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The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.

Nucleic acids research | Jan 1, 2005

The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics.

Pubmed ID: 15608240 RIS Download

Mesh terms: Animals | Databases, Genetic | Genes | Genome | Genomics | Genotype | Internet | Mice | Mice, Mutant Strains | Phenotype | Systems Integration | User-Computer Interface

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


Beta Cell Biology Consortium

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 1, 2015. Consortium that aims to facilitate interdisciplinary collaborations to advance the understanding of pancreatic islet development and function, with the goal of developing innovative therapies to correct the loss of beta cell mass in diabetes, including cell reprogramming, regeneration and replacement. They are responsible for collaboratively generating the necessary reagents, mouse strains, antibodies, assays, protocols, technologies and validation assays that are beyond the scope of any single research effort. The scientific goals for the BCBC are to: * Use cues from pancreatic development to directly differentiate pancreatic beta cells and islets from stem / progenitor cells for use in cell-replacement therapies for diabetes, * Determine how to stimulate beta cell regeneration in the adult pancreas as a basis for improving beta cell mass in diabetic patients, * Determine how to reprogram progenitor / adult cells into pancreatic beta-cells both in-vitro and in-vivo as a mean for developing cell-replacement therapies for diabetes, and * Investigate the progression of human type-1 diabetes using patient-derived cells and tissues transplanted in humanized mouse models. Many of the BCBC investigator-initiated projects involve reagent-generating activities that will benefit the larger scientific community. The combination of programs and activities should accelerate the pace of major new discoveries and progress within the field of beta cell biology.

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Jackson Laboratory

An independent, nonprofit organization focused on mammalian genetics research to advance human health. Their mission is to discover the genetic basis for preventing, treating, and curing human disease, and to enable research for the global biomedical community. Jackson Laboratory breeds and manages colonies of mice as resources for other research institutions and laboratories, along with providing software and techniques. Jackson Lab also conducts genetic research and provides educational material for various educational levels.

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GO

A community-based bioinformatics resource consisting of three structured controlled vocabularies (ontologies) for the annotation of gene products with respect to their molecular function, cellular component, and biological role in a species-independent manner. This initiative to standardize the representation of gene and gene product attributes across species and databases is an effort to address the need for consistent descriptions of gene products in different databases. The Gene Ontology project encourages input from the community into both the content of the GO and annotation using GO. There are three separate aspects to this effort: first, they write and maintain the ontologies themselves; second, they make cross-links between the ontologies and the genes and gene products in the collaborating databases; and third, they develop tools that facilitate the creation, maintenance and use of ontologies. The controlled vocabularies are structured so that users can query them at different levels: for example, uers can use GO to find all the gene products in the mouse genome that are involved in signal transduction, or users can zoom in on all the receptor tyrosine kinases. This structure also allows annotators to assign properties to gene products at different levels, depending on how much is known about a gene product.

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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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