The Mouse Genome Database (MGD): updates and enhancements

Abstract

The Mouse Genome Database (MGD) integrates genetic and genomic data for the mouse in order to facilitate the use of the mouse as a model system for understanding human biology and disease processes. A core component of the MGD effort is the acquisition and integration of genomic, genetic, functional and phenotypic information about mouse genes and gene products. MGD works within the broader bioinformatics community to define referential and semantic standards to facilitate data exchange between resources including the incorporation of information from the biomedical literature. MGD is also a platform for computational assessment of integrated biological data with the goal of identifying candidate genes associated with complex phenotypes. MGD is web accessible at http://www.informatics.jax.org. Recent improvements in MGD described here include the incorporation of an interactive genome browser, the enhancement of phenotype resources and the further development of functional annotation resources.

Figure 1

Mouse GBrowse: a screen shot of the MGI Mouse GBrowse interface. Using Mouse GBrowse, users can display MGD-specific annotations about genes, allele types (e.g. spontaneous, targeted, transgenic, etc.) and phenotype to gene associations. Each glyph displayed in the browser is hypertext linked to the appropriate detail page in MGD. Particularly note the phenotype tracks.

Figure 2

Mouse models and human diseases. Panel A: Search summary page of phenotypic alleles indicating observed phenotypes in mouse. The human diseases given in the column ‘Similar human diseases’ link to the page describing the relationship of this human disease to mouse (Panel B). Panel B: Detail page of human disease and mouse models for Hirschsprung disease. The associated gene section (arrow C) shows where orthologous mouse and human genes have been associated with this disease phenotype. The mouse models section (arrow D) specifies the genotypes of mouse models for this disease that have etiologies involving orthologs or etiologies which are distinct.

Figure 3

GO annotations as text. In response to user requests, we have created a lexicon and templates that enable computational generation of GO annotations in text form. This is provided to our web interface users in conjunction with the tabular presentation of the GO annotation information. Here, the GO text for gene Ednrb annotations is presented.