Domain Knowledge Integration and Semantical Quality Management –A Biology Case Study–

  • Marie-Noelle Terrasse
  • Eric Leclercq
  • Marinette Savonnet
  • Arnaud Da Costa
  • Pierre Naubourg
  • Magali Roux-Rouquie
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5232)


The management of semantical quality is a major challenge in the context of knowledge integration. In this paper, we describe a new approach to constraint management that emphasizes constraint traceability when moving from the semantical level to the operational one.

Our strategy for management of semantical quality is related to a metamo-deling-based approach to knowledge integration. We carry out knowledge integration “on the fly” by using transformations applied to models belonging to our metamodeling architecture. The resulting integrated models access available resources through web services whose input and output parameters are guarded by constraints. Integrated metamodels, models, web services and various constraints are produced by ETL (extract-transform-load) operations that are applied both at the model and concept levels. Our metamodeling architectures facilitate scaling up of constraint verification.


Model Driven Engineering metamodeling knowledge integration biological image annotation 


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  1. 1.
    Labarga, A., Valentin, F., Anderson, M., Lopez, R.: Web services at the european bioinformatics institute. Nucleic Acids Research Advance 35, W6–W11 (2007) CrossRefGoogle Scholar
  2. 2.
    Crampin, E., Halstead, M., Nielsen, P.H.P., Noble, D., Smith, N., Tawhai, M.: Computational physiology and the physiome project. Experimental Physiology 89(1), 1–26 (2002)CrossRefGoogle Scholar
  3. 3.
    Li: Enterprise interoperability – research roadmap – version 4.0. Technical report, European Community, Information Society Technologies (2006),
  4. 4.
    Atzeni, P., Torlone, R.: Managing heterogeneous data models in a graph-theoretic framework. In: Proceedings of the 3rd International Conference on Information and Knowledge Management, CIKM 1994, Gaithersburg, Maryland, USA (1994)Google Scholar
  5. 5.
    Jeusfeld, M., Johnen, U.: An executable meta model for re-engineering of database schemas. In: Proceedings of the 13th International Conference on Entity-relationship Approach, Manchester, UK (1994)Google Scholar
  6. 6.
    Lou, J.: Data model description and translation using the meta-model SOME. Ph.D thesis, EPFL, Lausanne, Switzerland (1997)Google Scholar
  7. 7.
    Falkenberg, E.D., Han Oei, J.: Meta model hierarchies from an object-role modeling perspective. In: Proceedings of the 1st International Conference on Object-Role Modeling, ORM-1, Magnetic Island, Australia (1994)Google Scholar
  8. 8.
    Frederiks, P., ter Hofstede, A., Lippe, E.: A unifying framework for conceptual data modelling concepts. Information and Software Technology 39(1), 15–25 (1997)CrossRefGoogle Scholar
  9. 9.
    Vassiliadis, P., Simitsis, A., Skiadopoulos, S.: Conceptual modeling for etl processes. In: DOLAP, pp. 14–21 (2002)Google Scholar
  10. 10.
    Czarnecki, K., Helsen, S.: Classification of model transformation approaches. In: Proceedings of the OOPSLA Workshop on Generative Techniques in the Context of Model-Driven Architecture (2003)Google Scholar
  11. 11.
    Bao, J., Hu, Z., Caragea, D., Reecy, J., Honavar, V.: A tool for collaborative construction of large biological ontologies (2006)Google Scholar
  12. 12.
    Terrasse, M.N., Roux, M.: Metamodeling architectures for complex data integration in biology. International Journal of Biomedical Engineering and Technology Special issue Warehousing and Mining Complex Data: Applications to Biology, Medicine, Behavior, Health and Environment 3(2) (to appear, 2009)Google Scholar
  13. 13.
    Da Costa, A., Leclercq, E., Gaudin, A., Gascuel, J., Terrasse, M.: Organizing metadata into models and ontologies for lowering annotation costs of a biological image database. Studies in Computational Intelligence (2008) ISSN : 1860-949XGoogle Scholar
  14. 14.
    Jones, A., Miller, M., Spellman, P., Pizarro, A.: Fuge: Funtionnal genomics experiment model specification. FuGE Working Group, Recommandation (draft) (2007)Google Scholar
  15. 15.
    Golbreich, C., Horrocks, I.: The OBO to OWL mapping, GO to OWL 1.1! In: Proceedings of the 3rd Int. Workshop on OWL: Experiences and Directions (OWLED 2007) (2007)Google Scholar
  16. 16.
    ODM: Ontology definition metamodel (August 2005),
  17. 17.
    Motik, B., Horrocks, I., Sattler, U.: Bridging the gap between owl and relational databases (2007)Google Scholar
  18. 18.
    Patel-Schneider, P., Horrocks, I.: A comparison of two modelling paradigms in the semantic web. ACM, New York (2006)Google Scholar
  19. 19.
    Besson, L., Savelli, J., Leclercq, E., Terrasse, M.N.: Ikosem’s generic model for syntactical and semantical image description: the core component of a framework for image database engineering. In: Proceedings of the 10th International Workshop on Multimedia Information Systems, Maryland, USA (2004)Google Scholar
  20. 20.
    Evermann, J., Wand, Y.: Ontology based object-oriented domain modelling: fundamental concepts. Requirements Engineering 10, 146–160 (2005)CrossRefGoogle Scholar
  21. 21.
    Mascardi, V., Corde, V., Rosso, P.: Comparison of upper-level ontologies. Technical Report DISI-TR-06-2, DISI (Univ. degli Studi di Genova) Italy (2006)Google Scholar
  22. 22.
    Evermann, J.: A UML and OWL description of Bunge’s upper-level ontology model. Software and Systems Modeling (2008), doi:10.1007/s10270-008-0082-3Google Scholar
  23. 23.
    Lu, S., Parsons, J.: Enforcing Ontological Rules in UML-Based Conceptual Modeling: Principles and Implementation. In: Halpin, T., Siau, K., Krogstie, J. (eds.) Proceedings of the Workshop on Evaluating Modeling Methods for Systems Analysis and Design (EMMSAD 2005), held in conjunctiun with the 17th Conference on Advanced Information Systems (CAiSE 2005), Porto, Portugal, EU, FEUP, Porto, Portugal, EU, pp. 451–462 (2005)Google Scholar
  24. 24.
    Noy, N.F.: Semantic integration: a survey of ontology-based approaches. SIGMOD Rec. 33(4), 65–70 (2004)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Marie-Noelle Terrasse
    • 1
  • Eric Leclercq
    • 1
  • Marinette Savonnet
    • 1
  • Arnaud Da Costa
    • 1
  • Pierre Naubourg
    • 1
  • Magali Roux-Rouquie
    • 2
  1. 1.LE2I UMR CNRS 5158University of BurgundyFrance
  2. 2.LIP6 CNRS-UPMCParisFrance

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