The Zebrafish Information Network (ZFIN): the zebrafish model organism database

Abstract

The Zebrafish Information Network (ZFIN) is a web based community resource that serves as a centralized location for the curation and integration of zebrafish genetic, genomic and developmental data. ZFIN is publicly accessible at http://zfin.org. ZFIN provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community contact data. Recent enhancements to ZFIN include: (i) an anatomical dictionary that provides a controlled vocabulary of anatomical terms, grouped by developmental stages, that may be used to annotate and query gene expression data; (ii) gene expression data; (iii) expanded support for genome sequence; (iv) gene annotation using the standardized vocabulary of Gene Ontology (GO) terms that can be used to elucidate relationships between gene products in zebrafish and other organisms; and (v) collaborations with other databases (NCBI, Sanger Institute and SWISS-PROT) to provide standardization and interconnections based on shared curation.

Figure 1

RNA in situ hybridization assay for the neurogenin 1 (neurog1) gene from 50%-epiboly through Bud developmental stages of the gastrula. Patterns are grouped by stage. Anatomical dictionary terms identify regions of gene expression. A text description describes observed patterns. Links are provided to relevant ZFIN gene record and stage descriptions.

Figure 2

GO annotation display for the neurog1 zebrafish gene. GO terms are grouped by ontologies. Evidence codes and references provide researchers with information to establish levels of confidence for the association. GO term links provide information describing the lineage of the GO term.