Zebrafish information network, the knowledgebase for <i>Danio rerio</i> research

TLDR

The Zebrafish Information Network (zfin.org) is the central, long‑standing repository for Danio rerio genetic and genomic data, curating genes, alleles, disease models, expression, phenotype, and function, and making them Findable, Accessible, Interoperable, and Reusable. This paper describes the formation of the Alliance of Genome Resources, a collaboration among ZFIN and six other model organism databases to create sustainable genome resources for studying human biology and disease. The authors provide an overview of ZFIN’s data, including recent gene‑page updates that add single‑cell RNA‑seq data, links to Alliance web pages, ribbon diagrams summarizing biological systems, Gene Ontology annotations, and integration with the Alliance of Genome Resources. The paper reports that ZFIN now offers updated gene pages with single‑cell RNA‑seq data, integrated Alliance links, ribbon diagrams of biological systems, Gene Ontology annotations, and overall data integration with the Alliance of Genome Resources.

Abstract

The Zebrafish Information Network (zfin.org) is the central repository for Danio rerio genetic and genomic data. The Zebrafish Information Network has served the zebrafish research community since 1994, expertly curating, integrating, and displaying zebrafish data. Key data types available at the Zebrafish Information Network include, but are not limited to, genes, alleles, human disease models, gene expression, phenotype, and gene function. The Zebrafish Information Network makes zebrafish research data Findable, Accessible, Interoperable, and Reusable through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. Recently, the Zebrafish Information Network and 6 other model organism knowledgebases have collaborated to form the Alliance of Genome Resources, aiming to develop sustainable genome information resources that enable the use of model organisms to understand the genetic and genomic basis of human biology and disease. Here, we provide an overview of the data available at the Zebrafish Information Network including recent updates to the gene page to provide access to single-cell RNA sequencing data, links to Alliance web pages, ribbon diagrams to summarize the biological systems and Gene Ontology terms that have annotations, and data integration with the Alliance of Genome Resources.