Abstract
In this paper, we propose a formulation for inference rules in Drug Interaction Ontology (DIO). Our formulation for inference rules is viewed from the standpoint of process-description. The relations in DIO are now described as resource-sensitive linear logical implications. The compositional reasoning on certain drug-interactions discussed in our previous work on DIO is represented as a construction of a linear logical proof. As examples of our formulation, we use some anti-cancer drug interactions.
Keywords
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Gene Ontology Consortium: Creating the Gene Ontology resource: design and implementation. Genome Res. 2001 11, 1425–1433 (2001)
Gene Ontology Consortium: The Gene Ontology Editorial Style Guide, http://www.geneontology.org/GO.usage.shtml
Girard, J.Y.: Linear Logic. Theoretical Computer Science 50, 1–102 (1987)
Girard, J.Y.: Linear Logic: its syntax and semantics. In: Girard, J.Y., Lafont, Y., Regnier, L. (eds.) Advances in Linear Logic. London Mathematical Society Lecture Note Series, Cambridge University Press, Cambridge (1995)
Goguen, J.: Data, Schema, Ontology, and Logic Integration. In: Carnielli, W., Dionisio, M., Mateus, P. (eds.) Logic Journal of the IGPL, vol. 13(6) (2006) (to appear)
Goguen, J.: Information Integration in Institutions. In: Moss, L. (ed.) Jon Barwise memorial volume, Indiana University Press (2006) (to appear)
Goguen, J.: Ontology, Society, and Ontotheology. In: Varzi, A., Vieu, L. (eds.) Formal Ontology in Information Systems, pp. 95–103. IOS Press, Amsterdam (2004)
Grenona, P., Smith, B.: SNAP and SPAN: Towards Dynamic Spatial Ontology. In: SPATIAL COGNITION AND COMPUTATION, vol(issue), start-end, Lawrence Erlbaum Associates, Inc., Mahwah
Hasebe, K., Jouannaud, J.P., Kremer, A., Okada, M., Zumkeller, R.: Formal Verification of Dynamic Real-Time State-Transition Systems Using Linear Logic. In: Proc. Software Science Conference, Nagoya, September 2003, 5 pages (2003)
Hodas, J.S., Miller, D.: Logic Programming in a Fragment of Intuitionistic LinearLogic. Journal of Information and Computation 110(2), 327–365 (1994)
Horrocks, I.: Description logics in ontology applications. In: Beckert, B. (ed.) TABLEAUX 2005. LNCS (LNAI), vol. 3702, pp. 2–13. Springer, Heidelberg (2005)
Institute for Formal Ontology and Medical Information Science (IFOMIS), http://www.ifomis.uni-saarland.de/
Masolo, C., Borgo, S., Gangemi, A., Guarino, N., Oltramari, A.: WonderWeb Deliverable D18 - Ontology Library (final), http://wonderweb.semanticweb.org/deliverables/D18.shtml
Mathijssen, R.H.J., van Alpen, R.J., Verweij, J., Walter, J.L., Nooter, K., Stoter, G., Sparreboom, A.: Clinical Pharmacokinetics and Metabolism of Irinotecan (CPT- 11). Clinical Cancer Research 7, 2182–2194 (2001)
McCarthy, J., Hayes, P.J.: Some Philosophical Problems from the Standpoint of Artificial Intelligence. Machine Intelligence 4, 463–502 (1969)
Miller, D.: A Survey of Linear Logic Programming. Computational Logic: The Newsletter of the European Network in Computational Logic 2(2), 63–67 (1995)
OBO. Open Biomedical Ontologies, http://obo.sourceforge.net/
Okada, M.: Linear Logic and Intuitionistic Logic. In: La revue internationale de philosophie, vol. 230, pp. 449–481 (2004) (special issue Intuitionism)
Okada, M.: An Introduction to Linear Logic: Phase Semantics and Expressiveness. In: Takahashi, M., Dezani, M., Okada, M. (eds.) Theories of Types and Proofs. Memoirs of Mathematical Society of Japan, vol. 2, pp. 255–295 (1998), second edition (1999)
Okada, M.: Girard’s Linear Logic and Applications (in Japanese, partly in English). In: a JSSS Tutorial Lecture Note (41 pages), Software Science Society of Japan (1993)
Smith, B., et al.: Basic Formal Ontology, http://ontology.buffalo.edu/bfp
Smith, B., Kumar, A.: On Controlled Vocabularies in Bioinformatics: A Case Study in the Gene Ontology. BIOSILICO: Drug Discovery Today 2, 246–252 (2004)
Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A.L., Rosse, C.: Relations in biomedical ontologies. Genome Biology 6, R46 (2005)
Smith, B., Rosse, C.: The Role of Foundational Relations in the Alignment of Biomedical Ontologies. In: Fieschi, M., et al. (eds.) Medinfo 2004, pp. 444–448. IOS Press, Amsterdam (2004)
Sattler, U.: Description Logics for Ontologies. In: Ganter, B., de Moor, A., Lex, W. (eds.) ICCS 2003. LNCS(LNAI), vol. 2746, Springer, Heidelberg (2003)
Stevens, R., Wroe, C., Lord, P., Goble, C.: Ontologies in Bioinformatics. In: Handbook on Ontologies in Information Systems, pp. 635–657. Springer, Heidelberg (2003)
Yoshikawa, S., Satou, K., Konagaya, A.: Drug Interaction Ontology (DIO) for Inferences of Possible Drug-drug Interactions. In: Fieschi, M., et al. (eds.) MEDINFO 2004, pp. 454–458. IOS Press, Amsterdam (2004)
Yoshikawa, S., Konagaya, A.: DIO: Drug Interaction Ontology - Application to Inferences in Possible Drug-drug Interactions. In: Proceedings of The, International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS 2003), Las Vegas, Nevada, USA, June 23-26, pp. 231–236 (2003)
Yoshikawa, S., Satou, K., Konagaya, A.: Application of Drug Interaction Ontology (DIO) for Possible Drug-drug Interactions. In: Proceedings of Chem-BioInformatics Society (2003), p. 320 (2003)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Okada, M., Sugimoto, Y., Yoshikawa, S., Konagaya, A. (2006). Drug Interaction Ontology (DIO) and the Resource-Sensitive Logical Inferences. In: Futatsugi, K., Jouannaud, JP., Meseguer, J. (eds) Algebra, Meaning, and Computation. Lecture Notes in Computer Science, vol 4060. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11780274_32
Download citation
DOI: https://doi.org/10.1007/11780274_32
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-35462-8
Online ISBN: 978-3-540-35464-2
eBook Packages: Computer ScienceComputer Science (R0)