Mouse Genome Informatics: Integration Nexus for Mammalian Biology
B Sinclair1, JA Blake 2, M Ringwald, CJ Bult, JA Kadin, JE Richardson, JT Eppig, Mouse Genome Informatics Group
1bobs@informatics.jax.org, Jackson Laboratory; 2jblake@informatics.jax.org, Jackson Laboratory
The Mouse Genome Informatics (MGI) information system functions as an integration nexus for mammalian biology. Combining computational and curational approaches to data acquisition and integration, the MGI system provides access to comprehensive experimental data in the domains of sequence, expression, gene function, molecular variation, phenotype, inbred strain characterization, homology, and tumor biology. In daily collaboration with Swiss-Prot, HUGO Nomenclature, and LocusLink, MGI curators resolve inconsistencies in sequence assignments to gene objects, mapping determinations, nomenclatures, and functional classifications. MGI provides the definitive index of mouse genes with their official nomenclature under the aegis of the International Committee on Standardized Genetic Nomenclature of Mice.
Recent innovations and updates in the MGI system include the curation and incorporation of ~60,000 RIKEN clones as part of the FANTOM project, the development and implementation of a Mammalian Phenotype (MP) ontology which is being used to annotate the over 10,000 alleles, the inclusion of GO annotations for over 12,000 genes, sequence representations for over 30,000 genes, incorporation of nearly 80,000 publications, enhancements to the mouseBLAST resource, and curated links to Swiss-Prot, DOTs, EnSEMBL, TIGR, InterPro, and other genomics and genetics resources.
In addition to full integration of the GO in the MGI system, the Mouse Anatomical Dictionary and Phenotype Classifications provide the mechanism for standard annotations of aspects of gene expression data, QTL analyses, and details about experimental mouse mutants. Annotation of mouse mutants combines molecular details with information about normal and dysfunctional phenotypes. Mouse phenotypes are associated via carefully defined relationships with human phenotypes, particularly diseases.
MGI developers and curators are collaborating with other Model Organism Database and genome annotation groups to build informatics resources for biology including the Gene Ontology, the GMOD and OBO sites, and the Sequence Ontology. We are working with members of the community of biologists including clinicians to refine and standardize the representations of phenotypes including disease states. The goal of this project is to provide access to the highest quality data for the laboratory mouse
The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are two primary components of the MGI database system. MGD is supported by NHGRI grant HG-00330. GXD is supported by National Institute of Child Health and Human Development grant HD33745. The GO work at MGI is supported by NHGRI grant HG-02273.