Developing a protein‐interactions ontology

The prediction and analysis of a protein’s function is an ongoing challenge in the field of genomics. With upcoming datasets on protein interactions [9], it is becoming evident that the function of a protein can only be understood when taking its interaction with other molecules into account. Most current approaches to the classification and description of protein function, such as the Gene Ontology [8], focus on single proteins. These annotation efforts should be paralleled by the development of ontologies dealing with the interactions of a protein with other biomolecules. Currently, most approaches to building such ontologies focus on metabolism [3,6]. So far, for interactions, only high-level classifications have been created [4], developed to assist information extraction from text. In addition to assisting text mining, a more fine-grained (in comparison to these classifications) ontology on protein interactions could be helpful in database development and information mining. As an ontology captures domain knowledge in a computer-understandable way, it can be used for inferencing, i.e. deriving new knowledge from existing data. There are two important points to consider in developing such a formal ontology: (a) it should be independent of its final use; and (b) it should not only restrict itself to a controlled vocabulary but the concepts should be related to each other in a semantically consistent manner, and rules governing these definitions and relations should be incorporated whenever necessary. Here we describe our approach for developing such an ontology.