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.

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Exploratory/Developmental Grants Phase II (R33)
Project #
5R33LM007299-02
Application #
6622199
Study Section
Genome Study Section (GNM)
Program Officer
Sim, Hua-Chuan
Project Start
2002-05-01
Project End
2006-04-30
Budget Start
2004-05-01
Budget End
2005-04-30
Support Year
2
Fiscal Year
2004
Total Cost
$440,259
Indirect Cost
Name
University of Arizona
Department
Administration
Type
Other Domestic Higher Education
DUNS #
806345617
City
Tucson
State
AZ
Country
United States
Zip Code
85721
Li, Xin; Chen, Hsinchun; Li, Jiexun et al. (2010) Gene function prediction with gene interaction networks: a context graph kernel approach. IEEE Trans Inf Technol Biomed 14:119-28
Li, Xin; Chen, Hsinchun; Huang, Zan et al. (2007) Global mapping of gene/protein interactions in PubMed abstracts: a framework and an experiment with P53 interactions. J Biomed Inform 40:453-64
Quinones, Karin D; Su, Hua; Marshall, Byron et al. (2007) User-centered evaluation of Arizona BioPathway: an information extraction, integration, and visualization system. IEEE Trans Inf Technol Biomed 11:527-36
Li, Jiexun; Su, Hua; Chen, Hsinchun et al. (2007) Optimal search-based gene subset selection for gene array cancer classification. IEEE Trans Inf Technol Biomed 11:398-405
Marshall, Byron; Su, Hua; McDonald, Daniel et al. (2006) Aggregating automatically extracted regulatory pathway relations. IEEE Trans Inf Technol Biomed 10:100-8
Li, Jiexun; Li, Xin; Su, Hua et al. (2006) A framework of integrating gene relations from heterogeneous data sources: an experiment on Arabidopsis thaliana. Bioinformatics 22:2037-43
Marshall, Byron; Su, Hua; McDonald, Daniel et al. (2005) Linking ontological resources using aggregatable substance identifiers to organize extracted relations. Pac Symp Biocomput :162-73
McDonald, Daniel M; Chen, Hsinchun; Su, Hua et al. (2004) Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser. Bioinformatics 20:3370-8
Leroy, Gondy; Chen, Hsinchun; Martinez, Jesse D (2003) A shallow parser based on closed-class words to capture relations in biomedical text. J Biomed Inform 36:145-58