The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources

Abstract

The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, nomenclature and reagents. New features at ZFIN include increased support for genomic regions and for non-coding genes, and support for more expressive Gene Ontology annotations. ZFIN has recently taken over maintenance of the zebrafish reference genome sequence as part of the Genome Reference Consortium. ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO). The recently launched Alliance portal (https://alliancegenome.org) provides a unified, comparative view of MOD, GO, and human data, and facilitates foundational and translational biomedical research.

Figure 1.

Non-coding genes in ZFIN’s Single Box Search. ZFIN data can be searched or browsed using the single box search (22). To search for a specific gene, enter the gene symbol in the Search box on any ZFIN page. To browse all genes in ZFIN, as shown in this figure, click on the ‘Go’ next to the search box on the ZFIN home page to get to the Search page (https://zfin.org/search?q=), then select the ‘Gene/Transcript’ category, and then select ‘Gene’ from the ‘Type’ filter. To further limit the Gene results list to non-coding genes, select ‘ncRNA Gene’ or one of the more specific ncRNA gene subtypes in the ‘Type’ filter.