Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse

Abstract

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the key community mouse database which supports basic, translational and computational research by providing integrated data on the genetics, genomics, and biology of the laboratory mouse. MGD serves as the source for biological reference data sets related to mouse genes, gene functions, phenotypes and disease models with an increasing emphasis on the association of these data to human biology and disease. We report here on recent enhancements to this resource, including improved access to mouse disease model and human phenotype data and enhanced relationships of mouse models to human disease.

Figure 1.

Disease Ontology Browser at Mouse Genome Informatics. Example of a new disease detail page and associated mouse and human data available for Leber congenital amaurosis. (A) Shown are the Disease Ontology (DO) term, definition, synonyms and IDs for this DO term. Additional matching terms at other resources are shown and linked when available at another resource. Graphical views of the ontology are also available. (B) The genes tab of the browser lists all human and mouse orthologs associated with the disease or subclasses of the disease. Mouse models are listed, if available. (C) The models tab lists the disease and genotype of mouse models of the disease along with supporting reference information and links to phenotype data for each model.

Figure 2.

Gene Ontology Browser. The new MGD ontology browsers have an autocomplete search feature and display linked matching terms. Shown here is an example from the Gene Ontology Browser. GO term names, definitions, IDs, superclasses (parent terms) and term relations are listed and terms are shown in a tree view. The example shown here is a search for ‘cell adhesion’ showing all terms containing this text string. The subclass ‘chorio-allantoic fusion’ is selected. Different branches may be viewed by clicking on the different parent terms under the defintion. Each biological term is connected to annotated genes via a link in the tree view following the term name; in this example, ten different genes are annotated to this biological process term. Other terms with subclasses are expanded by clicking on the triangle toggle to the left of the term name.

Figure 3.

Phenotype systems grid for Slc20a2^{tm1a(EUCOMM)Wtsi}. Shown is Phenotype systems grid from the allele detail page the for Slc20a2^{tm1a(EUCOMM)Wtsi} allele featuring DMDD data integrated with IMPC data and published data curated by MGI. Blue triangular toggles to the right of the system name may be opened for comparison of data details across genotypes. Further phenotype details including detailed phenotype terms and references may be accessed by clicking genotype links (e.g. ‘hm1’) or checkmarks on the phenotypes grid. Other included information on the allele detail page for this mutation (not shown) are links to the gene detail page, mutation origin and description, human disease information, links to repositories carrying the mouse mutation and references.