This project seeks to explore biomolecules in the context of networks of different biological pathways. The methods are built upon a combination of two complementary technologies, BioPAX and Instance Store. BioPAX is an emerging standard for the representation of biological pathway data exchange such as metabolic pathways, signal transduction pathways and gene regulatory networks. It is an ontology written in the Web Ontology Language (OWL) that describes genes, proteins, enzymes, and small molecules. Statements in OWL have a precise meaning and the strong formalism enables a collection of statements made in OWL to be reasoned over, as well as checked for consistency and contradictions. Instance Store takes an ontology and the data it describes formally in OWL and uses reasoning technology to ask question and make inferences about these data. Using the two technologies together should enable seamless integration of a number of data sources and facilitate the creation of tools.
Understanding and reasoning over pathway data will enhance life science and medical research, as well as environmental research such as bioremediation. It will also facilitate the development of semantic web technologies because of the data and use cases provided by the life sciences and be part of the World Wide Web consortium Life Science Initiative.
