Levels of ontology annotation of mouse phenotype data. The relationships between the levels of annotation are shown along with real annotations taken from the Hotplate SOP. a) The SOP is annotated using MP. Each parameter, representing a mouse trait, is defined using EQ. At the point of annotating individual mouse data, qualitative and quantitative parameters are handled differently. Qualitative parameters have a quality assigned to them, with a child-to-parent "is a" relationship to the parameter quality, and may be described using MP where a relevant concept exists. Quantitative parameters have a numerical value assigned to them. After comparison of the mutant line (cohort of individual mice) to the baseline data, statistically significant lines are annotated dynamically. Qualitative EQ data is annotated as being present at an increased or decreased frequency and quantitative data annotation using an increased or decreased based EQ statement, where the quality is a child of the parameter quality. In both cases, if a relevant MP term exists to define the direct phenotype it is assigned. The annotation of inferred phenotypes using MP terms is explained in the Discussion. b) Ontology terms are used to define two Hotplate SOP parameters. Example data is used to illustrate possible annotations of the mouse and the mutant strain. The annotations of the direct phenotypes allow association with an inferred phenotype.