Abstract
This paper presents an evaluation of state of the art black box justification finding algorithms on the NCBO BioPortal ontology corpus. This corpus represents a set of naturally occurring ontologies that vary greatly in size and expressivity. The results paint a picture of the performance that can be expected when finding all justifications for entailments using black box justification finding techniques. The results also show that many naturally occurring ontologies exhibit a rich justificatory structure, with some ontologies having extremely high numbers of justifications per entailment.
Chapter PDF
Similar content being viewed by others
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.
References
Readings in Model Based Diagnosis. Morgan Kaufmann Publishers Inc. (1992)
Baader, F., Peñaloza, R.: Axiom pinpointing in general tableaux. Journal of Logic Computation 20(1), 5–34 (2010)
Cuenca Grau, B., Halaschek-Wiener, C., Kazakov, Y.: History Matters: Incremental Ontology Reasoning Using Modules. In: Aberer, K., Choi, K.-S., Noy, N., Allemang, D., Lee, K.-I., Nixon, L.J.B., Golbeck, J., Mika, P., Maynard, D., Mizoguchi, R., Schreiber, G., Cudré-Mauroux, P. (eds.) ASWC 2007 and ISWC 2007. LNCS, vol. 4825, pp. 183–196. Springer, Heidelberg (2007)
Dolby, J., Fokoue, A., Kalyanpur, A., Kershenbaum, A., Schonberg, E., Srinivas, K., Ma, L.: Scalable semantic retrieval through summarization and refinement. In: AAAI 2007 (2007)
Glimm, B., Rudolph, S., Völker, J.: Integrated Metamodeling and Diagnosis in OWL 2. In: Patel-Schneider, P.F., Pan, Y., Hitzler, P., Mika, P., Zhang, L., Pan, J.Z., Horrocks, I., Glimm, B. (eds.) ISWC 2010, Part I. LNCS, vol. 6496, pp. 257–272. Springer, Heidelberg (2010)
Golbreich, C., Horrocks, I.: The OBO to OWL mapping, GO to OWL 1.1! In: OWLED 2007 (2007)
Grimm, S., Wissmann, J.: Elimination of Redundancy in Ontologies. In: Antoniou, G., Grobelnik, M., Simperl, E., Parsia, B., Plexousakis, D., De Leenheer, P., Pan, J. (eds.) ESWC 2011, Part I. LNCS, vol. 6643, pp. 260–274. Springer, Heidelberg (2011)
Grove, M.: OWLSight (October 2009), http://pellet.owldl.com/ontology-browser
Halaschek-Wiener, C., Katz, Y., Parsia, B.: Belief base revision for expressive description logics. In: OWLED 2006 (2006)
Horridge, M.: Justification Based Explanation in Ontologies. Ph.D. thesis, School of Computer Science, The University of Manchester (2011)
Horridge, M., Bechhofer, S.: The OWL API: A Java API for OWL ontologies. Semantic Web 2(1), 11–21 (2011)
Horridge, M., Parsia, B., Sattler, U.: Explanation of OWL entailments in Protégé-4. Poster and Demo Track, ISWC 2008 (2008)
Horridge, M., Parsia, B., Sattler, U.: Laconic and Precise Justifications in OWL. In: Sheth, A.P., Staab, S., Dean, M., Paolucci, M., Maynard, D., Finin, T., Thirunarayan, K. (eds.) ISWC 2008. LNCS, vol. 5318, pp. 323–338. Springer, Heidelberg (2008)
Ji, Q., Haase, P., Qi, G., Hitzler, P., Stadtmüller, S.: RaDON — Repair and Diagnosis in Ontology Networks. In: Aroyo, L., Traverso, P., Ciravegna, F., Cimiano, P., Heath, T., Hyvönen, E., Mizoguchi, R., Oren, E., Sabou, M., Simperl, E. (eds.) ESWC 2009. LNCS, vol. 5554, pp. 863–867. Springer, Heidelberg (2009)
Ji, Q., Qi, G., Haase, P.: A Relevance-Directed Algorithm for Finding Justifications of DL Entailments. In: Gómez-Pérez, A., Yu, Y., Ding, Y. (eds.) ASWC 2009. LNCS, vol. 5926, pp. 306–320. Springer, Heidelberg (2009)
Kalyanpur, A.: Debugging and Repair of OWL Ontologies. Ph.D. thesis, The Graduate School of the University of Maryland (2006)
Kalyanpur, A., Parsia, B., Hendler, J.: A tool for working with web ontologies. International Journal on Semantic Web and Information Systems 1 (2005)
Kalyanpur, A., Parsia, B., Horridge, M., Sirin, E.: Finding All Justifications of OWL DL Entailments. In: Aberer, K., Choi, K.-S., Noy, N., Allemang, D., Lee, K.-I., Nixon, L.J.B., Golbeck, J., Mika, P., Maynard, D., Mizoguchi, R., Schreiber, G., Cudré-Mauroux, P. (eds.) ASWC 2007 and ISWC 2007. LNCS, vol. 4825, pp. 267–280. Springer, Heidelberg (2007)
Knublauch, H.: Composing the semantic web: Explaining inferences, http://composing-the-semantic-web.blogspot.com/2007/08/explanining-inferences.html
Meyer, T., Lee, K., Booth, R., Pan, J.Z.: Finding maximally satisfiable terminologies for the description logic \(\mathcal{ALC}\). In: AAAI 2006 (2006)
Mungall, C.: OBO Flat File Format 1.4 syntax and semantics (February 2011), ftp://ftp.geneontology.org/pub/go/www/obo-syntax.html
Noy, N.F.: BioPortal: Ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research 37 (May 2009)
Reiter, R.: A theory of diagnosis from first principles. Artificial Intelligence 32, 57–95 (1987)
Scharrenbach, T., d’Amato, C., Fanizzi, N., Grütter, R., Waldvogel, B., Bernstein, A.: Default Logics for Plausible Reasoning with Controversial Axioms. In: Bobillo, F. (ed.) URSW 2010 (2010)
Schlobach, S., Cornet, R.: Non-standard reasoning services for the debugging of description logic terminologies. In: IJCAI 2003 (2003)
Schlobach, S., Huang, Z., Cornet, R., van Harmelen, F.: Debugging incoherent terminologies. Journal of Automated Reasoning 39, 317–349 (2007)
Shchekotykhin, K., Friedrich, G., Jannach, D.: On computing minimal conflicts for ontology debugging. In: ECAI 2008 (2008)
Smith, B.: The OBO Foundary: Coordinated evolution of ontology to support biomedical data integration. Nature Biotechnology
Stuckenschmidt, H.: Debugging OWL ontologies - a reality check. In: EON-SWSC 2008 (2008)
Suntisrivaraporn, B.: Polynomial-Time Reasoning Support for Design and Maintenance of Large-Scale Biomedical Ontologies. Ph.D. thesis, Technical University of Dresden (2009)
Suntisrivaraporn, B., Qi, G., Ji, Q., Haase, P.: A Modularization-Based Approach to Finding All Justifications for OWL DL Entailments. In: Domingue, J., Anutariya, C. (eds.) ASWC 2008. LNCS, vol. 5367, pp. 1–15. Springer, Heidelberg (2008)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Horridge, M., Parsia, B., Sattler, U. (2012). Extracting Justifications from BioPortal Ontologies. In: Cudré-Mauroux, P., et al. The Semantic Web – ISWC 2012. ISWC 2012. Lecture Notes in Computer Science, vol 7650. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35173-0_19
Download citation
DOI: https://doi.org/10.1007/978-3-642-35173-0_19
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-35172-3
Online ISBN: 978-3-642-35173-0
eBook Packages: Computer ScienceComputer Science (R0)