The recent explosion of information in the biomedical field has provided a greater opportunity to address significant problems related to human disease than at any time in the past. Biomedical researchers studying such processes as growth, differentiation, and cell death have defined a large number of genetic and biochemical pathways that regulate these processes, and have determined that disruption of these pathways are known to occur in most disease states. It is widely believed that elucidation of the genes and proteins that compose these biochemical pathways will define the molecular targets for future drug therapies. Increasingly, it is recognized that the various biochemical pathways that have been defined by researchers are cross connected and form an exceedingly complex network involving hundreds of genes and proteins. Therefore, before the promise of pathway mechanism based drug therapies can be realized, the nature of the effect that manipulating any one pathway might have on another must be understood. GeneScene is designed to utilize information derived from Medline, the primary repository of the abstracts of biomedical research reports, to help suggest possible interactions between genetic and biochemical pathways. It will assist in reviewing existing literature, identifying gaps in existing knowledge, comparing and integrating knowledge and data from different fields, and as such help lead the way to new and interesting hypotheses and field research. There are four parts to this goal: GeneScene will integrate the knowledge related to gene pathway analysis contained in several journals, allow researchers to browse and search the information and our knowledge representation, integrate text based knowledge regarding gene pathway analysis with gene array data, and allow personalization and collaboration by researchers. Our first objective is the extraction of gene pathway knowledge from text-based sources. Our second objective is to let researchers browse and search the knowledge map. Our third objective is to provide researchers the opportunity to cooperate and to integrate gene array data into the knowledge map.
