Skip to main content
SpringerLink
Log in

Vocabularies and Retrieval Tools in Biomedicine: Disentangling the Terminological Knot

  • Original Paper
  • Published:
Journal of Medical Systems Aims and scope Submit manuscript

Abstract

Terms like “thesaurus”, “taxonomy”, “classification”, “glossary”, “ontology” and “controlled vocabulary” can be used in diverse contexts, causing confusion and vagueness about their denotation. Is a thesaurus a tool to enrich a writer’s style or an indexing tool used in bibliographic retrieval? Or can it be both? A literature study was to clear the confusion, but rather than giving us consensus definitions, it provided us with conflicting descriptions. We classified these definitions into three domains: linguistics, knowledge management and bibliographic retrieval. The scope of the terms is therefore highly dependent on the context. We propose one definition per term, per context. In addition to this intra-conceptual confusion, there is also inter-conceptual vagueness. This leads to the introduction of misnomers, like “ontology” in the Gene Ontology. We examined some important (bio)medical systems for their compatibility with the definitions proposed in the first part of this paper. To conclude, an overview of these systems and their classification into the three domains is given.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

Notes

  1. http://en.wikipedia.org/wiki/Glossary_of_medical_terms_related_to_communications_disorders

  2. http://www.riziv.fgov.be/nl/glossary.htm

  3. http://www.termisti.refer.org/data/ivg/index.htm

  4. http://www.termisti.refer.org/data/autisme/frame.html

  5. http://users.ugent.be/∼rvdstich/eugloss/welcome.html

  6. The first column refers to the French term, the second to the German translation and the third column refers to the corresponding domain.

  7. http://www.plainenglish.co.uk/

  8. http://www.springerlink.com

  9. The BS 8723 standard consists of five parts, the first two of which broadly correspond to ISO 2788, whereas the combination of part one and four have approximately the same scope as ISO 5964 (multilingual thesauri). BS 8723–3 covers vocabularies other than thesauri, BS 8723–4 gives recommendations concerning interoperability of vocabularies and BS 8723–5 discusses exchange formats.

  10. Project Leader for NISO's Thesaurus Development Team

  11. DARPA stands for Defense Advanced Research Projects Agency

  12. http://acl.icnet.uk/∼mw/MDM0.73.owl

  13. The definition of topic maps proposed in ISO/IEC 13250 is a circular definition, thus not helping to grasp the exact meaning of ‘topic maps’:

    1. a)

      A set of information resources regarded by a topic map application as a bounded object set whose hub document is a topic map document conforming to the SGML architecture defined by this International Standard.

    2. b)

      Any topic map document conforming to the SGML architecture defined by this International Standard, or the document element (topicmap) of such a document.

    3. c)

      The document element type (topicmap) of the topic map document architecture.

  14. 3BT (Belgian Bilingual Biclassified Thesaurus) is a continuation of the ICPC2/ICD10 Thesaurus, but with French translations added to it. The designation “thesaurus” is a misnomer in this case, as the system does not meet all the criteria described in the ISO standards for thesauri: it has no associative relationships. However, some terms do have synonyms or entry terms that lead the system to the correct concept. Like ATC, ICD and ICPC, this is a specific, enumerative, documentary classification used for medical coding.

  15. http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Root

  16. http://lhncbc.nlm.nih.gov/lhc/servlet/Turbine/template/research,langproc,MedicalOntology.vm

References

  1. University of London Computer Centre (ULCC), UNESCO Thesaurus [cited 2009 26/02/2009]; Available from: http://www2.ulcc.ac.uk/unesco/#brow, 2003.

  2. Roget, P., Roget's II: The new thesaurus. [cited 2009 26/02/2009]; Third edition. Available from: www.bartleby.com/62, 1995.

  3. Kagolovsky, Y., and Moehr, J. R., Terminological problems in information retrieval. J. Med. Syst. 27(5):399–408, 2003.

    Article  Google Scholar 

  4. Harter, S. P., and Hert, C. A., Evaluation of information retrieval systems: Approaches, issues, and methods. Annu. Rev. Inf. Sci. Technol. (ARIST). 32:3–94, 1997.

    Google Scholar 

  5. Ananiadou, S., and McNaught, J., Text mining for biology and biomedicine. Norwood, Artech House, 2006.

    Google Scholar 

  6. CILF, Wörterbuch für Industrie und Technik. Paris, Conseil International de la Langue Française, 1993.

    Google Scholar 

  7. Mawson, C. O. S., Roget’s international thesaurus of English words and phrases, 1st edition. New York, Thomas Y. Crowell, 1922.

    Google Scholar 

  8. Kilgarriff, A., and Yallop, C., What's in a thesaurus? In Proceedings of the Second Conference on Language Resources and Evaluation. Athens, Greece, 2000.

  9. Wodtke, C., Mind your phraseology! Using controlled vocabularies to improve findability. [cited 2007 24/01/2007]; Available from: http://www.digital-web.com/articles/mind_your_phraseology/, 2002.

  10. Garshol, L. M., Metadata? Thesauri? Taxonomies? Topic maps! Making sense of it all. [cited 13/06/2006]; Available from: www.ontopia.net/topicmaps/materials/tm-vs-thesauri.html 2004.

  11. Davis, P. H., and Heywood, V. H., Principles of Angiosperm Taxonomy. Princeton NJ, Van Nostrand, p. 556, 1963.

    Google Scholar 

  12. ISO/IEC_11179–2, Information technology—Metadata registries (MDR)—Part 2: Classification. 2nd ed. ISO/IEC 11179 Metadata Registry (MDR) standard. Vol. 2. Geneva: ISO copyright office. 16, 2005.

  13. Agro, G., Classifications and Taxonomies. University of Texas, Austin, 2004.

    Google Scholar 

  14. Beck, H. and Pinto, H. S., Overview of approach, methodologies, standards, and tools for ontologies. University of Florida, Universidade Técnica de Lisboa, 2002.

  15. Sterkenburg, P., (Ed.), A practical guide to lexicography. Terminology and lexicography. Research and practice. Vol. 6. Amsterdam/Philadelphia: John Benjamins Publishing Company, 2003.

  16. Van Rees, R., Clarity in the usage of the terms ontology, taxonomy and classification. In CIB73, 2003.

  17. Cann, J., Principles of classification—suggestions for a procedure to be used by ICIS in developing international classification tables for the construction industry. NBS Services, ICIS, 1997.

  18. Indira Gandhi National Open University, Part II: classification schemes. In: Indexing languages, pp. 56–88. New Delhi: Indira Gandhi National Open University, pp. 56–88, 2006.

  19. Procter, P., LONGMAN dictionary of contemporary English. London, Longman Dictionaries, 1978.

    Google Scholar 

  20. Simpson, J. A., and Weiner, S. C., Oxford English dictionary, 2nd edition. London, Oxford University Press, 1989.

    Google Scholar 

  21. Merriam-Webster Inc., Merriam-Webster online dictionary. [cited 2007 20/03/2007]; Available from: http://www.merriam-webster.com, 2008.

  22. Ullrich, M., Maier, A., and Angele, J., Taxonomie, thesaurus, topic map, Ontologie—ein Vergleich. Ontoprise GmbH, 2003.

  23. Engineers Joint Council (Ed.), Thesaurus of engineering and scientific terms: a list of engineering and related terms and their relationships for use as a vocabulary reference in indexing and retrieving technical information. New York: Engineers Joint Council and the US Department of Defense. 690, 1967.

  24. ISO, Documentation—guidelines for the establishment and development of monolingual thesauri, 2nd edition. Geneva, ISO, 1986.

    Google Scholar 

  25. Aitchison, J., Gilchrist, A., and Bawden, D., Thesaurus construction and use: a practical manual, Vol. 1, 4th edition. London, Aslib IMI, p. 218, 2000.

    Google Scholar 

  26. ANSI/NISO, Guidelines for the construction, format, and management of monolingual controlled vocabularies. NISO Press, Bethesda, MD, p. 172, 2005.

    Google Scholar 

  27. BSI, Structured vocabularies for information retrieval—guide, Vol. 1. BSI British Standards, London, p. 10, 2005.

    Google Scholar 

  28. Chowdhury, G. G., Introduction to modern information retrieval, 2nd edition. Facet Publishing, London, 2003.

    Google Scholar 

  29. Hagedorn, K., The information architecture glossary. [cited 2006 04/07/2006]; Available from: http://argus-acia.com/white_papers/ia_glossary.pdf, 2000.

  30. Ribeiro-Neto, B., and Baeza-Yates, R. A., Modern information retrieval. ACM Press, New York, 1999.

    Google Scholar 

  31. Landau, S., Dictionaries: the art and craft of lexicography. Charles Scribner's Sons, New York, 1984.

    Google Scholar 

  32. ISO, Documentation—guidelines for the establishment and development of multilingual thesauri. ISO, Geneva, 1985.

    Google Scholar 

  33. ISO, Information and documentation. Guidelines for the establishment and development of thesauri [revision of ISO 2788 and 5964]. ISO/TC 46/SC9, 2007.

  34. Roe, S. K., and Thomas, A. R., The thesaurus: review, renaissance and revision. Haworth Information Press, Binghamton, NY, 2004.

    Google Scholar 

  35. Will, L., Glossary of terms relating to thesauri and other forms of structured vocabulary for information retrieval. [cited 2008 01–02–2008]; Available from: http://www.willpowerinfo.co.uk/glossary.htm, 2007.

  36. Studer, R., Oppermann, H., and Schnurr, H.-P., Die Bedeutung von Ontologien für das Wissensmanagement. Ontoprise GmbH, Karlsruhe, 2001.

    Google Scholar 

  37. Klein, G. O., and Smith, B., Concept systems and ontologies. Centre for medical terminology, Karolinska Institutet, Stockholm. Department of Philosophy, University at Buffalo, NY, p. 12, 2005.

    Google Scholar 

  38. Jonker, R., Termen en begrippen—Informatiebeheer. [cited 2007 15/01/2006]; Available from: http://labyrinth.opweb.nl/files/termenbegrippen.pdf, 2006.

  39. Jernst, What are the differences between a vocabulary, a taxonomy, a thesaurus, an ontology, and a meta-model?. 15/01/2003 [cited 10/05/2006]; Available from: www.metamodel.com/article.php?story=2003011223271, 2003.

  40. Gruber, T. R., Toward principles for the design of ontologies used for knowledge sharing. Int. J. Human-Comput. Stud. 43(5–6):907–928, 1995.

    Article  Google Scholar 

  41. Beckett, D., RDF/XML Syntax specification (revised). [cited 2008 26/11/2008]; Available from: http://www.w3.org/TR/rdf-syntax-grammar/, 2004.

  42. Dieng-Kuntz, R., et al., Building and using a medical ontology for knowledge management and cooperative work in a health care network. Comput. Biol. Med. 36(7–8):871–892, 2006.

    Article  Google Scholar 

  43. Kifer, M., Lausen, G., and Wu, J., Logical foundations of object-oriented and frame-based languages. University of Mannheim, 1990.

  44. Frohn, J., et al., FLORID: A prototype for F-logic. In: Proceedings of International Conference on Data Engineering. Birmingham, UK: IEEE Computer Science Press, 1997.

  45. Van Hamelen, F., et al., OIL: an ontology infrastructure for the semantic web. IEEE Intelligent Systems. 16(2):38–45, 2001.

    Article  Google Scholar 

  46. Bechhofer, S., et al., OWL web ontology language reference. In: Schreiber, Guus, M. Dean, (Ed.). W3C, 2004.

  47. Uschold, M., An ontology research pipeline. Applied Ontology. 1(1):13–16, 2005.

    Google Scholar 

  48. Garshol, L. M., Living with topic maps and RDF. [cited 2007 05/01/2007]; Available from: http://www.ontopia.net/topicmaps/materials/tmrdf.html, 2003.

  49. Ahmed, K., Introducing topic maps: a powerful, subject-oriented approach to structuring sets of information. (Content management). XML J. 3(10):22–27, 2002.

    Google Scholar 

  50. Pepper, S., The TAO of topic maps. In: XML Europe 2000. Paris, France, 2000.

  51. Hummel, B., Einsatz und Nutzenpotentiale von topic maps: Ein State-Of-The-Art Bericht. In: Fachbereich Informationswissenschaften. Fachhochschule Potsdam: Potsdam, 2004.

  52. Okkes, I. M., et al., ICPC-2-E: the electronic version of ICPC-2. Differences from the printed version and the consequences. Fam. Pract. 17(2):101–107, 2000.

    Article  Google Scholar 

  53. NN/LM, PubMed expert searching: using PubMed to get advanced results. [cited 2007 14/03/2007]; Available from: http://nnlm.gov/ner/training/material/NER_PES.doc, 2006.

  54. Greenberg, J., User comprehension and searching with information retrieval thesauri. Cat. Classif. Q. 37(3):103–120, 2004.

    Article  Google Scholar 

  55. Cataloging Policy and Support Office, Pre- vs. post-coordination and related issues. A. Management, Editor. Aquisitions and Bibliographic Access Directorate, Library Services, Library of Congress, 2007.

  56. Smith, B., Williams, J., and Schulze-Kremer, S., The ontology of the gene ontology. In: AMIA Annual Symposium. Washington D.C., 2003.

  57. Beier, J., and Tesche, T., Navigation and interaction in medical knowledge spaces using topic maps. Int. Congr. Ser. 1230:384–388, 2001.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Faculty of Translation Studies, University College Ghent, Ghent, Belgium

    Klaar Vanopstal & Joost Buysschaert

  2. Department of Applied Mathematics and Computer Science, Ghent University, Ghent, Belgium

    Klaar Vanopstal

  3. Faculty of Medicine and Health Sciences, Heymans Institute of Pharmacology, Ghent University, Ghent, Belgium

    Robert Vander Stichele

  4. Faculty of Arts and Philosophy, Department of Nordic Studies, Ghent University, Ghent, Belgium

    Godelieve Laureys

Authors
  1. Klaar Vanopstal
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Robert Vander Stichele
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Godelieve Laureys
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Joost Buysschaert
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Klaar Vanopstal.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Vanopstal, K., Vander Stichele, R., Laureys, G. et al. Vocabularies and Retrieval Tools in Biomedicine: Disentangling the Terminological Knot. J Med Syst 35, 527–543 (2011). https://doi.org/10.1007/s10916-009-9389-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10916-009-9389-z

Keywords

Search

Navigation