Large-scale international projects are underway to generate collections of knockout mouse mutants and subsequently to perform high throughput phenotype assessments, raising new challenges for computational researchers due to the complexity and scale of the phenotype data. Phenotypes can be described using ontologies in two differing methodologies. Traditionally an individual phenotypic character has either been defined using a single compound term, originating from a species-specific dedicated phenotype ontology, or alternatively by a combinatorial annotation, using concepts from a range of disparate ontologies, to define a phenotypic character as an entity with an associated quality (EQ). Both methods have their merits, which include the dedicated approach allowing use of community standard terminology, and the combinatorial approach facilitating cross-species phenotypic statement comparisons. Previously databases have favoured one approach over another. The EUMODIC project will generate large amounts of mouse phenotype data, generated as a result of the execution of a set of Standard Operating Procedures (SOPs) and will implement both ontological approaches to capture the phenotype data generated.