The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse

Abstract

The Mouse Genome Database (MGD, http://www.informatics.jax.org) is the international community resource for integrated genetic, genomic and biological data about the laboratory mouse. Data in MGD are obtained through loads from major data providers and experimental consortia, electronic submissions from laboratories and from the biomedical literature. MGD maintains a comprehensive, unified, non-redundant catalog of mouse genome features generated by distilling gene predictions from NCBI, Ensembl and VEGA. MGD serves as the authoritative source for the nomenclature of mouse genes, mutations, alleles and strains. MGD is the primary source for evidence-supported functional annotations for mouse genes and gene products using the Gene Ontology (GO). MGD provides full annotation of phenotypes and human disease associations for mouse models (genotypes) using terms from the Mammalian Phenotype Ontology and disease names from the Online Mendelian Inheritance in Man (OMIM) resource. MGD is freely accessible online through our website, where users can browse and search interactively, access data in bulk using Batch Query or BioMart, download data files or use our web services Application Programming Interface (API). Improvements to MGD include expanded genome feature classifications, inclusion of new mutant allele sets and phenotype associations and extensions of GO to include new relationships and a new stream of annotations via phylogenetic-based approaches.

Figure 1.

Screenshots of the upper portion of two locus detail pages. (A) The BioType Conflict indicator (upper right), when opened, displays the different biotype annotations for Psme2b-ps. In this case, MGI and NCBI assign this marker as a pseudogene, where VEGA and Ensembl have assigned the status as protein coding gene. Links are provided to the underlying evidence that support the biotype assignments by different annotation groups. (B) The strain-specific marker indicator (upper right), when opened, displays information about strains in which the gene (in this case Ren2) is found or, not found, in the genome, with supporting reference links.

Figure 2.

Screenshot of the results of querying for ‘wavy’ using the MGI Quick Search box. Note that heritable phenotypic markers that identify mutants whose underlying gene is not yet identified, such as Wf and Wtgr are retrieved, as well as genes (e.g. Pax1, with synonym of wavy tail), and other types of mutant alleles in defined genes (e.g. Pax1^un-ex, undulated extensive mutation of the Pax1 gene).