Interoperability between phenotype and anatomy ontologies

Abstract

Motivation: Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning.

Results: We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge.

Availability: http://bioonto.de/pmwiki.php/Main/PheneOntology.

Fig. 1.

The first distinction is drawn between phenes of objects and phenes of processes. We primarily classify phenes of objects into four main categories: structural, functional, qualitative and participatory phenes. Under the structural phenes, we show possible further classifications based on the relations we use in our method. Qualitative phenes can be further distinguished into those where only the quality is relevant and those where the quality's value is considered.