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.

The authors report the BioPAX which is a collaborative effort to create a data exchange format for biological pathway data. In this paper, the authors explore the potential for the BioPAX initiative and the BioPAX ontology to model and deliver the pathway data necessary for systems style bioinformatics. The authors demonstrate how to map different pathway database to the BioPAX ontology, and the way of using the BioPAX ontology to ask questions over different pathway databases.

Very relevant to my work. The additional files contain templates of OWL files that will represent pathways and molecular interactions within a pathway.

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.

BioPAX[1] is a collaborative effort to develop a data exchange format to facilitate integration of biological pathway knowledge. The BioPAX exchange format is currently specified in a combination of English and OWL. In this paper we explore a tension, present in the current BioPAX specification, between representation of records in biological databases and realist representations of biological entities and processes. We propose to reorganize the BioPAX ontology to represent both of these points of view and in the process correct shortcomings in its use of OWL. In doing so we note some issues in using OWL for data exchange. We propose extensions which would both serve accurately model such exchange and help users avoid some common errors when using OWL.