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A Formal Framework on the Semantics of Regulatory Relations and Their Presence as Verbs in Biomedical Texts

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Flexible Query Answering Systems (FQAS 2009)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 5822))

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Abstract

Relations used in biomedical ontologies and expressed in biomedical texts can be very general or very specific. Regulatory relations are used widely in regulatory networks, for example, and therefore they appear systematically and highly frequently in biomedical texts. This work focuses on the logical properties of positive and negative regulations, both as formal relations and the frequency of their usage as verbs in texts. The paper discusses whether there exists a weak transitivity-like property for the relations. Our corpora consist of biomedical patents, Medline abstracts and the British National Corpus (BNC). Finally, the paper discusses the use of the relations for semantic indexing in information retrieval.

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References

  1. Andreasen, T., Bulskov, H., Lassen, S., Zambach, T., Madsen, B.N., Thomsen, H.E., Jensen, P.A., Nilsson, J.F., Szymczak, B.A.: SIABO: Semantic Information Access through Biomedical Ontologies. In: KEOD (accepted, 2009)

    Google Scholar 

  2. Baader, F., Lutz, C., Suntisrivaraporn, B.: CEL a polynomial-time reasoner for life science ontologies, pp. 287–291. Springer, Heidelberg (2006)

    Google Scholar 

  3. Bodenreider, O.: The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 32, D267–D270 (2004)

    Article  Google Scholar 

  4. Chen, H., Sharp, B.M.: Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics 5(NIL), 147 (2004)

    Article  Google Scholar 

  5. Heinrich, R., Rapoport, S.M.: Metabolic regulation and mathematical models. Prog. Biophys. Molec. Biol. 32, 1 (1977)

    Article  MathSciNet  Google Scholar 

  6. Hoffmann, R.: Using the iHOP information resource to mine the biomedical literature on genes, proteins, and chemical compounds. In: Curr. Protoc. Bioinformatics, ch. 1, Unit1.16 (December 2007)

    Google Scholar 

  7. Kanehisa, M., Goto, S.: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000)

    Article  Google Scholar 

  8. Kilgarriff, A.: Assorted frequency lists and related documentation for the british national corpus, bnc (1995), http://www.kilgarriff.co.uk/bnc-readme.html

  9. Lassen, T., Zambach, S.: Verb frequence lists, BNC, Medline abstracts and biomedical patents (2008) (unpublished)

    Google Scholar 

  10. Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., Kanapin, A., Lewis, S., Mahajan, S., May, B., Schmidt, E., Vastrik, I., Wu, G., Birney, E., Stein, L., D’Eustachio, P.: Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37, D619–D622 (2009)

    Article  Google Scholar 

  11. Gene Ontology Consortium. GO Ontology Relations. geneontology (August 2009), http://www.org/GO.ontology-ext.relations.shtml

  12. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L.J., Eilbeck, K., Ireland, A., Mungall, C.J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S.A., Scheuermann, R.H., Shah, N., Whetzel, P.L., Lewis, S.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25, 1251–1255 (2007)

    Article  Google Scholar 

  13. Smith, B., Rosse, C.: The role of foundational relations in the alignment of biomedical ontologies. MEDINFO, 444–448 (2004)

    Google Scholar 

  14. Medline ®. National library of medicine (2008), http://www.ncbi.nlm.nih.gov/sites/entrez

  15. Zambach, S.: Logical implications for regulatory relations represented by verbs in biomedical texts. In: International Conference on Biomedical Ontology, Conference proceedings, Nature preceedings, p. 198 (July 2009)

    Google Scholar 

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Zambach, S. (2009). A Formal Framework on the Semantics of Regulatory Relations and Their Presence as Verbs in Biomedical Texts. In: Andreasen, T., Yager, R.R., Bulskov, H., Christiansen, H., Larsen, H.L. (eds) Flexible Query Answering Systems. FQAS 2009. Lecture Notes in Computer Science(), vol 5822. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04957-6_38

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  • DOI: https://doi.org/10.1007/978-3-642-04957-6_38

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-04956-9

  • Online ISBN: 978-3-642-04957-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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