The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information

Abstract

The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease. The MP Ontology supports different levels and richness of phenotypic knowledge and flexible annotations to individual genotypes. It continues to develop dynamically via collaborative input from research groups, mutagenesis consortia, and biological domain experts. The MP Ontology is currently used by the Mouse Genome Database and Rat Genome Database to represent phenotypic data.

Figure 1

Screen shot of the Mammalian Phenotype (MP) Browser in which the term 'lethality-embryonic/perinatal' was selected. At the top (yellow shading) the term, its synonym and MP unique identifier appear. The number of paths to term (in this case, one) indicates how many paths through the DAG structure can be traversed to reach the term. The main body of the browser page shows the selected term highlighted and within the context of the hierarchical path(s) of the MP Ontology. In this example page, three levels of the hierarchy are visible (Phenotype Ontology, its 34 sub-terms, and the two sub-terms that fall beneath 'lethality-embryonic/perinatal'. The plus sign, appearing for many of the terms on this page, indicates that these terms have additional sub-terms that can be viewed by clicking on the term to expand the view of that portion of the ontology. The number of genotypes and annotations following the term 'lethality-embryonic/perinatal' is a hypertext link to those data. This latter feature will be available in early 2005.

Figure 2

Example showing a portion of the MGI web display of the phenotype annotations for homozygotes for the Ccm1^tm1Dmar genetically engineered allele (the first targeted mutation from the Douglas Marchuk laboratory in the cerebral cavernous malformations 1 gene). Homozygotes are embryonic lethal, showing developmental and cardiac abnormalities. Note the organization of annotations under the high level phenotype categories and the link to OMIM where the mouse and human show similar phenotypic characteristics. See [30] to view the complete record for the Ccm1^tm1Dmar phenotypic allele. Searches for phenotypes at MGI can be done via the Alleles and Phenotypes Query Form [31].