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Literature Mining: Towards Better Understanding of Autism

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Artificial Intelligence in Medicine (AIME 2007)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 4594))

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Abstract

In this article we present a literature mining method RaJoLink that upgrades Swanson’s ABC model approach to uncovering hidden relations from a set of articles in a given domain. When these relations are interesting from medical point of view and can be verified by medical experts, they represent new pieces of knowledge and can contribute to better understanding of diseases. In our study we analyzed biomedical literature about autism, which is a very complex and not yet sufficiently understood domain. On the basis of word frequency statistics several rare terms were identified with the aim of generating potentially new explanations for the impairments that are observed in the affected population. Calcineurin was discovered as a joint term in the intersection of their corresponding literature. Similarly, NF-kappaB was recognized as a joint term. Pairs of documents that point to potential relations between the identified joint terms and autism were also automatically detected. Expert evaluation confirmed the relevance of these relations.

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References

  1. Ahn, K.S., Aggarwal, B.B.: Transcription Factor NF-{kappa}B: A Sensor for Smoke and Stress Signals. Annals of the New York Academy of Sciences 1056, 218–233 (2005)

    Article  Google Scholar 

  2. Araghi-Niknam, M., Fatemi, S.H.: Levels of Bcl-2 and P53 are altered in superior frontal and cerebellar cortices of autistic subjects. Cellular and Molecular Neurobiology 23(6), 945–952 (2003)

    Article  Google Scholar 

  3. Belmonte, M.K., Allen, G., Beckel-Mitchener, A., Boulanger, L.M., Carper, R.A., Webb, S.J.: Autism and abnormal development of brain connectivity. The Journal of Neuroscience 27(42), 9228–9231 (2004)

    Article  Google Scholar 

  4. Chen, H., Polo, S., Di Fiore, P.P., De Camilli, P.V.: Rapid Ca2+-dependent decrease of protein ubiquitination at synapses. Proceedings of the National Academy of Sciences of the United States of America 100(25), 14908–14913 (2003)

    Article  Google Scholar 

  5. Erin, N., Bronson, S.K., Billingsley, M.L.: Calcium-dependent interaction of calcineurin with Bcl-2 in neuronal tissue. Neuroscience 117(3), 541–555 (2003)

    Article  Google Scholar 

  6. Fatemi, S.H., Stary, J.M., Halt, A.R., Realmuto, G.R.: Dysregulation of Reelin and Bcl-2 proteins in autistic cerebellum. Journal of Autism and Developmental Disorders 31(6), 529–535 (2001)

    Article  Google Scholar 

  7. Fayyad, U., Piatetsky-Shapiro, G., Smyth, P.: Knowledge Discovery and Data Mining: Towards a Unifying Framework. In: Proceedings of the Second International Conference on Knowledge Discovery and Data Mining, Portland, Oregon, pp. 82–88 (1996)

    Google Scholar 

  8. Fortuna, B., Grobelnik, M., Mladenić, D.: Semi-automatic Data-driven Ontology Construction System. In: Proceedings of the 9th International multi-conference Information Society IS-2006, Ljubljana, Slovenia, pp. 223–226 (2006)

    Google Scholar 

  9. 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, 289–298 (2005)

    Article  Google Scholar 

  10. Huber, K.M., Gallagher, S.M., Warren, S.T., Bear, M.F.: Altered synaptic plasticity in a mouse model of fragile X mental retardation. Proceedings of the National Academy of Sciences of the United States of America 99(11), 7746–7750 (2002)

    Article  Google Scholar 

  11. Irwin, S., Galvez, R., Weiler, I.J., Beckel-Mitchener, A., Greenough, W.: Brain structure and the functions of FMR1 protein. In: Hagerman, R.J., Hagerman, P., J. Fragile X syndrome. The Johns Hopkins University Press, Baltimore, pp. 191–205 (2002)

    Google Scholar 

  12. Mattson, M.P.: NF-kappaB in the survival and plasticity of neurons. Neurochemical Research 30(6-7), 883–893 (2005)

    Article  Google Scholar 

  13. Ming, X., Stein, T.P., Brimacombe, M., Johnson, W.G., Lambert, G.H., Wagner, G.C.: Increased excretion of a lipid peroxidation biomarker in autism. Prostaglandins, Leukotrienes, and Essential Fatty Acids 73(5), 379–384 (2005)

    Article  Google Scholar 

  14. Pratt, W., Yetisgen-Yildiz, M.: LitLinker: Capturing Connections across the Biomedical Literature. In: Proceedings of the International Conference on Knowledge Capture (K-Cap 2003), Florida, pp. 105–112 (2003)

    Google Scholar 

  15. PubMed: Overview (January 2007) http://www.ncbi.nlm.nih.gov/

  16. Qiu, S., Korwek, K.M., Weeber, E.J.: A fresh look at an ancient receptor family: emerging roles for density lipoprotein receptors in synaptic plasticity and memory formation. Neurobiology of Learning and Memory 85(1), 16–29 (2006)

    Article  Google Scholar 

  17. Rusnak, F., Mertz, P.: Calcineurin: Form and Function. Physiological Reviews 80(4), 1483–1521 (2000)

    Google Scholar 

  18. Smalheiser, N.R., Swanson, D.R.: Using ARROWSMITH: a computer-assisted approach to formulating and assessing scientific hypotheses. Computer Methods and Programs in Biomedicine 57, 149–153 (1998)

    Article  Google Scholar 

  19. Swanson, D.R.: Medical literature as a potential source of new knowledge. Bulletin of the Medical Library Association 78(1), 29–37 (1990)

    Google Scholar 

  20. Van Someren, M., Urbančič, T.: Applications of machine learning: matching problems to tasks and methods. The Knowledge Engineering Review 20(4), 363–402 (2006)

    Article  Google Scholar 

  21. Vargas, D.L., Nascimbene, C., Krishnan, C., Zimmerman, A.W., Pardo, C.A.: Neuroglial activation and neuroinflammation in the brain of patients with autism. Annals of Neurology 57(1), 67–81 (2005)

    Article  Google Scholar 

  22. Weeber, M., Vos, R., Klein, H., De Jong-van den Berg, L.T., Aronson, A.R., Molema, G.: Generating Hypotheses by Discovering Implicit Associations in the Literature: A case Report of a Search for New Potential Therapeutic Uses for Thalidomide. Journal of the American Medical Informatics Association 10(3), 252–259 (2003)

    Article  Google Scholar 

  23. Winder, D.G., Sweatt, J.D.: Roles of serine/threonine phosphatases in hippocampal synaptic plasticity. Nature reviews Neuroscience 2(7), 461–474 (2001)

    Article  Google Scholar 

  24. Zou, J., Crews, F.: CREB and NF-kappaB Transcription Factors Regulate Sensitivity to Excitotoxic and Oxidative Stress Induced Neuronal Cell Death. Cellular and Molecular Neurobiology 26(4-6), 383–403 (2006)

    Article  Google Scholar 

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Riccardo Bellazzi Ameen Abu-Hanna Jim Hunter

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Urbančič, T., Petrič, I., Cestnik, B., Macedoni-Lukšič, M. (2007). Literature Mining: Towards Better Understanding of Autism. In: Bellazzi, R., Abu-Hanna, A., Hunter, J. (eds) Artificial Intelligence in Medicine. AIME 2007. Lecture Notes in Computer Science(), vol 4594. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73599-1_29

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  • DOI: https://doi.org/10.1007/978-3-540-73599-1_29

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-73598-4

  • Online ISBN: 978-3-540-73599-1

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