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. 2008 Jan;36(Database issue):D724-8.
doi: 10.1093/nar/gkm961. Epub 2007 Dec 23.

The Mouse Genome Database (MGD): mouse biology and model systems

Carol J Bult  1 , Janan T Eppig, James A Kadin, Joel E Richardson, Judith A Blake; Mouse Genome Database Group
Affiliations

The Mouse Genome Database (MGD): mouse biology and model systems

Carol J Bult et al. Nucleic Acids Res. 2008 Jan.

Abstract

The Mouse Genome Database, (MGD, http://www.informatics.jax.org/), integrates genetic, genomic and phenotypic information about the laboratory mouse, a primary animal model for studying human biology and disease. MGD data content includes comprehensive characterization of genes and their functions, standardized descriptions of mouse phenotypes, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information including comparative data on mammalian genes. Data within MGD are obtained from diverse sources including manual curation of the biomedical literature, direct contributions from individual investigator's laboratories and major informatics resource centers such as Ensembl, UniProt and NCBI. MGD collaborates with the bioinformatics community on the development of data and semantic standards such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. MGD provides a data-mining platform that enables the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the association of gene trap data with mouse genes and a new batch query capability for customized data access and retrieval.

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Figures

Figure 1.
Figure 1.
Screenshot showing the new MGI Batch Query Tool. Inputs into the query form (A) can be lists of sequence or gene identifiers. The output of the query (B) can be gene identifiers from other resources, genome location, gene nomenclature, functional annotations and phenotype annotations. Output from the batch query form can be displayed as a web form or as a tab-delimited file (C).
Figure 2.
Figure 2.
Screenshot showing the Gene Ontology Molecular Function annotation graph for a gene associated with OMIM disorder ‘Aniridia, type II’ (OMIM id 106210). The graph displays experimental GO annotations for the human gene (PAX6) associated with this disorder as well as annotations for orthologous genes in other organisms (mouse, rat, nematode, chicken and yeast) based on the OrthoDisease set. The graph nodes are color-coded to indicate the organism that is the source of the annotation. The full graph and table of annotations can be viewed at: http://proto.informatics.jax.org/prototypes/GOgraphEX/OrthoDisease_Graphs/ OMIM_DisorderGraphs/106210.html
See this image and copyright information in PMC

References

    1. Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, the Mouse Genome Informatics group. The Mouse Genome Database (MGD): new features facilitating a model system. Nucleic Acids Res. 2007;35:637. - PMC - PubMed
    1. Blake JA, Eppig JT, Bult CJ, Kadin JA, Richardson JE, Mouse Genome Database Group. The Mouse Genome Database (MGD): updates and enhancements. Nucleic Acids Res. 2006;34:D562–D567. - PMC - PubMed
    1. Eppig JT, Bult CJ, Kadin JA, Richardson JE, Blake JA, The Mouse Genome Database Group. The Mouse Genome Database (MGD): from genes to mice – a community resource for mouse biology. Nucleic Acids Res. 2005;33:D471–D475. - PMC - PubMed
    1. Hill DP, Begley DA, Finger JH, Hayamizu TF, McCright IJ, Smith CM, Beal JS, Corbani LE, Blake J, et al. The Mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Res. 2004;32:D568–D571. Available at http://www.informatics.jax.org/mgihome/GXD/aboutGXD.shtml. - PMC - PubMed
    1. Krupke DM, Naf D, Vincent MJ, Allio T, Mikaelian I, Sundberg JP, Bult CJ, Eppig JT. The Mouse Tumor Biology Database: integrated access to mouse cancer biology data. Exp. Lung Res. 2005;31:259–270. Available at http://tumor.informatics.jax.org. - PubMed

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