Introduction

1. Knowledge Discovery through Text Mining Biomedical Documents Relating Climate and Cancer Incidence Research Alliance in Math and Science Oak Ridge National Laboratory http://info.ornl.gov/sites/rams2012/k_gaster Katherine Gaster Wofford College Mentor: Georgia Tourassi, Ph.D. Computational Sciences and Engineering Division Introduction Conclusions Results • Relationship between climate and health widely studied • Climatic temperature stress increases cardiovascular disease risk • Solar UV radiation increases skin cancer risk • Cancer incidence rates expected to rise dramatically • Cancer risk factors: genetic vs. environmental • Objective: Investigate possible link between climate and cancer incidence • How: Knowledge discovery via text mining of biomedical literature • Why: Efficient way to assist scientific hypothesis formation • Discovered expectedassociations • Skin cancer risk and UV exposure • Breast cancer / prostate cancer risk and genetic profile • Text mining revealed expected associations between climatic factors and cancer types • Unexpected association discovered: increased skin cancer risk in kidney transplant recipients • Supplementary articles clustered as expected Total documents: 3 Total Piranha Categories: 1 Unknown 100% Total Document Categories: 1 All Article… 100% Top Terms: uv photobiol, phot… .rs carcinogenesis bl ish ed Total documents: 6 Total Piranha Categories: 1 unknown 100% Total Document Categories: 1 All Article… 100% Top Terms: herit, heritable, prostate, pros … genetics, ge ne… brca population-based Figure 1. Expected association: cancer risk and UV exposure. Figure 5. Document clustering of original articles. Original threshold values, no stop words. Figure 6. Document clustering of original and supplementary articles. Original threshold values, no stop words. Discovered unexpected association: increased skin cancer risk in kidney transplant recipients Future Work Methodology Melanoma of the Skin Incidence Rates by State, 2008 Total documents: 3 Total Piranha Categories: 1 unknown 100% Total Document Categories: 1 All Article… 100% Top Terms: renal nmsc, nmsc:, nmscs dermatol keratoses:, ker… transplanted, t… Figure 2.Expected association: breast or prostate cancer risk and genetic profile. • Implement investigation linking actual transplant records and cancer incidence data • Determine if higher association exists between skin cancer and kidney transplants in sunny climates • Generate new hypotheses that may be tested with traditional, long term epidemiological studies • Develop model to predict future expected cancer incidence based on environmental factors Figure 3. Map depicting relative melanoma incidence for each U.S. state in 2008. Figure 4.Unexpected association: kidney transplants and skin cancer. • Obtained additional publications to investigate association further • Completed literature search for publications referring to kidney transplants and skin cancer • Analyzed supplementary documents with and without original documents • Study design • Literature search to find relevant publications • Text mining using Piranha software • Investigate impact of Piranha’s key features • Crandall, C.G., & Gonzalez-Alonso, J. (2010). Cardiovascular Function in the Heat-Stressed Human. Acta Physiologica, 407-23. • Jemal, A., Center, M. M., & DeSantis, C. (2010). Global Patterns of Cancer Incidence and Mortality Rates and Trends. Cancer Epidemiology Biomarkers & Prevention,1893-907. • U.S. cancer statistics: an interactive atlas [Image]. (n.d.). Retrieved from http://apps.nccd.cdc.gov/DCPC_INCA/DCPC_INCA.aspx • van der Leun, J. C., & de Gruijl, F. R. (2002). Climate change and skin cancer [Abstract]. Photochemical and Photobiological Sciences, 324-26. The Research Alliance in Math and Science program is sponsored by the Office of Advanced Scientific Computing Research, U.S. Department of Energy. The work was performed at the Oak Ridge National Laboratory, which is managed by UT-Battelle, LLC under Contract No. De-AC05-00OR22725. This work has been authored by a contractor of the U.S. Government, accordingly, the U.S. Government retains a nonexclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes.The author would like to thank Dr. Georgia Tourassi and Dr. Robert Patton for their support and assistance with this research. I would also like to thank Kara Kruse and Rashida Askia for their continued support and assistance, and Debbie McCoy for the opportunity to perform this research and her continued support and assistance.