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The mouse genome database (MGD): new features facilitating a model system.

The mouse genome database (MGD, http://www.informatics.jax.org/), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGD's primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and expert human curation. MGD collaborates with the bioinformatics community on the development of data and semantic standards, and it incorporates key ontologies into the MGD annotation system, including the Gene Ontology (GO), the Mammalian Phenotype Ontology, and the Anatomical Dictionary for Mouse Development and the Adult Anatomy. MGD is the authoritative source for mouse nomenclature for genes, alleles, and mouse strains, and for GO annotations to mouse genes. MGD provides a unique platform for data mining and hypothesis generation where one can express complex queries simultaneously addressing phenotypic effects, biochemical function and process, sub-cellular location, expression, sequence, polymorphism and mapping data. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the incorporation of single nucleotide polymorphism data and search tools, the addition of PIR gene superfamily classifications, phenotype data for NIH-acquired knockout mice, images for mouse phenotypic genotypes, new functional graph displays of GO annotations, and new orthology displays including sequence information and graphic displays.

Pubmed ID: 17135206

Authors

  • Eppig JT
  • Blake JA
  • Bult CJ
  • Kadin JA
  • Richardson JE
  • Mouse Genome Database Group

Journal

Nucleic acids research

Publication Data

January 4, 2007

Associated Grants

  • Agency: NHGRI NIH HHS, Id: HG000330

Mesh Terms

  • Animals
  • Computer Graphics
  • Databases, Genetic
  • Disease Models, Animal
  • Genomics
  • Genotype
  • Internet
  • Mice
  • Mice, Knockout
  • Models, Animal
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Proteins
  • Sequence Homology
  • Systems Integration
  • User-Computer Interface