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About MouseMine

MouseMine contains a subset of the data from MGI, concentrating on essential mouse genomic information, MGI-curated annotations (GO, MP, OMIM), and supporting publications, external database references, and curator notes. Human and comparative data (human genes, coordinates, OMIM annotations, Homologene clusters) are included as well. MouseMine also contains some data not currently found in MGI, including the Disease Ontology and mouse/human synteny blocks. Over time, we will expand MouseMine's data coverage to include more of MGI (e.g., sequences), as well as selected additional data (e.g. pathways). For more information, see About MouseMine.

Data Category Data Source

Genome

Mouse genome feature catalog. All mouse features from MGI, including nomenclature, synonyms, ids, genome coordinates and cross-references (external database IDs). MGI
Human genes, including symbols, names, ids, and genome coordinates. MGI
Genes from other model organisms, including symbols, names, ids, and genome coordinates. FlyMine RatMine WormMine YeastMine ZebrafishMine

Proteins

Mouse proteins and protein fragments, including sequences, keywords, identifiers, etc. UniProt
Association of mouse proteins to mouse genes. NOTE: due to a limitation in the data model, MouseMine does NOT currently contain associations of proteins to non-gene features (e.g., gene segments). MGI
Protein domains annotated to specific protein regions. InterPro

Function

Mouse GO annotations. High quality associations of mouse genes (and other features) to biological processes, molecular functions, and cellular localizations. MGI
GO@MGI
Gene Ontology (GO). Gene Ontology project.

Expression

Expression annotations. Results from assays of endogenous gene expression in wild type and mutant mice. GXD (Gene Expression Database) @MGI
EMAPA anatomy ontology. EMAPA is the abstract (stage-aggregated) mouse developmental anatomy ontology, developed by the Edinburgh Mouse Atlas Project. EMAP (Edinburgh Mouse Atlas Project) and GXD

Interactions

Mouse and human protein-protein interaction data from BioGrid and IntAct. BioGrid
IntAct
Mouse micro RNA (miRNA) interaction data from MGI. MGI

Pathways

Pathways and their associations to genes and proteins. Reactome

Phenotype

The MGI catalog of mouse alleles, including targeted, engineered, induced, and spontaneous mutants. MGI
Phenotypes (MP terms) annotated to specific mouse genotypes. From these, additional annotations are computed (derived) from phenotypes to mouse genes and alleles.
Mammalian Phenotype (MP) ontology

Disease

Disease names, synonyms, and identifiers from the Online Mendelian Inheritance in Man database. OMIM (via MGI)
Mouse disease model annotations, i.e., associations of human diseases to specific mouse models (genotypes). From these, additional annotations are computed (derived) from diseases to mouse genes and alleles. MGI
Human disease gene annotations, i.e., associations of human genes with specific diseases. OMIM (via MGI)
The Disease Ontology (DO) is a standardized ontology for human disease terms, phenotype characteristics and related medical vocabulary disease concepts. Disease Ontology project.

Homology

Mouse-Human Orthologies Homologene and Panther
Mouse-Human Synteny Blocks. Computed/extrapolated from ortholog pairs and their coordinates. (Usage note: InterMine does not yet provide any facilities for mapping (interpolating) coordinates using synteny blocks. Implementation of such a service is on the "to do" list.) MGI

Literature

All publications from MGI. MGI