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Generating explanations for biomedical queries

Published online by Cambridge University Press:  17 December 2013

ESRA ERDEM  and
UMUT OZTOK
ESRA ERDEM
Affiliation:
Sabancı University, Orhanlı, Tuzla, İstanbul 34956, Turkey (e-mail: esraerdem@sabanciuniv.edu, uoztok@sabanciuniv.edu)
UMUT OZTOK
Affiliation:
Sabancı University, Orhanlı, Tuzla, İstanbul 34956, Turkey (e-mail: esraerdem@sabanciuniv.edu, uoztok@sabanciuniv.edu)
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Abstract

We introduce novel mathematical models and algorithms to generate (shortest or k different) explanations for biomedical queries, using answer set programming. We implement these algorithms and integrate them in BioQuery-ASP. We illustrate the usefulness of these methods with some complex biomedical queries related to drug discovery, over the biomedical knowledge resources PharmGKB, DrugBank, BioGRID, CTD, SIDER, Disease Ontology, and Orphadata.

Keywords

answer set programmingexplanation generationquery answeringbiomedical queries
Type
Regular Papers
Information
Theory and Practice of Logic Programming , Volume 15 , Issue 1 , January 2015 , pp. 35 - 78
Copyright
Copyright © Cambridge University Press 2013 

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References

Apt, K. R. and Bol, R. N. 1994. Logic programming and negation: A survey. Journal of Logic Programming 19/20, 9–71.Google Scholar
Baral, C. 2003. Knowledge Representation, Reasoning and Declarative Problem Solving. Cambridge University Press, Cambridge, UK.Google Scholar
Bodenreider, O., Coban, Z. H., Doganay, M. C., Erdem, E. and Kosucu, H. 2008. A preliminary report on answering complex queries related to drug discovery using answer set programming. In Proc. of the Third International Workshop on Applications of Logic Programming to the (Semantic) Web and Web Services (ALPSWS 2008).Google Scholar
Brain, M. and Vos, M. D. 2005. Debugging logic programs under the answer set semantics. In Proc. of the Third International Workshop on Answer Set Programming (ASP 2005), De Vos, M. and Provetti, A. (Eds.). Online CEUR-WS.org/Vol-142/page141.pdf.Google Scholar
Brewka, G., Eiter, T. and Truszczynski, M. 2011. Answer set programming at a glance. Communications of the ACM 54, 92–103.CrossRefGoogle Scholar
Chong, C. R. and Sullivan, D. J. 2007. New uses for old drugs. Nature 448, 645–646.Google Scholar
Davis, A. P., King, B. L., Mockus, S., Murphy, C. G., Saraceni-Richards, C., Rosenstein, M., Wiegers, T. and Mattingly, C. J. 2011. The comparative toxicogenomics database: Update 2011. Nucleic Acids Research 39, D1067–1072.Google Scholar
Eiter, T., Ianni, G., Schindlauer, R. and Tompits, H. 2006. Effective integration of declarative rules with external evaluations for Semantic-Web reasoning. In Proc. of the Third European Conference on the Semantic Web: Research and Applications (ESWC 2006), Sure, Y. and Domingue, J. (Eds.). Springer-Verlag, Berlin, 273–287.Google Scholar
Erdem, E., Erdem, Y., Erdogan, H. and Oztok, U. 2011. Finding answers and generating explanations for complex biomedical queries. In Proc. of the Twenty-Fifth AAAI Conference on Artificial Intelligence (AAAI 2011), Burgard, W. and Roth, D. (Eds.). AAAI Press, 785–790.Google Scholar
Erdem, E., Erdogan, H. and Oztok, U. 2011. BIOQUERY-ASP: Querying biomedical ontologies using answer set programming. In Proc. of the Fifth International RuleML2011@BRF Challenge, Bragaglia, S., Viegas Damasio, C., Montali, M., Preece, A., Petrie, C., Proctor, M. and Straccia, U. (Eds.). Online CEUR-WS.org/Vol-560/paper8.pdf.Google Scholar
Erdem, E. and Yeniterzi, R. 2009. Transforming controlled natural language biomedical queries into answer set programs. In Proc. of the BioNLP 2009 Workshop, Cohen, K. Bretonnel, Demner-Fushman, D., Ananiadou, S., Pestian, J., Tsujii, J. and Webber, B. (Eds.). Association for Computational Linguistics, 117–124.Google Scholar
Ferraris, P. and Lifschitz, V. 2005. Weight constraints as nested expressions. Theory and Practice of Logic Programming 5, 45–74.Google Scholar
Gebser, M., Kaminski, R., Koenig, A. and Schaub, T. 2011. Advances in gringo series 3. In Proc of the 11th International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR 2011), Delgrande, J. P. and Faber, W. (Eds.). Springer-Verlag, Berlin, 345–351.Google Scholar
Gebser, M., Kaufmann, B., Neumann, A. and Schaub, T. 2007. Clasp: A conflict-driven answer set solver. In Proc of the 9th International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR 2007), Baral, C., Brewka, G. and Schlipf, J. (Eds.). Springer-Verlag, Berlin, 260–265.Google Scholar
Gebser, M., Puehrer, J., Schaub, T. and Tompits, H. 2008. A meta-programming technique for debugging answer-set programs. In Proc. of the 23rd National Conference on Artificial Intelligence (AAAI 2008), Fox, D. and Gomes, C. (Eds.). AAAI Press, 448–453.Google Scholar
Gelder, A. V., Ross, K. A. and Schlipf, J. S. 1991. The well-founded semantics for general logic programs. Journal of the ACM 38, 620–650.Google Scholar
Gelfond, M. and Lifschitz, V. 1988. The stable model semantics for logic programming. In Proc. of the Fifth International Conference and Symposium on Logic Programming (ICLP 1988), Kowalski, R. A. and Bowen, K. A. (Eds.). MIT Press, 1070–1080.Google Scholar
Gelfond, M. and Lifschitz, V. 1991. Classical negation in logic programs and disjunctive databases. New Generation Computing 9, 365–385.CrossRefGoogle Scholar
Gower, T. 2009. Born again. Proto Magazine Summer, 14–19.Google Scholar
Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V., Djoumbou, Y., Eisner, R., Guo, A. C. and Wishart, D. S. 2010. Drugbank 3.0: A comprehensive resource for “omics” research on drugs. Nucleic Acids Research 39, D1035–1041.Google Scholar
Kuhn, M., Campillos, M., Letunic, I., Jensen, L. J. and Bork, P. 2010. A side effect resource to capture phenotypic effects of drugs. Molecular Systems Biology 6, 343.CrossRefGoogle ScholarPubMed
Lifschitz, V. 2002. Answer set programming and plan generation. Artificial Intelligence 138, 39–54.Google Scholar
Lifschitz, V. 2008. What is answer set programming? In Proc. of the Twenty-Third AAAI Conference on Artificial Intelligence (AAAI 2008), Fox, D. and Gomes, C. (Eds.). AAAI Press, 1594–1597.Google Scholar
Marek, V. and Truszczyński, M. 1999. Stable models and an alternative logic programming paradigm. In The Logic Programming Paradigm: A 25-Year Perspective, Springer, Berlin, 375–398.Google Scholar
McDonagh, E. M., Whirl-Carrillo, M., Garten, Y., Altman, R. B. and Klein, T. E. 2011. From pharmacogenomic knowledge acquisition to clinical applications: The PharmGKB as a clinical pharmacogenomic biomarker resource. Biomarkers in Medicine 5, 795–806.Google Scholar
Niemelä, I. 1999. Logic programs with stable model semantics as a constraint programming paradigm. Annals of Mathematics and Artificial Intelligence 25, 241–273.Google Scholar
Nogueira, M., Balduccini, M., Gelfond, M., Watson, R. and Barry, M. 2001. An A-Prolog decision support system for the space shuttle. In Proc. of the Third International Symposium on Practical Aspects of Declarative Languages (PADL 2001), Ramakrishnan, I. V. (Ed.). Springer-Verlag, Berlin, 169–183.CrossRefGoogle Scholar
Oetsch, J., Puehrer, J. and Tompits, H. 2010. Catching the ouroboros: On debugging non-ground answer-set programs. Theory and Practice of Logic Programming 10, 513–529.CrossRefGoogle Scholar
Oetsch, J., Puehrer, J. and Tompits, H. 2011. Stepping through an answer-set program. In Proc. of the Eleventh International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR 2011), Delgrande, J. P. and Faber, W. (Eds.). Springer-Verlag, Berlin, 134–147.CrossRefGoogle Scholar
Oztok, U. 2012. Generating explanations for complex biomedical queries. MS Thesis, Sabanci University.Google Scholar
Pontelli, E., Son, T. C. and El-Khatib, O. 2009. Justifications for logic programs under answer set semantics. Theory and Practice of Logic Programming 9, 1–56.Google Scholar
Ricca, F., Grasso, G., Alviano, M., Manna, M., Lio, V., Iiritano, S. and Leone, N. 2012. Team-building with answer set programming in the Gioia-Tauro seaport. Theory and Practice of Logic Programming 12, 361–381.CrossRefGoogle Scholar
Schriml, L. M., Arze, C., Nadendla, S., Chang, Y.-W. W., Mazaitis, M., Felix, V., Feng, G. and Kibbe, W. A. 2012. Disease ontology: A backbone for disease semantic integration. Nucleic Acids Research 40, D940–946.Google Scholar
Simons, P., Niemelä, I. and Soininen, T. 2002. Extending and implementing the stable model semantics. Artificial Intelligence 138, 181–234.Google Scholar
Stark, C., Breitkreutz, B.-J., Reguly, T., Boucher, L., Breitkreutz, A. and Tyers, M. 2006. BioGRID: A general repository for interaction datasets. Nucleic Acids Research 34, D535–539.Google Scholar
Syrjanen, T. 2006. Debugging inconsistent answer set programs. In Proc. of the Eleventh International Workshop on Non-Monotonic Reasoning (NMR 2006), Dix, J. and Hunter, A. (Eds.). Online http://www.in.tu-clausthal.de/uploads/media/NMR_Proc_TR4.pdf.Google Scholar
Tiihonen, J., Soininen, T. and Sulonen, R. 2003. A practical tool for mass-customising configurable products. In Proc. of the 14th International Conference on Engineering Design (ICED03), Folkeson, A., Gralén, K., Norell, M. and Sellgren, U. (Eds.). Design Society, 1290–1299.Google Scholar
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