The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics

Abstract

The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse and the authoritative source for phenotype and functional annotations of mouse genes. MGD includes a complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics (MGI, http://www.informatics.jax.org/) resource. MGD contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. Major improvements to the Mouse Genome Database include comprehensive update of genetic maps, implementation of new classification terms for genome features, development of a recombinase (cre) portal and inclusion of all alleles generated by the International Knockout Mouse Consortium (IKMC).

Figure 1.

New classification terms for MGD markers and genome features. The definitions for the terms are displayed when a user ‘mouses over’ a term. Numbers following the term are the current number of entities in that class within MGD. Updated nightly.

Figure 2.

Details for the specificity of the recombinase bearing knockin allele, Tgfb3tm1(cre)Vk in sensory organs. Information shown includes molecular description, links to strain availability, other tissues showing recombinase activity and a gallery of images for Tgfb3tm1(cre)Vk in sensory organs. Arrow shows how images may be moved and enlarged to enable better inspection. The table in the lower portion shows detailed annotations for the sensory organ recombinase activities.

Figure 3.

Screenshot showing a biotype conflict note for the Cecr6 gene. In this instance, the Ensembl annotation pipeline has assigned a status of ‘pseudogene’ to Cecr6 and the NCBI annotation pipeline has assigned it a status of ‘protein-coding gene.’ MGI provides links to the underlying evidence for both gene predictions so that users can examine the evidence used to support the gene structure and biotype assignments by different annotation groups.