The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics

@article{Blake2011TheMG,
  title={The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics},
  author={Judith A. Blake and Carol J. Bult and James A. Kadin and Joel E. Richardson and Janan T. Eppig},
  journal={Nucleic Acids Research},
  year={2011},
  volume={39},
  pages={D842 - D848}
}
The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse and the authoritative source for phenotype and functional annotations of mouse genes. MGD includes a complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics (MGI, http://www… 

Figures and Tables from this paper

The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse

TLDR
Improvements to MGD include expanded genome feature classifications, inclusion of new mutant allele sets and phenotype associations and extensions of GO to include new relationships and a new stream of annotations via phylogenetic-based approaches.

Mouse Genome Informatics (MGI): reflecting on 25 years

TLDR
Some of the major changes in research approaches over that last quarter century are reviewed, how these changes are reflected in the MGI resource you use today, and what may be around the next corner.

Integration of global resources for human genetic variation and disease

TLDR
Building a systematic link to phenotypes manifested in model organisms will be of particular importance with the advent of new, large‐scale phenotyping projects such as the International Mouse Phenotyping Consortium, and improved semantic description and funding and organizational innovations are required.

The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data

TLDR
The Mammalian Phenotype Ontology is a structured vocabulary for describing mammalian phenotypes and serves as a critical tool for efficient annotation and comprehensive retrieval of phenotype data, providing a standard underpinning to mouse phenotype descriptions for existing and future experimental and large-scale phenotyping projects.

BioMart as an integration solution for the International Knockout Mouse Consortium

TLDR
The use of the BioMart data management system is described to provide integrated access to International Knockout Mouse Consortium data and other related mouse resources, invaluable for researchers involved in the elucidation of gene function and the role of individual genes in human disease.

Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases

TLDR
The predictive and analytical power of the Manteia system is demonstrated to predict candidate genes responsible for human genetic diseases.

From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes

TLDR
A set of human orthologs of known essential genes in the mouse shows characteristics fully consistent with essential function in human and thus provides a resource to inform and facilitate interpretation of sequence data in studies of human disease.

GeneWeaver: a web-based system for integrative functional genomics

TLDR
GeneWeaver is a curated repository of genomic experimental results with an accompanying tool set for dynamic integration of these data sets, enabling users to interactively address questions about sets of biological functions and their relations to sets of genes.

Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions

TLDR
A computational, knowledge-based approach to automatically infer gene functions from phenotypic manifestations has been developed and applied to yeast, nematode worm, zebrafish, fruit fly, fruitfly, and mouse phenotypes.

Disease model curation improvements at Mouse Genome Informatics

TLDR
The merged Medical Subject Headings (MeSH) and OMIM disease vocabulary created by the Comparative Toxicogenomics Database (CTD) project is evaluated and an extended version of the vocabulary is created to meet the genetic disease-specific curation needs at MGI.
...

References

SHOWING 1-10 OF 29 REFERENCES

The Mouse Genome Database: enhancements and updates

TLDR
Improvements in MGD described here includes integration of mouse gene trap allele and sequence data, integration of gene targeting information from the International Knockout Mouse Consortium, deployment of an MGI Biomart, and enhancements to the batch query capability for customized data access and retrieval.

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

TLDR
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.

The Mouse Genome Database genotypes::phenotypes

TLDR
Improvements in MGD described here include the unified mouse gene catalog for NCBI Build 37 of the reference genome assembly, and improved representation of mouse mutants and phenotypes.

The mammalian phenotype ontology: enabling robust annotation and comparative analysis

TLDR
A tool, the Mammalian Phenotype (MP) ontology, is described for classifying and organizing phenotypic information related to the mouse and other mammalian species and aids in the discovery of candidate disease genes and molecular signaling pathways.

The Rat Genome Database 2009: variation, ontologies and pathways

TLDR
By curating, storing, integrating, visualizing and promoting rat data, RGD ensures that the investment made into rat genomics and genetics can be leveraged by all interested investigators.

The mouse Gene Expression Database (GXD): 2007 update

TLDR
The utility of GXD has been greatly enhanced by a large increase in data content, obtained from the literature and provided by researchers doing large-scale in situ and cDNA screens, and the query and display features have been refined to make it easier for users to interrogate the data.

MouseCyc: a curated biochemical pathways database for the laboratory mouse

TLDR
A new database of curated metabolic pathways for the laboratory mouse called MouseCyc, integrated with genetic and genomic data for the Laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human.

Ensembl Genomes: Extending Ensembl across the taxonomic space

TLDR
Ensembl Genomes is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform.

The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium

The International Knockout Mouse Consortium (IKMC) aims to mutate all protein-coding genes in the mouse using a combination of gene targeting and gene trapping in mouse embryonic stem (ES) cells and

The vertebrate genome annotation (Vega) database

TLDR
The Vertebrate Genome Annotation (Vega) database was first made public in 2004 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome.