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

Nucleic acids research | Jan 15, 2008

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.

Pubmed ID: 18158299 RIS Download

Mesh terms: Animals | Databases, Genetic | Genomics | Internet | Mice | Models, Animal | Mutagenesis | Phenotype | Software | User-Computer Interface

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This is a list of tools and resources that we have found mentioned in this publication.


HGNC

A worldwide authority that approves standardized nomenclature to gene name and symbol (short-form abbreviation) for each known human gene and stores all approved symbols in the HGNC database. Approved symbols are also browse-able by chromosome. Each symbol is unique and each gene is only given one approved gene symbol. In preference each symbol maintains parallel construction in different members of a gene family and can also be used in other species, especially the mouse. Over 38,000 symbols have been approved; the vast majority of these are for protein-coding genes, but also include symbols for pseudogenes, non-coding RNAs, phenotypes and genomic features. Individual new symbols are requested by scientists, journals and databases, and groups of new symbols by those working on gene families or specific regions of the genome. Gene symbol and name proposals may be submitted to them to be accredited with HGNC approved nomenclature for use in publications, databases and presentations.

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RGD

Centralized database that collects, manages, and distributes data generated from ongoing rat genetic and genomic research efforts and makes these data widely available to the scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. It also facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include a comprehensive description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources.

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