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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 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).
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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).

Mentions: The new MGI Batch Query Tool (http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=batchQF) provides the ability to access information about nomenclature, genome location, function or phenotype associations for many genes/markers in a single query (Figure 1). The allowable input into the Batch Query Tool includes current gene symbols, Ensembl gene ids, EntrezGene ids, VEGA gene ids, MGI ids, RefSeq ids and GenBank sequence accession ids. These data can be uploaded as a file or pasted into a text box on the query form. Users can specify the desired output and output format (web or tab-delimited text). The Batch Query Tool is particularly useful for researchers who use non-MGI gene accession identifiers in their analyses but who want to connect those identifiers to the rich functional and phenotypic annotations for mouse genes contained in MGD.Figure 1.


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

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

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).
Mentions: The new MGI Batch Query Tool (http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=batchQF) provides the ability to access information about nomenclature, genome location, function or phenotype associations for many genes/markers in a single query (Figure 1). The allowable input into the Batch Query Tool includes current gene symbols, Ensembl gene ids, EntrezGene ids, VEGA gene ids, MGI ids, RefSeq ids and GenBank sequence accession ids. These data can be uploaded as a file or pasted into a text box on the query form. Users can specify the desired output and output format (web or tab-delimited text). The Batch Query Tool is particularly useful for researchers who use non-MGI gene accession identifiers in their analyses but who want to connect those identifiers to the rich functional and phenotypic annotations for mouse genes contained in MGD.Figure 1.

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