gene pathway text mining and visualization - Artificial Intelligence ...

542 MEDICAL INFORMATICSanalysis and future exploration. The network display was inspired by themanually created pathway maps researchers often make when readingPubMed abstracts and articles. We are currently evaluating the utility of thevisualizer to enhance cancer researchers’ access to research findings.Having extracting and analyzed large numbers of gene-pathway relations,our future research direction has focused on consolidating or aggregating therelations. Aggregating relations combines equivalent relations, even thoughthey may have been expressed with different words (i.e., non-mutant genesare often called wild-type genes). Such a task requires a deeperunderstanding of the relations. Knowing which relations say the same thingor express contradictory findings allows the visualizer to display only uniquerelations as well as point out possibly interesting contradictions forresearchers to pursue. Such information has the potential to improve theranking of relations returned from a search as well as to present a lesscluttered gene network for visual analysis. In addition, as relations are morefully understood, they can be automatically linked to other existingknowledge sources such as the UMLS semantic network and the REFSEQdatabase. Expert formed relations from the database could then be mergedwith the automatically extracted relations to increase the accuracy andcoverage of the network.5. ACKNOWLEDGEMENTSThis research was sponsored by the following grant: NIH/NLM, 1 R33LM07299-01, 2002-2005, “Genescene: a Toolkit for Gene PathwayAnalysis.”REFERENCESAnanko, E. A., N. L. Podkolodny, et al. (2002). "GeneNet: a Database on Structure AndFunctional Organisation of Gene Networks," Nucleic Acid Research 30(1): 398-401.Ashburner, M., C. A. Ball, et al. (2000). "Gene Ontology: Tool For the Unification ofBiology,” Nature Genetics 25: 25-29.Breitkreutz, B.-J., C. Stark, et al. (2003). "Osprey: A Network Visualization System,”Genome Biology 4(3): R22.Brill, E. (1993). A Corpus-Based Approach To Language Learning. Computer Science.Philadelphia, University of Pennsylvania.Buchholz, S. N. (2002). Memory-Based Grammatical Relation Finding. Computer Science.Tilburg, University of Tilburg: 217.Chen, H. And K. J. Lynch (1992). “Automatic Construction of Networks of ConceptsCharacterizing Document Databases," IEEE Transactions on Systems, Man AndCybernetics 22(5): 885-902.