Mouse Genome Database (MGD)

Mouse Genome Database (MGD) provides integrated genetic, genomic, phenotype, and functional annotations for the laboratory mouse to support genotype-to-phenotype analysis and translational research into human biology and disease.

Key Features:

• Comprehensive gene and genome catalog: Maintains a complete catalog of mouse genes and genome features integrating DNA and protein sequence data.
• Data integration: Incorporates data from manual curation of biomedical literature, researcher submissions, and downloads from Ensembl, UniProt, and NCBI.
• Non-redundant unified dataset: Produces a non-redundant unified dataset used for gene nomenclature, mutation, allele, and strain classification.
• Genotype–phenotype representation: Represents relationships between genes, sequences, and standardized phenotype descriptions to provide a consensus view from genotype to phenotype.
• Ontology-based functional annotation: Uses the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology for evidence-supported functional and phenotype annotations.
• Human disease associations: Links phenotype annotations to human disease entries via Online Mendelian Inheritance in Man (OMIM).
• IKMC and allele integration: Integrates alleles generated by the International Knockout Mouse Consortium (IKMC) and includes mouse gene trap allele and sequence information.
• Recombinase (cre) portal and classification updates: Includes a recombinase (cre) portal, comprehensive updates to genetic maps, and new classification terms for genome features.
• Programmatic data access: Provides programmatic and bulk data access mechanisms such as Batch Query, BioMart, and a web services API.

Scientific Applications:

• Modeling human disease: Enables use of the laboratory mouse to investigate human biology and disease through integrated genotype, phenotype, and functional data.
• Gene function analysis: Supports functional interpretation of genes and gene products via GO-based annotations linked to experimental evidence.
• Genotype-to-phenotype mapping: Facilitates mapping of alleles and mutations to standardized phenotype terms for comparative and mechanistic studies.
• Allele and knockout analysis: Supports analysis of IKMC-generated alleles and gene trap alleles for loss-of-function and genetic perturbation studies.
• Nomenclature and classification: Provides authoritative resources for accurate gene nomenclature, mutation annotation, allele definition, and strain classification.

Methodology:

Manual curation of biomedical literature and researcher submissions, integration of data from Ensembl, UniProt, and NCBI, use of Gene Ontology (GO) and Mammalian Phenotype (MP) Ontology for evidence-supported annotations, linkage to OMIM, and incorporation of IKMC and gene trap allele datasets.