MGD: the Mouse Genome Database

Abstract

The Mouse Genome Database (MGD) (http://www.informatics.jax.org) one component of a community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology. MGD strives to provide an extensively integrated information resource with experimental details annotated from both literature and on-line genomic data sources. MGD curates and presents the consensus representation of genotype (sequence) to phenotype information including highly detailed information about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse. Recent developments include a general implementation of database structures for controlled vocabularies and the integration of a phenotype classification system.

Figure 1

(A) The Allele and Phenotype Query Form permits queries based on Phenotype Classifications. In this example, the Phenotype Classification ‘tumors, increased incidence’ and Allele Type ‘Transgene induced (gene targeted)’ with only Conditional mutants returned. (B) The query presented in panel A returns a summary page of alleles defined by the criteria in A. In this case, 8 alleles met the criteria. The symbol, name and molecular description of these alleles are provided. Links are provided to the detail pages for each allele. (C) The top part of the detail page for the mutant phenotype of Brac1^tm2Cxd details the Phenotype Classification terms for this particular mutation. Here, the details of the genotype that underlie the phenotype are represented. Each Phenotype Classification term is associated with one or more allele pairs and with the information known about the remaining genetic background. Thus, phenotypes are associated with genotypes, rather than simply with the allele.