Abstract
Ontologies in the biomedical domain are becoming a key element for data integration and search. The usefulness of the applications which use ontologies is often directly influenced by the quality of ontologies, as incorrect or incomplete ontologies might lead to wrong or incomplete results for the applications. Therefore, there is an increasing need for repairing defects in ontologies. In this paper we focus on completing ontologies. We provide an algorithm for completing the is-a structure in \({\cal{EL}}\) ontologies which covers many biomedical ontologies. Further, we present an implemented system based on the algorithm as well as an evaluation using three biomedical ontologies.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Baader, F., Brandt, S., Lutz, C.: Pushing the \(\mathcal{EL}\) envelope. In: 19th Int. Joint Conf. on Artificial Intelligence, pp. 364–369 (2005)
Bienvenu, M.: Complexity of abduction in the \(\mathcal{EL}\) family of lightweight description logics. In: 11th Int. Conf. on Principles of Knowledge Representation and Reasoning, pp. 220–230 (2008)
Calvanese, D., Ortiz, M., Simkus, M., Stefanoni, G.: The complexity of explaining negative query answers in DL-Lite. In: 13th Int. Conf. on Principles of Knowledge Representation and Reasoning, pp. 583–587 (2012)
Cimiano, P., Buitelaar, P., Magnini, B.: Ontology Learning from Text: Methods, Evaluation and Applications. IOS Press (2005)
Colucci, S., Di Noia, T., Di Sciascio, E., Donini, F., Mongiello, M.: A uniform tableaux-based approach to concept abduction and contraction in \(\mathcal{ALN}\). In: Int. Workshop on Description Logics, pp. 158–167 (2004)
Corcho, O., Roussey, C., Vilches, L.M., Pérez, I.: Pattern-based OWL ontology debugging guidelines. In: Workshop on Ontology Patterns, pp. 68–82 (2009)
Donini, F., Colucci, S., Di Noia, T., Sciasco, E.D.: A tableaux-based method for computing least common subsumers for expressive description logics. In: 21st Int. Joint Conf. on Artificial Intelligence, pp. 739–745 (2009)
Du, J., Qi, G., Shen, Y.-D., Pan, J.: Towards practical abox abduction in large OWL DL ontologies. In: 25th AAAI Conf. on Artificial Intelligence, pp. 1160–1165 (2011)
Elsenbroich, C., Kutz, O., Sattler, U.: A case for abductive reasoning over ontologies. In: OWL: Experiences and Directions (2006)
Flouris, G., Manakanatas, D., Kondylakis, H., Plexousakis, D., Antoniou, G.: Ontology Change: Classification and Survey. Knowledge Engineering Review 23(2), 117–152 (2008)
Haase, P., Stojanovic, L.: Consistent Evolution of OWL Ontologies. In: Gómez-Pérez, A., Euzenat, J. (eds.) ESWC 2005. LNCS, vol. 3532, pp. 182–197. Springer, Heidelberg (2005)
Hartung, M., Terwilliger, J., Rahm, E.: Recent advances in schema and ontology evolution. In: Schema Matching and Mapping, pp. 149–190 (2011)
Hearst, M.: Automatic acquisition of hyponyms from large text corpora. In: 14th Int. Conf. on Computational Linguistics, pp. 539–545 (1992)
Hubauer, T., Lamparter, S., Pirker, M.: Automata-based abduction for tractable diagnosis. In: Int. Workshop on Description Logics, pp. 360–371 (2010)
Ivanova, V., Bergman, J.L., Hammerling, U., Lambrix, P.: Debugging taxonomies and their alignments: the ToxOntology - MeSH use case. In: 1st Int. Workshop on Debugging Ontologies and Ontology Mappings, pp. 25–36 (2012)
Ivanova, V., Lambrix, P.: A unified approach for aligning taxonomies and debugging taxonomies and their alignments. In: Cimiano, P., Corcho, O., Presutti, V., Hollink, L., Rudolph, S. (eds.) ESWC 2013. LNCS, vol. 7882, pp. 1–15. Springer, Heidelberg (2013)
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)
Jiménez-Ruiz, E., Cuenca Grau, B., Horrocks, I., Berlanga, R.: Ontology integration using mappings: Towards getting the right logical consequences. 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. 173–187. Springer, Heidelberg (2009)
Kalyanpur, A., Parsia, B., Sirin, E., Cuenca-Grau, B.: Repairing unsatisfiable concepts in OWL ontologies. In: Sure, Y., Domingue, J. (eds.) ESWC 2006. LNCS, vol. 4011, pp. 170–184. Springer, Heidelberg (2006)
Kalyanpur, A., Parsia, B., Sirin, E., Hendler, J.: Debugging Unsatisfiable Classes in OWL Ontologies. J. of Web Semantics 3(4), 268–293 (2006)
Kazakov, Y., Krötzsch, M., Simančík, F.: Concurrent classification of \(\mathcal{EL}\) ontologies. In: Aroyo, L., Welty, C., Alani, H., Taylor, J., Bernstein, A., Kagal, L., Noy, N., Blomqvist, E. (eds.) ISWC 2011, Part I. LNCS, vol. 7031, pp. 305–320. Springer, Heidelberg (2011)
Klarman, S., Endriss, U., Schlobach, S.: Abox abduction in the description logic \(\mathcal{ALC}\). J. of Automated Reasoning 46, 43–80 (2011)
Lambrix, P., Dragisic, Z., Ivanova, V.: Get my pizza right: Repairing missing is-a relations in \(\mathcal{ALC}\) ontologies. In: Takeda, H., Qu, Y., Mizoguchi, R., Kitamura, Y. (eds.) JIST 2012. LNCS, vol. 7774, pp. 17–32. Springer, Heidelberg (2013)
Lambrix, P., Ivanova, V.: A unified approach for debugging is-a structure and mappings in networked taxonomies. J. of Biomedical Semantics 4, 10 (2013)
Lambrix, P., Liu, Q.: Debugging the missing is-a structure within taxonomies networked by partial reference alignments. Data & Knowledge Engineering 86, 179–205 (2013)
Lambrix, P., Liu, Q., Tan, H.: Repairing the Missing is-a Structure of Ontologies. In: Gómez-Pérez, A., Yu, Y., Ding, Y. (eds.) ASWC 2009. LNCS, vol. 5926, pp. 76–90. Springer, Heidelberg (2009)
Lambrix, P., Strömbäck, L., Tan, H.: Information Integration in Bioinformatics with Ontologies and Standards (chapter 8). In: Bry, F., Małuszyński, J. (eds.) Semantic Techniques for the Web. LNCS, vol. 5500, pp. 343–376. Springer, Heidelberg (2009)
Lambrix, P., Wei-Kleiner, F., Dragisic, Z., Ivanova, V.: Repairing missing is-a structure in ontologies is an abductive reasoning problem. In: 2nd Int. Workshop on Debugging Ontologies and Ontology Mappings, pp. 33–44 (2013)
Meilicke, C., Stuckenschmidt, H., Tamilin, A.: Repairing Ontology Mappings. In: 22nd Nat. Conf. on Artificial Intelligence, pp. 1408–1413 (2007)
Qi, G., Ji, Q., Haase, P.: A conflict-based operator for mapping revision. In: Bernstein, A., Karger, D.R., Heath, T., Feigenbaum, L., Maynard, D., Motta, E., Thirunarayan, K. (eds.) ISWC 2009. LNCS, vol. 5823, pp. 521–536. Springer, Heidelberg (2009)
Schlobach, S.: Debugging and Semantic Clarification by Pinpointing. In: Gómez-Pérez, A., Euzenat, J. (eds.) ESWC 2005. LNCS, vol. 3532, pp. 226–240. Springer, Heidelberg (2005)
Wang, P., Xu, B.: Debugging ontology mappings: a static approach. Computing and Informatics 27, 21–36 (2008)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer International Publishing Switzerland
About this paper
Cite this paper
Dragisic, Z., Lambrix, P., Wei-Kleiner, F. (2014). Completing the is-a Structure of Biomedical Ontologies. In: Galhardas, H., Rahm, E. (eds) Data Integration in the Life Sciences. DILS 2014. Lecture Notes in Computer Science(), vol 8574. Springer, Cham. https://doi.org/10.1007/978-3-319-08590-6_7
Download citation
DOI: https://doi.org/10.1007/978-3-319-08590-6_7
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-08589-0
Online ISBN: 978-3-319-08590-6
eBook Packages: Computer ScienceComputer Science (R0)