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

Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA, Mouse Genome Database Gro - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA. carol.bult@jax.org

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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Related in: MedlinePlus

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
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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

Mentions: The comparative data resources in MGD now includes links to the TreeFam (9) resource and the availability of graphical displays of mammalian genes organized by the OrthoDisease (10) sets (Figure 2). TreeFam provides curated information about ortholog and paralog assignments and the evolutionary history of various gene families. Hypertext links to TreeFam are from the Genes and Markers or the Mammalian Orthology detail pages in MGD.Figure 2.


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

Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA, Mouse Genome Database Gro - Nucleic Acids Res. (2007)

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
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238849&req=5

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
Mentions: The comparative data resources in MGD now includes links to the TreeFam (9) resource and the availability of graphical displays of mammalian genes organized by the OrthoDisease (10) sets (Figure 2). TreeFam provides curated information about ortholog and paralog assignments and the evolutionary history of various gene families. Hypertext links to TreeFam are from the Genes and Markers or the Mammalian Orthology detail pages in MGD.Figure 2.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA. carol.bult@jax.org

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.

Show MeSH
Related in: MedlinePlus