Abstract
SummaryThe Mouse Genome Database (MGD, www.informatics.jax.org) is the international scientific database for genetic, genomic, and biological data on the laboratory mouse to support the research requirements of the biomedical community. To accomplish this goal, MGD provides broad data coverage, serves as the authoritative standard for mouse nomenclature for genes, mutants, and strains, and curates and integrates many types of data from literature and electronic sources. Among the key data sets MGD supports are: the complete catalog of mouse genes and genome features, comparative homology data for mouse and vertebrate genes, the authoritative set of Gene Ontology (GO) annotations for mouse gene functions, a comprehensive catalog of mouse mutations and their phenotypes, and a curated compendium of mouse models of human diseases. Here, we describe the data acquisition process, specifics about MGD's key data areas, methods to access and query MGD data, and outreach and user help facilities. genesis 53:458–473, 2015. © 2015 The Authors. Genesis Published by Wiley Periodicals, Inc.
Highlights
The laboratory mouse is widely recognized as an important animal model for investigating genetic and cellular systems relevant to human biology and disease
Scientific curators and analysts identify and prioritize newly published articles for inclusion in Mouse Genome Database (MGD) based on novelty and whether a model for human disease is included
Mouse GO annotations are derived by curation of the scientific literature, through inferences based on orthology from experimental data in other organisms, notably human and rat (Reference Genome Group of the Gene Ontology Consortium, 2009), and through inferences based on protein structural domains (Mitchell et al, 2015)
Summary
The laboratory mouse is widely recognized as an important animal model for investigating genetic and cellular systems relevant to human biology and disease It has the advantages of being a small mammal in which all life stages can be accessed, for which a completely sequenced, well annotated reference genome is publicly available, and for which there are myriad genomic tools available for comparative and experimental manipulation. Other new resources for complex traits and QTL (Quantitative Trait Loci), including the Collaborative Cross (Collaborative Cross Consortium, 2012; Threadgill and Churchill, 2012) and Diversity Outbred mice (Churchill et al, 2012; Svenson et al, 2012) are beginning to bear fruit in analysis of complex and multigenic diseases (Chesler, 2014; Logan et al, 2013; Philip et al, 2011) These exquisite genetic resources for mice help unravel the functional components of the mouse (and mammalian) genomes, at the level of the individual gene, complex interactions, and systemic effects (Bucan et al, 2012). We comment on the ongoing changes and challenges of maintaining and evolving MGD as an international community data resource for mouse genomics and biology
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