Abstract
This article addresses the task of mining named relationships between concepts from biomedical literature for indexing purposes or for scientific discovery from medical literature. This research builds on previous work on concept mining from medical literature for indexing purposes and proposes to learn semantic relationships names between concepts learnt. Previous ConceptMiner system did learn pairs of concepts, expressing a relationship between two concepts, but did not learn relationships semantic names. Building on ConceptMiner, RelationshipMiner is interested in learning as well the relationships with their name identified from the Unified Medical Language System (UMLS) knowledge-base as a basis for creating higher-level knowledge structures, such as rules, cases, and models, in future work. Current system is focused on learning semantically typed relationships as predefined in the UMLS, for which a dictionary of synonyms and variations has been created. An evaluation is presented showing that actually this relationship mining task improves the concept mining task results by enabling a better screening of the relationships between concepts for relevant ones.
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References
Bichindaritz, I.: Mémoire: Case Based Reasoning Meets the Semantic Web in Biology and Medicine. In: Funk, P., González Calero, P.A. (eds.) ECCBR 2004. LNCS (LNAI), vol. 3155, pp. 47–61. Springer, Heidelberg (2004)
Bichindaritz, I., Akineni, S.: Case Mining from Biomedical Literature. In: Perner, P., Imiya, A. (eds.) MLDM 2005. LNCS (LNAI), vol. 3587, pp. 682–691. Springer, Heidelberg (2005)
Dorre, J., Gerstl, P., Seiffert, R.: Text mining: Finding nuggets in mountains of textual data. In: Chaudhuri, S., Madigan, D., Fayyad, U. (eds.) Proceedings of the fifth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 398–401. ACM press, New York (1999)
Friedman, C., Kra, P., Yu, H., Krauthammer, M., Rzhetsky, A.: GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17(suppl. 1), S74–S82 (2001)
Fuller, S., Revere, D., Bugni, P., Martin, G.M.: A knowledgebase system to enhance scientific discovery: Telemakus. Biomed. Digit. Libr. 1(1), 2 (2004)
Han, J., Kamber, M.: Data mining concepts and techniques, 1st edn. Morgan Kaufmann, San Mateo (2000)
Hearst, M.A.: Untangling Text Data Mining. In: Dale, R., Church, K. (eds.) Proceedings of the 37th Annual Meeting of the Association for Computational Linguistics, pp. 3–10. Association for Computational Linguistics, Morristown (1999)
Hristovski, D., Peterlin, B., Mitchell, J.A., Humphrey, S.M.: Using literature-based discovery to identify disease candidate genes. International Journal of Medical Informatics 74(2-4), 28–98 (2005)
Nasukawa, T., Nagano, T.: Text Analysis and Knowledge Mining System. Knowledge management Special Issue. IBM systems journal 40, 967–984 (2001)
National Library of Medicine: The Specialist NLP Tools [Last access, April 1, 2005] (2004), http://specialist.nlm.nih.gov
National Library of Medicine: MetaMap Transfer (MMTx) (last access, April 1, 2005) (2005), http://mmtx.nlm.nih.gov
National Library of Medicine: The Unified Medical Language System (last access, April 1, 2005) (2005), http://umls.nlm.nih.gov
Swanson, D.R.: Information discovery from complementary literatures: Categorizing viruses as potential weapons. Journal of the American Society for Information Science 52(10), 797–812 (2001)
Swanson, D.R., Smalheiser, N.R.: An interactive system for finding complementary literatures: A stimulus to scientific discovery. Artificial Intelligence 9, 183–203 (1997)
Weeber, M., Vos, R., De Jong-van Den Berg, L.T., Aronson, A.R., Molena, G.: Generating hypotheses by discovering implicit associations in the literature: A case report of a search for new potential therapeutic uses for thalidomide. J. Am. Med. Inform. Assoc. 10(3), 252–259 (2003)
Yang, Q., Hong, C.: Case Mining from Large Databases. In: Ashley, K.D., Bridge, D.G. (eds.) ICCBR 2003. LNCS (LNAI), vol. 2689, pp. 691–702. Springer, Heidelberg (2003)
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Bichindaritz, I. (2006). Named Relationship Mining from Medical Literature. In: Perner, P. (eds) Advances in Data Mining. Applications in Medicine, Web Mining, Marketing, Image and Signal Mining. ICDM 2006. Lecture Notes in Computer Science(), vol 4065. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11790853_6
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DOI: https://doi.org/10.1007/11790853_6
Publisher Name: Springer, Berlin, Heidelberg
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