements, define jargon, and present tools and templates that can help with the acquisition and organization of data as they are being prepared for submission to ZFIN. This information will also appear in the ZFIN wiki, where it will be updated as our services evolve over time.
Genes / Markers
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Engineered Foreign Genes
Errata and Notes