The application of an ontology design pattern for functional abnormalities to phenotype ontologies and the extraction of an ontology of anatomical functions

Functions play an important role throughoutbiology. Although molecular functions are cov-ered in the Gene Ontology, there is currently nopublicly available ontology of anatomical func-tions. Ontological considerations on the natureof functional abnormalities and their represen-tation in current phenotype ontologies showthat we can automatically extract a skeletonfor such an ontology of anatomical functionsby using a combination of process, phenotypeand anatomy ontologies. We provide an onto-logical analysis of the nature of functions andfunctional abnormalities. From this analysis,we derive an approach to the automatic ex-traction of anatomical functions from existingontologies using a combination of natural lan-guage processing, graph-based analysis of theontologies and formal inferences. Alternatively,we introduce a new relation to relate materialobjects to processes that realize the functionof the object to avoid a needless duplication ofprocesses already present in the Gene Ontol-ogy in a new ontology of anatomical functions.We discuss several limitations of the currentontologies that still need to be addressed to en-sure a consistent and complete representationof anatomical functions and functional abnor-malities.