Methodologically Designing a Hierarchically Organized Concept-Based Terminology Database to Improve Access to Biomedical Documentation

  • Antonio Vaquero
  • Fernando Sáenz
  • Francisco Alvarez
  • Manuel de Buenaga
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4277)


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 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.


Software Engineering Machine Translation Language Resource Linguistic Resource Lexical 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.


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  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) ISBN 972-8939-00-0Google Scholar
  2. 2.
    Maña, M., Mata, J., Domínguez, J.L., Vaquero, A., Alvarez, F., Gomez, J., Gachet, D., De Buenaga, M.: 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. In: En Actas del XXII Congreso de la Sociedad Española de Procesamiento del Lenguaje (SEPLN) (2006)Google Scholar
  3. 3.
    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
  4. 4.
    Moreno, A.: Diseño e Implementación de un Lexicón Computacional para Lexicografía y Traducción Automática. Estudios de Lingüística Española, vol. (9) (2000)Google Scholar
  5. 5.
    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
  6. 6.
    Wittenburg, P., Broeder, D., Piepenbrock, R., van der Veer, K.: Databases for Linguistic Purposes: a case study of being always too early and too late. In: Proceedings of the EMELD Workshop (2004)Google Scholar
  7. 7.
    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, pp. 1061–1067 (2000)Google Scholar
  8. 8.
    Tiedemann, J.: MatsLex: A multilingual lexical database for machine translation. In: Proc. of the 3rd International Conference on Language Resources and Evaluation, pp. 1909–1912 (2002)Google Scholar
  9. 9.
    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
  10. 10.
    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
  11. 11.
    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
  12. 12.
    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
  13. 13.
    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
  14. 14.
    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, pp. 527–534 (1998)Google Scholar
  15. 15.
    Welty, C., Guarino, N.: Supporting ontological analysis of taxonomic relationships. Data and Knowledge Engineering 39(1), 51–74 (2001)zbMATHCrossRefGoogle Scholar
  16. 16.
    Bodenreider, O.: Circular Hierarchical Relationships in the UMLS: Etiology, Diagnosis, Treatment, Complications and Prevention. In: Proceedings of the AMIA Symposium (2001)Google Scholar
  17. 17.
    Feliu, J., Vivaldi, J., Cabré, M.T.: Ontologies: a review. Working Paper, 34. Barcelona: Institut Universitari de Lingüística Aplicada. DL 23, 735 (WP) (2002)Google Scholar
  18. 18.
    Evans, R., Kilgarriff, A.: MRDs, Standards and How to do Lexical Engineering. In: Proc. of 2nd Language Engineering Convention, pp. 125–132 (1995)Google Scholar
  19. 19.
    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
  20. 20.
    Martin, P.: Correction and Extension of WordNet 1.7. In: Proc. of the 11th International Conference on Conceptual Structures, pp. 160–173 (2003)Google Scholar
  21. 21.
    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
  22. 22.
    Philpot, A., Hovy, E., Pantel, P.: The Omega Ontology. 2005. In: IJCNLP Workshop on Ontologies and Lexical Resources, pp. 59–66 (2005)Google Scholar
  23. 23.
    Makagonov, P., Ruiz Figueroa, A., Sboychakov, K., Gelbukh, A.: 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
  24. 24.
    Makagonov, P., Ruiz Figueroa, A., Sboychakov, K., Gelbukh, A.: 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
  25. 25.
    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 Country (2005)Google Scholar
  26. 26.
    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 Alvarez
    • 2
  • Manuel de Buenaga
    • 3
  1. 1.Facultad de Informática, Departamento de Sistemas Informáticos y ProgramaciónUniversidad Complutense de MadridMadridSpain
  2. 2.Universidad Autónoma de SinaloaCuliacán, SinaloaMéxico
  3. 3.Departamento de Sistemas InformáticosUniversidad Europea de MadridMadridSpain

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