Ontology-Based Aggregation of Biological Pathway Datasets

The massive accumulation of biological data in the past decades has generated a significant amount of biological knowledge which is represented in one way as biological pathways. The existence of over 150 pathway databases reflects the diversity of the biological data and heterogeneity of data models, storage formats and access methods. To address an intriguing biological question, it is not uncommon for a biologist to query more one pathway database to acquire a more complete picture of current understanding of biology. To facility life scientists in searching biological pathway data, we designed a biological pathway aggregator which aggregates various pathway datasets via the BioPAX ontology, a community-developed ontology based upon the concept of semantic Web for integrating and exchanging biological pathway data. Our aggregator is composed of modules that retrieve the data from various sources, transform the raw data to BioPAX format, persist the converted data in the persistent data store, and enable queries by other applications