Collecting Community-Based Mappings in an Ontology Repository

  • Natalya F. Noy
  • Nicholas Griffith
  • Mark A. Musen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5318)


Several ontology repositories provide access to the growing collection of ontologies on the Semantic Web. Some repositories collect ontologies automatically by crawling the Web; in other repositories, users submit ontologies themselves. In addition to providing search across multiple ontologies, the added value of ontology repositories lies in the metadata that they may contain. This metadata may include information provided by ontology authors, such as ontologies’ scope and intended use; feedback provided by users such as their experiences in using the ontologies or reviews of the content; and mapping metadata that relates concepts from different ontologies. In this paper, we focus on the ontology-mapping metadata and on community-based method to collect ontology mappings. More specifically, we develop a model for representing mappings collected from the user community and the metadata associated with the mapping. We use the model to bring together more than 30,000 mappings from 7 sources. We also validate the model by extending BioPortal–a repository of biomedical ontologies that we have developed—to enable users to create single concept-to-concept mappings in its graphical user interface, to upload and download mappings created with other tools, to comment on the mappings and to discuss them, and to visualize the mappings and the corresponding metadata.


Ontology Mapping Biomedical Ontology Ontology Match Ontology Alignment Sural Artery 
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.


  1. 1.
    Bernstein, P., Green, T., Melnik, S., Nash, A.: Implementing mapping composition. The VLDB Journal The International Journal on Very Large Data Bases 17(2), 333–353 (2008)CrossRefGoogle Scholar
  2. 2.
    Buitelaar, P., Eigner, T., Declerck, T.: OntoSelect: A dynamic ontology library with support for ontology selection. In: Demo Session at the International Semantic Web Conference, ISWC 2004 (2004)Google Scholar
  3. 3.
    d’Aquin, M., Baldassarre, C., Gridinoc, L., Angeletou, S., Sabou, M., Motta, E.: Watson: A gateway for next generation semantic web applications. In: Poster session at the International Semantic Web Conference, ISWC 2007 (2007)Google Scholar
  4. 4.
    Ding, L., Finin, T., Joshi, A., Pan, R., Cost, R.S., Sachs, J., Doshi, V., Reddivari, P., Peng, Y.: Swoogle: A search and metadata engine for the semantic web. In: Thirteenth ACM Conference on Information and Knowledge Management (CIKM 2004), Washington DC (2004)Google Scholar
  5. 5.
    Euzenat, J.: An api for ontology alignment. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds.) ISWC 2004. LNCS, vol. 3298, pp. 698–712. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  6. 6.
    Euzenat, J., Isaac, A., Meilicke, C., Shvaiko, P., Stuckenschmidt, H., Šváb, O., Svátek, V., Hage, W.R.V., Yatskevich, M.: Results of the Ontology Alignment Evaluation Initiative 2007. In: 2nd International Workshop on Ontology Matching (OM 2007) at ISWC (2007)Google Scholar
  7. 7.
    Euzenat, J., Shvaiko, P.: Ontology matching. Springer, Berlin (2007)zbMATHGoogle Scholar
  8. 8.
    Falconer, S.M., Storey, M.-A.: A cognitive support framework for ontology mapping. In: Aberer, K., Choi, K.-S., Noy, N., Allemang, D., Lee, K.-I., Nixon, L., Golbeck, J., Mika, P., Maynard, D., Mizoguchi, R., Schreiber, G., Cudré-Mauroux, P. (eds.) ASWC 2007 and ISWC 2007. LNCS, vol. 4825. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  9. 9.
    Guha, R., Kumar, R., Raghavan, P., Tomkins, A.: Propagation of trust and distrust. In: 13th International Conference on World Wide Web (WWW 2004), New York, USA (2004)Google Scholar
  10. 10.
    Isaac, A., Matthezing, H., van der Meij, L., Schlobach, S., Wang, S., Zinn, C.: Putting ontology alignment in context: usage scenarios, deployment and evaluation in a library case. In: Bechhofer, S., Hauswirth, M., Hoffmann, J., Koubarakis, M. (eds.) ESWC 2008. LNCS, vol. 5021. Springer, Heidelberg (2008)Google Scholar
  11. 11.
    Jonquet, C., Musen, M.A., Shah, N.: A System for Ontology-Based Annotation of Biomedical Data. In: Bairoch, A., Cohen-Boulakia, S., Froidevaux, C. (eds.) DILS 2008. LNCS (LNBI), vol. 5109, pp. 144–152. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  12. 12.
    Lindberg, D., Humphreys, B., McCray, A.: The unified medical language system. Methods of Information in Medicine 32(4), 281 (1993)Google Scholar
  13. 13.
    Madhavan, J., Bernstein, P.A., Doan, A., Halevy, A.: Corpus-based schema matching. In: International Conference on Data Engineering (ICDE), Tokyo, Japan (2005)Google Scholar
  14. 14.
    McCann, R., Shen, W., Doan, A.: Matching schemas in online communities: A Web 2.0 approach. In: The 24th Int. Conf. on Data Engineering (ICDE 2008), Cancun, Mexico (2008)Google Scholar
  15. 15.
    Mungall, C.: Mappings in OBO Foundry (2008),
  16. 16.
    Noy, N., Guha, R., Musen, M.A.: User ratings of ontologies: Who will rate the raters? In: AAAI Symp. on Knowledge Collection from Volunteer Contributors, Stanford, CA (2005)Google Scholar
  17. 17.
    Noy, N., Tudorache, T.: Collaborative ontology development on the (semantic) web. In: AAAI Spring Symposium on Semantic Web and Knowledge Engineering (SWKE), Stanford, CA (2008)Google Scholar
  18. 18.
    Noy, N.F., Chugh, A., Alani, H.: The CKC Challenge: Exploring tools for collaborative knowledge construction. IEEE Intelligent Systems 23(1), 64–68 (2008)CrossRefGoogle Scholar
  19. 19.
    Noy, N.F., Musen, M.A.: The PROMPT suite: Interactive tools for ontology merging and mapping. International Journal of Human-Computer Studies 59(6), 983–1024 (2003)CrossRefGoogle Scholar
  20. 20.
    Palma, R., Hartmann, J., Haase, P.: OMV: Ontology Metadata Vocabulary for the Semantic Web. Technical report (2008),
  21. 21.
    Rector, A., Rogers, J., Pole, P.: The GALEN High Level Ontology. In: 14th International Congress of the European Federation for Medical Informatics, MIE 1996, Denmark, (1996)Google Scholar
  22. 22.
    Rosse, C., Mejino, J.L.V.: A reference ontology for bioinformatics: The Foundational Model of Anatomy. Journal of Biomedical Informatics (2004)Google Scholar
  23. 23.
    Rubin, D.L., et al.: The National Center for Biomedical Ontology: Advancing biomedicine through structured organization of scientific knowledge. OMICS: A Journal of Integrative Biology 10(2) (2006)Google Scholar
  24. 24.
    Sioutos, N., de Coronado, S., Haber, M., Hartel, F., Shaiu, W., Wright, L.: NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information. Journal of Biomedical Informatics 40(1), 30–43 (2007)CrossRefGoogle Scholar
  25. 25.
    Smith, B., et al.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25(11), 1251–1255 (2007)CrossRefGoogle Scholar
  26. 26.
    Šváb, O., Svátek, V., Stuckenschmidt, H.: A study in empirical and “casuistic” analysis of ontology mapping results. In: Franconi, E., Kifer, M., May, W. (eds.) ESWC 2007. LNCS, vol. 4519, Springer, Heidelberg (2007)Google Scholar
  27. 27.
    Watts, D.: Six Degrees: The New Science of Networks, Vintage (2004)Google Scholar
  28. 28.
    Zacharias, V., Braun, S.: SOBOLEO - social bookmarking and lightweight ontology engineering. In: Workshop on Social and Collaborative Construction of Structured Knowledge at WWW 2007 (2007)Google Scholar
  29. 29.
    Zhang, S., Bodenreider, O.: Alignment of multiple ontologies of anatomy: Deriving indirect mappings from direct mappings to a reference. In: AMIA Annual Symposium (2005)Google Scholar
  30. 30.
    Zhang, S., Bodenreider, O.: Hybrid alignment strategy for anatomical ontologies: results of the 2007 ontology alignment contest. In: 2nd International Workshop on Ontology Matching (OM 2007) at ISWC 2007 (2007)Google Scholar
  31. 31.
    Zhdanova, A., Shvaiko, P.: Community-driven ontology matching. In: 3rd European Semantic Web Conference, Budva, Montenegro, p. 3449 (2006)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Natalya F. Noy
    • 1
  • Nicholas Griffith
    • 1
  • Mark A. Musen
    • 1
  1. 1.Stanford UniversityStanfordUS

Personalised recommendations