Advertisement

Thinking Precedes Action: Using Software Engineering for the Development of a Terminology Database to Improve Access to Biomedical Documentation

  • Antonio Vaquero
  • Fernando Sáenz
  • Francisco Álvarez
  • Manuel de Buenaga
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4345)

Abstract

Relational databases have been used to represent lexical knowledge since the days of machine-readable dictionaries. However, although software engineering provides a methodological framework for the construction of databases, most developing efforts focus on content, implementation and time-saving issues, and forget about the software engineering aspects of software and database construction. We have defined a methodology for the development of lexical resources that covers this and other aspects, by following a sound software engineering approach to formally represent knowledge. Nonetheless, the conceptual model from which it departs has some major limitations that need to be overcome. Based on a short analysis of common problems in existing lexical resources, we present an upgraded conceptual model as a first step towards the methodological development of a hierarchically organized concept-based terminology database, to improve the access to medical information as part of the SINAMED and ISIS projects.

Keywords

Software Engineering Machine Translation Algebraic Property Language Resource Linguistic Resource 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Sáenz, F., Vaquero, A.: Applying Relational Database Development Methodologies to the Design of Lexical Databases. In: Database Systems 2005, IADIS Virtual Multi Conference on Computer Science and Information Systems (MCCSIS) (2005)Google Scholar
  2. 2.
    Maña, M., et al.: Los proyectos SINAMED e ISIS: Mejoras en el Acceso a la Información Biomédica Mediante la Integración de Generación de Resúmenes, Categorización Automática de Textos y Ontologías. En Actas del XXII Congreso de la Sociedad Española de Procesamiento del Lenguaje (SEPLN) (2006)Google Scholar
  3. 3.
    Pressman, R.: Software Engineering. In: Dorfman, M., Thayer, R.H. (eds.) Software Engineering, Wiley-IEEE Computer Society Press (1999)Google Scholar
  4. 4.
    York, S., Gómez-Pérez, A., Daelemans, W., Reinberger, M., Guarino, N., Fridman, N.: Why Evaluate Ontology Technologies? Because It Works! IEEE Intelligent Systems 19(4), 74–81 (2004)CrossRefGoogle Scholar
  5. 5.
    Sáenz, F., Vaquero, A.: Towards a Development Methodology for Managing Linguistic Knowledge Bases. Research and Development in Intelligent Systems XIX. Springer, Cambridge (2002)Google Scholar
  6. 6.
    Pfleeger, S.: Software Engineering: Theory and Practice, 2nd edn. Prentice-Hall, Englewood Cliffs (2001)Google Scholar
  7. 7.
    Bouaud, J., Bachimont, B., Charlet, J., Zweigenbaum, P.: Acquisition and Structuring of an Ontology within Conceptual Graphs. In: Proceedings of the ICCS 1994 Workshop on Knowledge Acquisition using Conceptual Graph Theory (1994)Google Scholar
  8. 8.
    Bachimont, B.: Engagement sémantique et engagement ontologique: conception et réalisation d’ontologies en Ingénierie des connaissances. In: Charlet, J., Zacklad, M., Kassel, G., Bourigault, D. (eds.) Ingénierie des connaissances, évolutions récentes et nouveaux defies (2000)Google Scholar
  9. 9.
    Bläser, B., Schwall, U., Storrer, A.: Reusable Lexical Database Tool for Machine Translation. In: Proceedings of the International Conference on Computational Linguistics - COLING 1992, vol. II, pp. 510–516 (1992)Google Scholar
  10. 10.
    Moreno, A.: Diseño e Implementación de un Lexicón Computacional para Lexicografía y Traducción Automática. Estudios de Lingüística Española, vol. 9 (2000)Google Scholar
  11. 11.
    Hayashi, L.S., Hatton, J.: Combining UML, XML and Relational Database Technologies - The Best of all Worlds for Robust Linguistic Databases. In: Proceedings of the IRCS Workshop on Linguistic Databases (2001)Google Scholar
  12. 12.
    Wittenburg, P., et al.: Databases for Linguistic Purposes: a case study of being always too early and too late. In: Proceedings of the EMELD Workshop (2004)Google Scholar
  13. 13.
    Moreno, A., Pérez, C.: Reusing the Mikrokosmos Ontology for Concept-Based Multilingual Terminology Databases. In: Proc. of the 2nd International Conference on Language Resources and Evaluation (2000)Google Scholar
  14. 14.
    Tiedemann, J.M.: A multilingual lexical database for machine translation. In: Proc. of the 3rd International Conference on Language Resources and Evaluation (2002)Google Scholar
  15. 15.
    Lieberman, M.: The Use of SNOMED to Enhance Querying of a Clinical Data Warehouse. A thesis presented to the Division of Medical Informatics and Outcomes Research and the Oregon Health & Sciences University School of Medicine in partial fulfillment of the requirements for the degree of Master of Science (2003)Google Scholar
  16. 16.
    Nirenburg, S., McShane, M., Beale, S.: The Rationale for Building Resources Expressly for NLP. In: Proc. of the 4th International Conference on Language Resources and Evaluation (2004)Google Scholar
  17. 17.
    McShane, M., Nirenburg, S., Beale, S.: An implemented, integrative approach to ontology-based NLP and interlingua. Working Paper #06-05, Institute for Language and Information Technologies, University of Maryland Baltimore County (2005)Google Scholar
  18. 18.
    Cimino, J.: Desiderata for Controlled Medical Vocabularies in the Twenty-first Century. Methods of Information in Medicine 37(4-5), 394–403 (1998)Google Scholar
  19. 19.
    Ide, N., Veronis, J.: Extracting Knowledge Bases from Machine-Readable Dictionaries: Have we wasted our time? In: Proc. of the First International Conference on Building and Sharing of Very Large-Scale Knowledge Bases (1993)Google Scholar
  20. 20.
    Guarino, N.: Some Ontological Principles for Designing Upper Level Lexical Resources. In: Rubio, A., et al. (eds.) Proc. of the First International Conference on Language Resources and Evaluation (1998)Google Scholar
  21. 21.
    Welty, C., Guarino, N.: Supporting ontological analysis of taxonomic relationships. Data and Knowledge Engineering 39(1) (2001)Google Scholar
  22. 22.
    Bodenreider, O.: Circular Hierarchical Relationships in the UMLS: Etiology, Diagnosis, Treatment, Complications and Prevention. In: Proceedings of the AMIA Symposium (2001)Google Scholar
  23. 23.
    Feliu, J., Vivaldi, J., Cabré, M.T.: Ontologies: a review. Working Paper, 34. Barcelona: Institut Universitari de Lingüística Aplicada (2002)Google Scholar
  24. 24.
    Evans, R., Kilgarriff, A.: MRDs, Standards and How to do Lexical Engineering. In: Proc. of 2nd Language Engineering Convention (1995)Google Scholar
  25. 25.
    Burgun, A., Bodenreider, O.: Aspects of the Taxonomic Relation in the Biomedical Domain. In: Proc. of the 2nd International Conference on Formal Ontologies in Information Systems (2001)Google Scholar
  26. 26.
    Martin, P.: Correction and Extension of WordNet 1.7. In: Proc. of the 11th International Conference on Conceptual Structures (2003)Google Scholar
  27. 27.
    Oltramari, A., Prevot, L., Borgo, S.: Theoretical and Practical Aspects of Interfacing Ontologies and Lexical Resources. In: Proc. of the 2nd Italian SWAP workshop (2005)Google Scholar
  28. 28.
    Philpot, A., Hovy, E., Pantel, P.: The Omega Ontology. In: IJCNLP Workshop on Ontologies and Lexical Resources (2005)Google Scholar
  29. 29.
    Makagonov, P., et al.: Learning a Domain Ontology from Hierarchically Structured Texts. In: Proc. of Workshop Learning and Extending Lexical Ontologies by using Machine Learning Methods at 22nd International Conference on Machine Learning (2005)Google Scholar
  30. 30.
    Makagonov, P., et al.: Studying Evolution of a Branch of Knowledge by Constructing and Analyzing Its Ontology. In: Kop, C., Fliedl, G., Mayr, H.C., Métais, E. (eds.) Natural Language Processing and Information Systems. 11th International Conference on Applications of Natural Language to Information Systems (2006)Google Scholar
  31. 31.
    Nirenburg, S., McShane, M., Zabludowski, M., Beale, S., Pfeifer, C.: Ontological Semantic text processing in the biomedical domain. Working Paper #03-05, Institute for Language and Information Technologies, University of Maryland Baltimore County (2005)Google Scholar
  32. 32.
    Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C.J., Neuhaus, F., Rector, A., Rosse, C.: Relations in Biomedical Ontologies. Genome Biology, 6(5) (2005)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Antonio Vaquero
    • 1
  • Fernando Sáenz
    • 1
  • Francisco Álvarez
    • 2
  • Manuel de Buenaga
    • 3
  1. 1.Facultad de Informática, Departamento de Ingeniería del Software e Inteligencia ArtificialUniversidad Complutense de MadridMadridSpain
  2. 2.Universidad Autónoma de SinaloaCuliacán, SinaloaMéxico
  3. 3.Departamento de Sistemas InformáticosUniversidad Europea de MadridVillaviciosa de Odón. MadridSpain

Personalised recommendations