The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes

Abstract

The Zebrafish Information Network (ZFIN, http://zfin.org), the model organism database for zebrafish, provides the central location for curated zebrafish genetic, genomic and developmental data. Extensive data integration of mutant phenotypes, genes, expression patterns, sequences, genetic markers, morpholinos, map positions, publications and community resources facilitates the use of the zebrafish as a model for studying gene function, development, behavior and disease. Access to ZFIN data is provided via web-based query forms and through bulk data files. ZFIN is the definitive source for zebrafish gene and allele nomenclature, the zebrafish anatomical ontology (AO) and for zebrafish gene ontology (GO) annotations. ZFIN plays an active role in the development of cross-species ontologies such as the phenotypic quality ontology (PATO) and the gene ontology (GO). Recent enhancements to ZFIN include (i) a new home page and navigation bar, (ii) expanded support for genotypes and phenotypes, (iii) comprehensive phenotype annotations based on anatomical, phenotypic quality and gene ontologies, (iv) a BLAST server tightly integrated with the ZFIN database via ZFIN-specific datasets, (v) a global site search and (vi) help with hands-on resources.

Figure 1.

The genotype page summarizes genotype specific data for mib^ta52b/ta52b and provides extensive cross-linking to all mib^ta52b/ta52b data in ZFIN.

Figure 2.

Phenotype summary page for mib^ta52b/ta52b. Publication, genotype and ‘observed in’ link to their respective pages. Figures and thumbnail images link to curated phenotype details.

Figure 3.

A typical published figure with curated phenotype annotations. ‘Whole organism’, ‘shield’, ‘germ ring’, ‘notochord’ and ‘somite’ are entities derived from the zebrafish AO. ‘Gastrulation’ and ‘embryonic morphogenesis’ are entities derived from the GO. ‘Increased thickness’, ‘decreased length’, ‘malformed’, ‘fused with’, ‘arrested’, ‘disrupted’ and ‘abnormal’ are PATO qualities. Links are provided to the genotype page, stage description, anatomy term pages, GO details page and the full text of the publication. Figure reproduced from Reim and Brand (11).