Summarizing Phenotype Evolution Patterns from Report Cases
- 157 Downloads
The need to represent and manage time is implicit in several reasoning processes in medicine. However, this is predominantly obvious in the field of many neurodegenerative disorders, which are characterized by insidious onsets, progressive courses and variable combinations of clinical manifestations in each patient. Therefore, the availability of tools providing high level descriptions of the evolution of phenotype manifestations from patient data is crucial to promote early disease recognition and optimize the diagnostic process. Although many case reports published in the literature do not provide exhaustive temporal information except only key time references, such as disease onset, diagnosis or monitoring time, automatically comparing cases described by temporal clinical manifestation sequences can provide valuable knowledge about the data evolution. In this paper, we demonstrate the usefulness of representing patient case reports of a neurodegenerative disorder as a set of temporal clinical manifestations semantically annotated with a domain phenotype ontology and registered with a time-stamped value. Novel techniques are presented to query and match sets of different manifestation sequences from multiple patient cases, with the aim of automatically inferring phenotype evolution patterns of generic patients for clinical studies. The method was applied to 25 patient report cases from a Spanish study of the domain of cerebrotendinous xanthomatosis. Five evolution patterns were automatically generated to analyze the patient data. The results were evaluated against 49 relevant conclusions drawn from the study, with a precision of 93 % and a recall of 70 %.
KeywordsOWL Ontology Temporal constraint network Phenotype Semantic web Cerebrotendinous xanthomatosis
The work presented in this paper has been developed in the funded national project Gestión de Terminologías Médicas para Arquetipos (TIN2009-14159-C05-05) by the Ministerio de Educación y Ciencia.
Conflict of interest
The authors declare that they have no conflict of interest.
- 3.Pustejovsky, J., Castaño, J., Ingria, R., Saurí, R., Gaizauskas, R., Setzer, A., Katz, G. TimeML: robust specification of event and temporal expressions in text. Proc of the Fifth International Workshop on Computational Semantics. http://www.timeml.org/site/publications/timeMLpubs/IWCS-v4.pdf. Accessed 10 June 2012, 2003.
- 4.Marín, R., Cárdenas, M. A., Balsa, M., and Sánchez, J. L., Obtaining solutions in fuzzy constraint networks. Int. J. Approx. Reason. 16(3–4):261–288, 1996.Google Scholar
- 5.McGuinness, D., and van Harmelen, F. OWL web ontology language overview. http://www.w3.org/TR/owl-features/. Accessed 10 June 2012, 2004
- 6.Hobbs, J. R., and Pan, F. Time ontology in OWL. http://www.w3.org/TR/owl-time/. Accessed 10 June 2012, 2006.
- 8.Tao, C., Wei, W. Q., Solbrig, H. R., Savova, G., Chute, C. G. CNTRO: a semantic web ontology for temporal relation inferencing in clinical narratives. Proc of the AMIA Annual Symposium pp 787–791. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041418/. Accessed 10 June 2012, 2010.
- 9.Zhou, L., Parsons, S., and Hripcsak, G., The evaluation of a temporal reasoning system in processing clinical discharge summaries. J. Am. Med. Inform. Assoc. 15:99e106, 2008.Google Scholar
- 10.Mannila, H., and Moen, P., Similarity between event types in sequences. In: Mohania, M., and Tjoa, A. M. (Eds.), Proc of the first intl. conf. on data warehousing and knowledge discovery. Springer, London, pp. 271–280, 1999.Google Scholar
- 14.Seidenberg, J., and Rector, A. Web ontology segmentation: analysis, classification and use. In: Proc of the 15th International Conference on World. New York: ACM, pp 23–26, 2006.Google Scholar
- 17.O’Connor, M., and Das, A. SQWRL: a Query Language for OWL. In: Proc of the Fifth International Workshop on OWL: experiences and directions. http://bmir.stanford.edu/file_asset/index.php/1723/BMIR-2009-1395.pdf Accessed 10 June 2012, 2009.
- 18.Pilo, B. Xantomatosis Cerebrotendinosa en España: mutaciones, aspectos clínicos y terapéuticos. Dissertation, University of Alcalá de Henares, 2009.Google Scholar
- 21.Drummond, N., and Shearer, R. The open world assumption. http://www.cs.man.ac.uk/~drummond/presentations/OWA.pdf. Accessed 10 June 2012, 2006.