SIABO - Semantic Information Access through Biomedical Ontologies

Troels Andreasen, Henrik Bulskov, Tine Lassen, Sine Zambach, Per Anker Jensen, Bodil Nistrup Madsen, Hanne Erdman Thomsen, Jørgen Fischer Nilsson, Bartlomiej Antoni Szymczak



The scientific aim of the project presented in this paper is to provide an approach to representing, organizing, and accessing conceptual content of biomedical texts using a formal ontology. The ontology is based on UMLS resources supplemented with domain ontologies developed in the project. The approach introduces the notion of ‘generative ontologies’, i.e., ontologies providing increasingly specialized concepts reflecting the phrase structure of natural language. Furthermore, we propose a novel so-called ‘ontological semantics’ which maps noun phrases from texts and queries into nodes in the generative ontology. This enables an advanced form of data mining of texts identifying paraphrases and concept relations and measuring distances between key concepts in texts. Thus, the project gains its identity in its attempt to provide a formal underpinning of conceptual similarity or relatedness of meaning.


  1. Andreasen, T., Fischer Nilsson, J., 2004. Grammatical Specification of Domain Ontologies. In Data & Knowledge Engineering, 48, p. 221-230
  2. Budanitsky, A., Hirst, G., 2006. Evaluating WordNetbased measures of semantic distance. Computational Linguistics, 32(1).
  3. Jensen, P., Fischer Nilsson, J., 2006. Ontology-based Semantics for Prepositions. In Syntax and Semantics of Prepositions, Text, Speech and Language Technology, Vol. 29. Springer.
  4. Ben-Avi, G., Francez, N., 2004. Categorial Grammar with Ontology-refined Types. In Proceedings of CG04.
  5. Fillmore, C. J., 1968. The Case for Case. In Universals in Linguistic Theory. Holt, Rinehart, and Winston. New York, pp. 1-88.
  6. Hearst, M., 1992. Automatic acquisition of hyponyms from large text corpora. In Proceedings of the 14th International Conference on Computational Linguistics, Association for Computational Linguistics, Volume 2, pp. 539 - 545.
  7. Madsen, B. N., Pedersen, B. S. & Thomsen, H. E., 2002. Semantic Relations in Content-based Querying Systems: a Research Presentation from the OntoQuery Project. In Ontologies and Lexical Knowledge Bases. Proceedings of the 1st International Workshop, OntoLex 2000. OntoText Lab., Sofia, pp. 72-82.
  8. Madsen, B.N., Thomsen, H.E., and Vikner, C., 2005. Multidimensionality in terminological concept modelling. In: Terminology and Content Development, TKE 2005, 7th International Conference on Terminology and Knowledge Engineering, Copenhagen: 161-173.
  9. Nilsson, J. F., 2001. A Logico-Algebraic Framework for Ontologies. ONTOLOG. In Ontology-based Interpretation of Noun Phrases, Proceedings of the First Inernational. OntoQuery Workshop, Kolding.
  10. Nirenburg, S., Raskin, V., 2004. Ontological Semantics. MIT Press.
  11. Rada, R. & Bicknell, E., 1989. Ranking documents with a thesaurus. Journal of the American Society for Information Science, 40(5).
  12. Resnik, P., 1999. Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language. Journal of Artificial Intelligence Research.

Paper Citation

in Harvard Style

Andreasen T., Bulskov H., Lassen T., Zambach S., Anker Jensen P., Nistrup Madsen B., Erdman Thomsen H., Fischer Nilsson J. and Antoni Szymczak B. (2009). SIABO - Semantic Information Access through Biomedical Ontologies . In Proceedings of the International Conference on Knowledge Engineering and Ontology Development - Volume 1: KEOD, (IC3K 2009) ISBN 978-989-674-012-2, pages 171-176. DOI: 10.5220/0002297801710176

in Bibtex Style

author={Troels Andreasen and Henrik Bulskov and Tine Lassen and Sine Zambach and Per Anker Jensen and Bodil Nistrup Madsen and Hanne Erdman Thomsen and Jørgen Fischer Nilsson and Bartlomiej Antoni Szymczak},
title={SIABO - Semantic Information Access through Biomedical Ontologies},
booktitle={Proceedings of the International Conference on Knowledge Engineering and Ontology Development - Volume 1: KEOD, (IC3K 2009)},

in EndNote Style

JO - Proceedings of the International Conference on Knowledge Engineering and Ontology Development - Volume 1: KEOD, (IC3K 2009)
TI - SIABO - Semantic Information Access through Biomedical Ontologies
SN - 978-989-674-012-2
AU - Andreasen T.
AU - Bulskov H.
AU - Lassen T.
AU - Zambach S.
AU - Anker Jensen P.
AU - Nistrup Madsen B.
AU - Erdman Thomsen H.
AU - Fischer Nilsson J.
AU - Antoni Szymczak B.
PY - 2009
SP - 171
EP - 176
DO - 10.5220/0002297801710176