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Selection and Combination of Heterogeneous Mappings to Enhance Biomedical Ontology Matching

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Book cover Knowledge Engineering and Knowledge Management (EKAW 2016)

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Abstract

This paper presents a novel background knowledge approach which selects and combines existing mappings from a given biomedical ontology repository to improve ontology alignment. Current background knowledge approaches usually select either manually or automatically a limited number of different ontologies and use them as a whole for background knowledge. Whereas in our approach, we propose to pick up only relevant concepts and relevant existing mappings linking these concepts all together in a specific and customized background knowledge graph. Paths within this graph will help to discover new mappings. We have implemented and evaluated our approach using the content of the NCBO BioPortal repository and the Anatomy benchmark from the Ontology Alignment Evaluation Initiative. We used the mapping gain measure to assess how much our final background knowledge graph improves results of state-of-the-art alignment systems. Furthermore, the evaluation shows that our approach produces a high quality alignment and discovers mappings that have not been found by state-of-the-art systems.

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Notes

  1. 1.

    http://bioportal.bioontology.org/.

  2. 2.

    http://oaei.ontologymatching.org/2015/anatomy/index.html.

  3. 3.

    Unified Medical Language System.

  4. 4.

    Not all mappings in BioPortal are manually produced, see Sect. 5.1 for more information about NCBO BioPortal mappings.

  5. 5.

    http://oaei.ontologymatching.org/2015/.

  6. 6.

    http://data.bioontology.org/documentation.

  7. 7.

    http://www.bioontology.org/wiki/index.php/BioPortal_Mappings.

  8. 8.

    We have created the graph using the graph database Neo4J (https://neo4j.com/).

  9. 9.

    http://oaei.ontologymatching.org/2015/results/anatomy/index.html.

References

  1. Aleksovski, Z., Kate, W.T., Van Harmelen, F.: Exploiting the structure of background knowledge used. In: 1st International Conference on Ontology Matching, vol. 225, pp. 13–24 (2006)

    Google Scholar 

  2. Annane, A., Emonet, V., Azouaou, F., Jonquet, C.: Multilingual mapping reconciliation between english-french biomedical ontologies. In: 6th International Conference on Web Intelligence, Mining, Semantics, WIMS, pp. 13:1–13:12 (2016)

    Google Scholar 

  3. Bodenreider, O.: The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 32, 267–270 (2004)

    Article  Google Scholar 

  4. Cheatham, M., et al.: Results of the ontology alignment evaluation initiative 2015. In: 10th ISWC Workshop on Ontology Matching, pp. 60–115 (2015)

    Google Scholar 

  5. Chen, X., Xia, W., Jiménez-Ruiz, E., Cross, V.V.: Extending an ontology alignment system with bioportal: a preliminary analysis. In: ISWC, pp. 313–316 (2014)

    Google Scholar 

  6. Smith, B., et al.: The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25(11), 1251–1255 (2007)

    Article  Google Scholar 

  7. Euzenat, J., Shvaiko, P.: Ontology Matching. Springer, Heidelberg (2013)

    Book  MATH  Google Scholar 

  8. Faria, D., et al.: Automatic background knowledge selection for matching biomedical ontologies. PloS one 9(11), e111226 (2014)

    Article  MathSciNet  Google Scholar 

  9. Faria, D., Jiménez-Ruiz, E., Pesquita, C., Santos, E., Couto, F.M.: Towards annotating potential incoherences in bioportal mappings. In: Mika, P., et al. (eds.) ISWC 2014, Part II. LNCS, vol. 8797, pp. 17–32. Springer, Heidelberg (2014)

    Google Scholar 

  10. Ghazvinian, A., Noy, N.F., Musen, M.A.,et al.: Creating mappings for ontologies in biomedicine: simple methods work. In: AMIA, pp. 198–202 (2009)

    Google Scholar 

  11. 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)

    Chapter  Google Scholar 

  12. Gross, A., Hartung, M., Kirsten, T., Rahm, E.: Mapping composition for matching large life science ontologies. In: ICBO, pp. 109–116 (2011)

    Google Scholar 

  13. Hartung, M., Gross, A., Kirsten, T., Rahm, E.: Effective mapping composition for biomedical ontologies. In: ESWC, pp. 176–190 (2012)

    Google Scholar 

  14. Jiménez-Ruiz, E., Grau, B.C., Solimando, A., Cross, V.V.: Logmap family results for OAEI 2015. In: 10th International Workshop on Ontology Matching, pp. 171–175 (2015)

    Google Scholar 

  15. Jonquet, C., Shah, N., Musen, M.: The open biomedical annotator. In: AMIA Summit on Translational Bioinformatics, pp. 56–60 (2009)

    Google Scholar 

  16. Locoro, A., David, J., Euzenat, J.: Context-based matching: design of a flexible framework and experiment. J. Data Semant. 3(1), 25–46 (2014)

    Article  Google Scholar 

  17. Mascardi, V., Locoro, A., Rosso, P.: Automatic ontology matching via upper ontologies: a systematic evaluation. IEEE Trans. Knowl. Data Eng. 22(5), 609–623 (2010)

    Article  Google Scholar 

  18. Quix, C., Roy, P., Kensche, D.: Automatic selection of background knowledge for ontology matching. In: International Workshop on Semantic Web Information Management, p. 5. ACM (2011)

    Google Scholar 

  19. Sabou, M., d’Aquin, M., Motta, E.: Exploring the semantic web as background knowledge for ontology matching. In: Spaccapietra, S., Pan, J.Z., Thiran, P., Halpin, T., Staab, S., Svatek, V., Shvaiko, P., Roddick, J. (eds.) Journal on Data Semantics XI. LNCS, vol. 5383, pp. 156–190. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  20. Safar, B., Reynaud, C., Calvier, F.: Techniques d’alignement d’ontologies basées sur la structure dune ressource complémentaire. 1ères Journées Francophones sur les Ontologies, pp. 21–35 (2007)

    Google Scholar 

  21. Shvaiko, P., Euzenat, J.: Ontology matching: state of the art and future challenges. IEEE Trans. Knowl. Data Eng 25(1), 158–176 (2013)

    Article  Google Scholar 

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Acknowledgment

This work was achieved during a LIRMM-ESI collaboration within the SIFR project funded in part by the French National Research Agency (grant ANR-12-JS02-01001), as well as by University of Montpellier, the CNRS and the EU H2020 MSCA program.

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Authors and Affiliations

  1. Université de Montpellier, Laboratoire d’Informatique, de Robotique et de Microélectronique (LIRMM), Montpellier, France

    Amina Annane, Zohra Bellahsene & Clement Jonquet

  2. Ecole Nationale Supérieure en Informatique (ESI), Algiers, Algeria

    Amina Annane & Faiçal Azouaou

  3. Center for Biomedical Informatics Research, Stanford University, Stanford, USA

    Clement Jonquet

Authors
  1. Amina Annane
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  2. Zohra Bellahsene
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  3. Faiçal Azouaou
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  4. Clement Jonquet
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Correspondence to Amina Annane .

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Editors and Affiliations

  1. Linköping University, Linköping, Sweden

    Eva Blomqvist

  2. University of Bologna, Bologna, Italy

    Paolo Ciancarini

  3. University of Bologna, Bologna, Italy

    Francesco Poggi

  4. University of Bologna, Bologna, Italy

    Fabio Vitali

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Annane, A., Bellahsene, Z., Azouaou, F., Jonquet, C. (2016). Selection and Combination of Heterogeneous Mappings to Enhance Biomedical Ontology Matching. In: Blomqvist, E., Ciancarini, P., Poggi, F., Vitali, F. (eds) Knowledge Engineering and Knowledge Management. EKAW 2016. Lecture Notes in Computer Science(), vol 10024. Springer, Cham. https://doi.org/10.1007/978-3-319-49004-5_2

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  • DOI: https://doi.org/10.1007/978-3-319-49004-5_2

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  • Publisher Name: Springer, Cham

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