towards an integrative human pathway database for systems biology applications
While there are more than 217 online pathway databases of different coverage and quality as of September 2007, our knowledge of human pathways is still far from complete. It has been challenging to develop pathway tools and database resources that could expand the coverage of existing annotated pathway data by integrating these resources both at the syntactic and semantic levels. While developing the Human Pathway Database (HPD), we use data warehousing techniques and a unified pathway data model to integrate a total of 1,895 pathways and 10,631 molecular entities from four different annotated and predicted pathway resources in human. HPD provides a comprehensive and integrated view linking human proteins, genes, RNAs, signaling reactions, gene regulatory events for future systems biology applications. We studied pathways in the database for their merging potentials and showed a preliminary pathway merging result as 2-D clusters. We also examined pathway scale and the distribution of pathway-spanning proteins, pathway characteristics that suggest small pathways and large pathways may still be under-represented in the HPD. We also found many proteins with important energy metabolism, cell growth, and cell differentiation functions span across vast number of pathways. The raw data for HPD can be queried at: http://discover.uits.indiana.edu:8340/spathway/s_pathway/
data integration signaling pathways bio-molecular pathway