ZFIN, The zebrafish model organism database: Updates and new directions

Abstract

The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for genetic and genomic data from zebrafish (Danio rerio) research. ZFIN staff curate detailed information about genes, mutants, genotypes, reporter lines, sequences, constructs, antibodies, knockdown reagents, expression patterns, phenotypes, gene product function, and orthology from publications. Researchers can submit mutant, transgenic, expression, and phenotype data directly to ZFIN and use the ZFIN Community Wiki to share antibody and protocol information. Data can be accessed through topic-specific searches, a new site-wide search, and the data-mining resource ZebrafishMine (http://zebrafishmine.org). Data download and web service options are also available. ZFIN collaborates with major bioinformatics organizations to verify and integrate genomic sequence data, provide nomenclature support, establish reciprocal links, and participate in the development of standardized structured vocabularies (ontologies) used for data annotation and searching. ZFIN-curated gene, function, expression, and phenotype data are available for comparative exploration at several multi-species resources. The use of zebrafish as a model for human disease is increasing. ZFIN is supporting this growing area with three major projects: adding easy access to computed orthology data from gene pages, curating details of the gene expression pattern changes in mutant fish, and curating zebrafish models of human diseases.

Keywords: curation; data mining; human disease models; ontology.

Figure 1. Selected Data Types in ZFIN

The numbers of genes, genetic features, transgenic insertions, gene ontology (GO) annotations, gene expression patterns, and phenotypes in ZFIN from 2001 to 2014.

Figure 2. ZFIN’s New Search Interface

The new search provides rapid searching and browsing. Results can be refined using the filters on the left. In this example, the search term is “cerebellum”. The search has been narrowed by selecting the Expression category, and the results have been further refined by selecting these filters: standard/control experimental conditions, wild-type genotypes, and figures with images showing gene expression. The search results in the right-hand panel provide the requested details: figures that have images showing gene expression in the cerebellum in wild-type zebrafish in standard/control conditions.