Towards Annotating Potential Incoherences in BioPortal Mappings

  • Daniel Faria
  • Ernesto Jiménez-Ruiz
  • Catia Pesquita
  • Emanuel Santos
  • Francisco M. Couto
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8797)

Abstract

BioPortal is a repository for biomedical ontologies that also includes mappings between them from various sources. Considered as a whole, these mappings may cause logical errors, due to incompatibilities between the ontologies or even erroneous mappings.

We have performed an automatic evaluation of BioPortal mappings between 19 ontology pairs using the mapping repair systems of LogMap and AgreementMakerLight. We found logical errors in 11 of these pairs, which on average involved 22% of the mappings between each pair. Furthermore, we conducted a manual evaluation of the repair results to identify the actual sources of error, verifying that erroneous mappings were behind over 60% of the repairs.

Given the results of our analysis, we believe that annotating BioPortal mappings with information about their logical conflicts with other mappings would improve their usability for semantic web applications and facilitate the identification of erroneous mappings. In future work, we aim to collaborate with BioPortal developers in extending BioPortal with these annotations.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al.: Gene Ontology: tool for the unification of biology. Nature Genetics 25(1), 25–29 (2000)CrossRefGoogle Scholar
  2. 2.
    Bodenreider, O.: The unified medical language system (UMLS): integrating biomedical terminology. Nucleic Acids Research 32, 267–270 (2004)CrossRefGoogle Scholar
  3. 3.
    Borgida, A., Serafini, L.: Distributed description logics: Assimilating information from peer sources. J. Data Sem. 1, 153–184 (2003)CrossRefGoogle Scholar
  4. 4.
    Cuenca Grau, B., Horrocks, I., Motik, B., Parsia, B., Patel-Schneider, P.F., Sattler, U.: OWL 2: The next step for OWL. J. Web Sem. 6(4), 309–322 (2008)CrossRefGoogle Scholar
  5. 5.
    Dowling, W.F., Gallier, J.H.: Linear-time algorithms for testing the satisfiability of propositional Horn formulae. J. Log. Prog. 1(3), 267–284 (1984)MathSciNetCrossRefMATHGoogle Scholar
  6. 6.
    Euzenat, J.: Semantic precision and recall for ontology alignment evaluation. In: Int’l Joint Conf. on Artif. Intell (IJCAI), pp. 348–353 (2007)Google Scholar
  7. 7.
    Euzenat, J., Meilicke, C., Stuckenschmidt, H., Shvaiko, P., Trojahn, C.: Ontology alignment evaluation initiative: Six years of experience. J. Data Sem. 15, 158–192 (2011)CrossRefGoogle Scholar
  8. 8.
    Euzenat, J., Shvaiko, P.: Ontology matching. Springer (2007)Google Scholar
  9. 9.
    Faria, D., Pesquita, C., Santos, E., Palmonari, M., Cruz, I.F., Couto, F.M.: The agreementmakerlight ontology matching system. In: Meersman, R., Panetto, H., Dillon, T., Eder, J., Bellahsene, Z., Ritter, N., De Leenheer, P., Dou, D. (eds.) ODBASE 2013. LNCS, vol. 8185, pp. 527–541. Springer, Heidelberg (2013)Google Scholar
  10. 10.
    Fridman Noy, N., Shah, N.H., Whetzel, P.L., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D.L., Storey, M.A.D., Chute, C.G., Musen, M.A.: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research 37(Web-Server-Issue) (2009)Google Scholar
  11. 11.
    Gallo, G., Urbani, G.: Algorithms for testing the satisfiability of propositional formulae. J. Log. Prog. 7(1), 45–61 (1989)MathSciNetCrossRefMATHGoogle Scholar
  12. 12.
    Ghazvinian, A., Noy, N.F., Jonquet, C., Shah, N., Musen, M.A.: What four million mappings can tell you about two hundred ontologies. In: Bernstein, A., Karger, D.R., Heath, T., Feigenbaum, L., Maynard, D., Motta, E., Thirunarayan, K. (eds.) ISWC 2009. LNCS, vol. 5823, pp. 229–242. Springer, Heidelberg (2009)CrossRefGoogle Scholar
  13. 13.
    Ghazvinian, A., Noy, N.F., Musen, M.A.: Creating mappings for ontologies in biomedicine: Simple methods work. In: AMIA Annual Symposium (AMIA) (2009)Google Scholar
  14. 14.
    Golbeck, J., Fragoso, G., Hartel, F.W., Hendler, J.A., Oberthaler, J., Parsia, B.: The National Cancer Institute’s Thésaurus and Ontology. J. Web Sem. 1(1), 75–80 (2003)CrossRefGoogle Scholar
  15. 15.
    Golbreich, C., Horridge, M., Horrocks, I., Motik, B., Shearer, R.: OBO and OWL: Leveraging Semantic Web Technologies for the Life Sciences. In: Aberer, K., et al. (eds.) ISWC/ASWC 2007. LNCS, vol. 4825, pp. 169–182. Springer, Heidelberg (2007)Google Scholar
  16. 16.
    Jiménez-Ruiz, E., Cuenca Grau, B., Horrocks, I.: On the feasibility of using OWL 2 DL reasoners for ontology matching problems. In: OWL Reasoner Evaluation Workshop (2012)Google Scholar
  17. 17.
    Jiménez-Ruiz, E., Cuenca Grau, B.: LogMap: Logic-based and Scalable Ontology Matching. 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. 273–288. Springer, Heidelberg (2011)CrossRefGoogle Scholar
  18. 18.
    Jiménez-Ruiz, E., Cuenca Grau, B., Horrocks, I., Berlanga, R.: Ontology integration using mappings: Towards getting the right logical consequences. In: Aroyo, L., et al. (eds.) ESWC 2009. LNCS, vol. 5554, pp. 173–187. Springer, Heidelberg (2009)Google Scholar
  19. 19.
    Jiménez-Ruiz, E., Cuenca Grau, B., Horrocks, I., Berlanga, R.: Logic-based Assessment of the Compatibility of UMLS Ontology Sources. J. Biomed. Semant. 2(suppl. 1), S2 (2011)Google Scholar
  20. 20.
    Jiménez-Ruiz, E., Cuenca Grau, B., Zhou, Y., Horrocks, I.: Large-scale interactive ontology matching: Algorithms and implementation. In: Europ. Conf. on Artif. Intell. (ECAI) (2012)Google Scholar
  21. 21.
    Jiménez-Ruiz, E., Meilicke, C., Grau, B.C., Horrocks, I.: Evaluating mapping repair systems with large biomedical ontologies. In: Description Logics, pp. 246–257 (2013)Google Scholar
  22. 22.
    Kalyanpur, A., Parsia, B., Horridge, M., Sirin, E.: Finding all justifications of OWL DL entailments. In: Aberer, K., et al. (eds.) ISWC/ASWC 2007. LNCS, vol. 4825, pp. 267–280. Springer, Heidelberg (2007)Google Scholar
  23. 23.
    Kazakov, Y., Krötzsch, M., Simančík, F.: Concurrent classification of 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)CrossRefGoogle Scholar
  24. 24.
    Konev, B., Walther, D., Wolter, F.: The Logical Difference Problem for Description Logic Terminologies. In: Armando, A., Baumgartner, P., Dowek, G. (eds.) IJCAR 2008. LNCS (LNAI), vol. 5195, pp. 259–274. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  25. 25.
    Meilicke, C.: Alignments Incoherency in Ontology Matching. Ph.D. thesis, University of Mannheim (2011)Google Scholar
  26. 26.
    Meilicke, C., Stuckenschmidt, H.: Incoherence as a basis for measuring the quality of ontology mappings. In: Ontology Matching Workshop (2008)Google Scholar
  27. 27.
    Meilicke, C., Stuckenschmidt, H., Tamilin, A.: Repairing ontology mappings. In: Proc. of AAAI Conf. on Artif. Intell., pp. 1408–1413 (2007)Google Scholar
  28. 28.
    Meilicke, C., Stuckenschmidt, H., Tamilin, A.: Reasoning support for mapping revision. J. Log. Comput. 19(5) (2009)Google Scholar
  29. 29.
    Noy, N.F., Griffith, N., Musen, M.A.: Collecting community-based mappings in an ontology repository. In: Sheth, A.P., Staab, S., Dean, M., Paolucci, M., Maynard, D., Finin, T., Thirunarayan, K. (eds.) ISWC 2008. LNCS, vol. 5318, pp. 371–386. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  30. 30.
    Pathak, J., Chute, C.G.: Debugging Mappings between Biomedical Ontologies: Preliminary Results from the NCBO BioPortal Mapping Repository. In: Int’l Conf. on Biomedical Ontology (ICBO) (2009)Google Scholar
  31. 31.
    Pesquita, C., Faria, D., Santos, E., Couto, F.M.: To repair or not to repair: reconciling correctness and coherence in ontology reference alignments. In: Ontology Matching (OM) (2013)Google Scholar
  32. 32.
    Rosse, C., Mejino Jr., J.: A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed. Informatics 36(6), 478–500 (2003)CrossRefGoogle Scholar
  33. 33.
    Salvadores, M., Alexander, P.R., Musen, M.A., Noy, N.F.: BioPortal as a dataset of linked biomedical ontologies and terminologies in RDF. Semantic Web 4(3), 277–284 (2013)Google Scholar
  34. 34.
    Santos, E., Faria, D., Pesquita, C., Couto, F.: Ontology alignment repair through modularization and confidence-based heuristics. arXiv:1307.5322 preprint (2013)Google Scholar
  35. 35.
    Santos, E., Faria, D., Pesquita, C., Couto, F.M.: Ontology alignment repair through modularization and confidence-based heuristics. CoRR abs/1307.5322 (2013)Google Scholar
  36. 36.
    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)Google Scholar
  37. 37.
    Shvaiko, P., Euzenat, J.: Ontology matching: State of the art and future challenges. IEEE Trans. Knowledge and Data Eng. (2012)Google Scholar
  38. 38.
    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. Biotech. 25(11) (2007)Google Scholar
  39. 39.
    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)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Daniel Faria
    • 1
  • Ernesto Jiménez-Ruiz
    • 2
  • Catia Pesquita
    • 1
    • 3
  • Emanuel Santos
    • 3
  • Francisco M. Couto
    • 1
    • 3
  1. 1.LASIGE, Faculdade de CiênciasUniversidade de LisboaPortugal
  2. 2.Department of Computer ScienceUniversity of OxfordUK
  3. 3.Departamento de Informática, Faculdade de CiênciasUniversidade de LisboaPortugal

Personalised recommendations