Zebrafish information network, the knowledgebase for Danio rerio research

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.

Keywords: Danio rerio; database; knowledgebase; zebrafish.

Fig. 1.

The ZFIN gene page. Web page providing information as it relates to a gene. The top portion provides general information about the gene, and the left navigation panel allows users to navigate directly to areas of interest. Arrows indicate new links or information provided by the Alliance.

Fig. 2.

Expression section of the gene page. Section of the gene page providing information about where and when the gene is expressed. Links to all expression data, Alliance and Bgee for cross-species expression data, high throughput data, and Thisse expression data are provided. Circles indicate new links. The wild-type expression summary provides an overview of expression data, with color blocks indicating where annotations exist. Clicking on shaded boxes opens a table with more detailed gene expression information as shown.

Fig. 3.

Phenotype section of the gene page. Section of the gene page providing mutant and gene knockdown phenotype information. Links to Alliance gene page provided in Cross-Species Comparison section. The phenotype summary provides a high-level overview of systems, stages, MFs, and BPs that have annotations. Clicking shaded boxes opens a table where more detailed annotation information is provided, as shown. Image reproduced/adapted with permission. Lun K, Brand M. A series of no isthmus (noi) alleles of the zebrafish pax2.1 gene reveals multiple signaling events in development of the midbrain-hindbrain boundary. Development 1998 Aug;125(16):3049-62. doi: 10.1242/dev.125.16.3049. PMID: 9671579.

Fig. 4.

Human disease section of the gene page. Provides information about human diseases associated with the gene via orthology to human genes and experimentally validated models of human disease. Links to Alliance disease pages (circled) provide access to multispecies disease information including associated genes, and experimental models.

Fig. 5.

Gene ontology section of the gene page. This section provides an overview of the GO MF, BP, and CC annotations for a gene. Shaded boxes indicate presence of data; clicking shaded boxes, as shown, opens a table where more detailed annotation information is provided.