ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

Abstract

ZFIN, the Zebrafish Model Organism Database (http://zfin.org), is the central resource for zebrafish genetic, genomic, phenotypic and developmental data. ZFIN curators manually curate and integrate comprehensive data involving zebrafish genes, mutants, transgenics, phenotypes, genotypes, gene expressions, morpholinos, antibodies, anatomical structures and publications. Integrated views of these data, as well as data gathered through collaborations and data exchanges, are provided through a wide selection of web-based search forms. Among the vertebrate model organisms, zebrafish are uniquely well suited for rapid and targeted generation of mutant lines. The recent rapid production of mutants and transgenic zebrafish is making management of data associated with these resources particularly important to the research community. Here, we describe recent enhancements to ZFIN aimed at improving our support for mutant and transgenic lines, including (i) enhanced mutant/transgenic search functionality; (ii) more expressive phenotype curation methods; (iii) new downloads files and archival data access; (iv) incorporation of new data loads from laboratories undertaking large-scale generation of mutant or transgenic lines and (v) new GBrowse tracks for transgenic insertions, genes with antibodies and morpholinos.

Figure 1.

In the past 2 years, mutant and transgenic features (Genetic Features) as well as transgenic constructs have been among the most rapidly growing data types at ZFIN. *2012 data through 8 August 2012.

Figure 2.

The Genomic Feature page provides detailed information about the genomic feature. This is an example of a viral insertion feature including affected gene, previous name, associated construct, type of mutation, protocol used, laboratory of origin, mapping information, associated GenBank accessions, current sources and genotypes.

Figure 3.

Transgenic insertions now have a dedicated GBrowse track. Like other items shown in Gbrowse, transgenic insertions shown on this track are linked to their feature records in ZFIN.

Figure 4.

Example of a figure page at ZFIN with phenotype summary statements. Clicking the complete hyperlinked phenotype statement opens a Phenotype Statement summary page (not shown). Clicking the icon at the end of the statement (red arrow) opens a pop-up window with additional ontology term information as shown. Click on a hyperlinked term name from the pop-up to redirect to the term detail page for additional information and the ability to navigate the ontology. Represented are examples of a ‘normal or recovered’ phenotype statement, the use of a relational quality (boxed phenotype statement) and post-composition, which is displayed in the pop-up where the AO term retinal rod cell is post-composed with the GO cellular component term photoreceptor outer segment.