Abstract
In this article we present a study which demonstrates the ability of the method RaJoLink to uncover candidate hypotheses for future discoveries from rare terms in existing literature. The method is inspired by Swanson’s ABC model approach to finding hidden relations from a set of articles in a given domain. The main novelty is in a semi-automated way of suggesting which relations might have more potential for new discoveries and are therefore good candidates for further investigations. In our previous articles we reported on a successful application of the method RaJoLink in the autism domain. To support the evaluation of the method with a well-known example from the literature, we applied it to the migraine domain, aiming at reproducing Swanson’s finding of magnesium deficiency as a possible cause of migraine. Only literature which was available at the time of the Swanson’s experiment was used in our test. As described in this study, in addition to actually uncovering magnesium as a candidate for formulating the hypothesis, RaJoLink pointed also to interferon, interleukin and tumor necrosis factor as candidates for potential discoveries connecting them with migraine. These connections were not published in the titles contemporary to the ones used in the experiment, but have been recently reported in several scientific articles. This confirms the ability of the RaJoLink method to uncover seeds of future discoveries in existing literature by using rare terms as a beacon.
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References
PubMed. Overview, http://www.ncbi.nlm.nih.gov/ (accessed, September 2008)
Koestler, A.: The act of creation. MacMillan Company, New York (1964)
Swanson, D.R.: Undiscovered public knowledge. Libr Q 56(2), 103–118 (1986)
Swanson, D.R.: Migraine and magnesium: Eleven neglected connections. Perspectives in Biology and Medicine 31, 526–557 (1988)
Swanson, D.R.: Medical literature as a potential source of new knowledge. Bull. Med. Libr. Assoc. 78(1), 29–37 (1990)
Weeber, M., Vos, R., Klein, H., de Jong-van den Berg, L.T.W.: Using concepts in literature-based discovery: Simulating Swanson’s Raynaud–fish oil and migraine–magnesium discoveries. J. Am. Soc. Inf. Sci. Tech. 52(7), 548–557 (2001)
Srinivasan, P., Libbus, B.: Mining MEDLINE for implicit links between dietary substances and diseases. Bioinformatics 20 (suppl.1), i290–i296 (2004)
Hristovski, D., Peterlin, B., Mitchell, J.A., Humphrey, S.M.: Using literature-based discovery to identify disease candidate genes. Int. J. Med. Inform. 74(2-4), 289–298 (2005)
Yetisgen-Yildiz, M., Pratt, W.: Using statistical and knowledge-based approaches for literature-based discovery. J. Biomed. Inform. 39(6), 600–611 (2006)
Urbančič, T., Petrič, I., Cestnik, B., Macedoni-Lukšič, M.: Literature mining: towards better understanding of autism. In: Bellazzi, R., Abu-Hanna, A., Hunter, J. (eds.) AIME 2007. LNCS (LNAI), vol. 4594, pp. 217–226. Springer, Heidelberg (2007)
Petrič, I., Urbančič, T., Cestnik, B.: Discovering hidden knowledge from biomedical literature. Informatica 31(1), 15–20 (2007)
Petrič, I., Urbančič, T., Cestnik, B., Macedoni-Lukšič, M.: Literature mining method RaJoLink for uncovering relations between biomedical concepts. Journal of Biomedical Informatics 42, 219–227 (2009)
Belmonte, M.K., Allen, G., Beckel-Mitchener, A., Boulanger, L.M., Carper, R.A., Webb, S.J.: Autism and abnormal development of brain connectivity. J. Neurosci. 24(42), 9228–9231 (2004)
Persico, A.M., Bourgeron, T.: Searching for ways out of autism maze: genetic, epigenetic and environmental clues. Trends in neurosciences 29(7) (July 2006)
Nelson, S.J., Johnston, D., Humphreys, B.L.: Relationships in Medical Subject Headings. In: Bean, C.A., Green, R. (eds.) Relationships in the organization of knowledge, pp. 171–184. Kluwer Academic Publishers, New York (2001)
Smalheiser, N.R., Swanson, D.R.: Using ARROWSMITH: a computer-assisted approach to formulating and assessing scientific hypotheses. Comput. Methods Programs Biomed. 57(3), 149–153 (1998)
Swanson, D.R., Smalheiser, N.R., Torvik, V.I.: Ranking indirect connections in literature-based discovery: The role of Medical Subject Headings (MeSH). J. Am. Soc. Inf. Sci. Tec. 57(11), 1427–1439 (2006)
Altura, B.M.: Calcium antagonist properties of magnesium: implications for antimigraine actions. Magnesium 4(4), 169–175 (1985)
Blake, C., Pratt, W.: Automatically Identifying Candidate Treatments from Existing Medical Literature. In: Proceedings of AAAI Spring Symposium on Mining Answers from Texts and Knowledge Bases, Stanford, CA (2002)
Lindsay, R.K., Gordon, M.D.: Literature-based discovery by lexical statistics. Journal of the American Society for Information Science and Technology 50(7), 574–587 (1999)
Srinivasan, P.: Text Mining: Generating Hypotheses from MEDLINE. Journal of the American Society for Information Science and Technology 55(5), 396–413 (2004)
Hearst, M.A.: Untangling text data mining. In: Dale, R. (ed.) Proceedings of the 37th Annual Meeting of the Association for Computational Linguistics, pp. 3–10. Morgan Kaufmann Publishers, San Francisco (1999)
Covelli, V., Munno, I., Pellegrino, N.M., Di Venere, A., Jirillo, E., Buscaino, G.A.: Exaggerated spontaneous release of tumor necrosis factor-alpha/cachectin in patients with migraine without aura. Acta Neurol. (Napoli) 12(4), 257–263 (1990)
Covelli, V., Munno, I., Pellegrino, N.M., Altamura, M., Decandia, P., Marcuccio, C., Di Venere, A., Jirillo, E.: Are TNF-alpha and IL-1 beta relevant in the pathogenesis of migraine without aura? Acta Neurol. (Napoli) 13(2), 205–211 (1991)
Shimomura, T., Araga, S., Esumi, E., Takahashi, K.: Decreased serum interleukin-2 level in patients with chronic headache. Headache 31(5), 310–313 (1991)
van Hilten, J.J., Ferrari, M.D., Van der Meer, J.W., Gijsman, H.J., Looij Jr., B.J.: Plasma interleukin-1, tumour necrosis factor and hypothalamic-pituitary-adrenal axis responses during migraine attacks. Cephalalgia 11(2), 65–67 (1991)
Detry-Morel, M., Boschi, A., Gehenot, M., Geubel, A.: Bilateral transient visual obscurations with headaches during alpha-II interferon therapy: a case report. Eur. J. Ophthalmol. 5(4), 271–274 (1995)
Gunderson, C.H.: The impact of new pharmaceutical agents on the cost of neurologic care. Neurology 45(3 Pt. 1), 569–572 (1995)
Gidal, B.E., Wagner, M.L., Privitera, M.D., Dalmady-Israel, C., Crismon, M.L., Fagan, S.C., Graves, N.M.: Current developments in neurology, Part I: Advances in the pharmacotherapy of headache, epilepsy, and multiple sclerosis. Ann Pharmacother 30(11), 1272–1276 (1996)
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Urbančič, T., Petrič, I., Cestnik, B. (2009). RaJoLink: A Method for Finding Seeds of Future Discoveries in Nowadays Literature. In: Rauch, J., Raś, Z.W., Berka, P., Elomaa, T. (eds) Foundations of Intelligent Systems. ISMIS 2009. Lecture Notes in Computer Science(), vol 5722. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04125-9_16
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