e-Science and biological pathway semantics

Abstract

Background: The development of e-Science presents a major set of opportunities and challenges for the future progress of biological and life scientific research. Major new tools are required and corresponding demands are placed on the high-throughput data generated and used in these processes. Nowhere is the demand greater than in the semantic integration of these data. Semantic Web tools and technologies afford the chance to achieve this semantic integration. Since pathway knowledge is central to much of the scientific research today it is a good test-bed for semantic integration. Within the context of biological pathways, the BioPAX initiative, part of a broader movement towards the standardization and integration of life science databases, forms a necessary prerequisite for its successful application of e-Science in health care and life science research. This paper examines whether BioPAX, an effort to overcome the barrier of disparate and heterogeneous pathway data sources, addresses the needs of e-Science.

Results: We demonstrate how BioPAX pathway data can be used to ask and answer some useful biological questions. We find that BioPAX comes close to meeting a broad range of e-Science needs, but certain semantic weaknesses mean that these goals are missed. We make a series of recommendations for re-modeling some aspects of BioPAX to better meet these needs.

Conclusion: Once these semantic weaknesses are addressed, it will be possible to integrate pathway information in a manner that would be useful in e-Science.

Figure 1

Image showing the human insulin signaling pathway from BioCarta.

Figure 2

Image showing the human glycolysis pathway from BioCarta.

Figure 3

Image showing part of the human glycolysis pathway from HumanCyc.

Figure 4

Image showing part of the human glycolysis pathway from KEGG.

Figure 5

Image showing the ontology and the mapping of a reaction from the glycolysis pathway. The black arrows indicate the physical entity subclasses of the reaction (protein and smallMolecule). The green and blue arrows refer to interaction subclasses. The green arrows indicate the properties of the catalysis class (CONTROLLER and CONTROLLED); the blue arrows indicate the properties of the class biochemicalReaction (LEFT, RIGHT, and E.C.#)

Figure 6

Image showing the mapping of the biochemical reaction beta-D-glucose-6-phosphate <=>D-fructose-6-phosphate from the glycolysis pathway in BioCarta to BioPAX [30]. Figure courtesy of Michael Cary and Gary Bader.