Ontologies

  • Liana Stanescu
  • Dumitru Dan Burdescu
  • Marius Brezovan
  • Cristian Gabriel Mihai
Chapter
Part of the SpringerBriefs in Electrical and Computer Engineering book series (BRIEFSELECTRIC)

Abstract

Medical images can be described properly only by using a set of specific words. In practice, this constraint can be satisfied by the usage of ontologies. In this chapter, we focus on the existing definitions for ontologies and usability. Several design criteria and development tools are presented to illustrate the means available for creating and maintaining ontologies. Ontologies are frequently used in medical domain, and for this reason, several aspects related to the applicability of the ontology in this domain are presented. Existing ontologies are provided in formats that are not always easy to interpret and use. A high flexibility is obtained when an ontology is created from scratch using a custom approach. Because of this, we are describing a custom approach for obtaining an ontology using a medical source of information like MeSH. The content of an ontology needs to be stored in a specific format. The Topic Maps standard was proved to be an efficient mechanism that can be successfully used to represent the content of our ontology.

Keywords

Coherence Stratification Saccharomyces Editing MeSH 

References

  1. 1.
    Moriya N, Hasharon R Ontology. The specification of a shared conceptualization, A review document source. http://www.iqlue.com/prosearch/ProSearchOntology.jsp?type=CMP. Accessed 26 Aug 2011
  2. 2.
    Staab S, Studer R (eds) (2009) Handbook on ontologies, 2nd edn. Series: International handbooks on information systems, Springer, HeidelbergGoogle Scholar
  3. 3.
    Gruber TR (1993) A translation approach to portable ontology specifications. Knowl Acquis 5:199–220CrossRefGoogle Scholar
  4. 4.
    Noy NF, McGuinness DL (2001) Ontology development 101: a guide to creating your first ontology, Stanford University, Stanford. http://www-ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html
  5. 5.
    The Generalized Upper Model. http://www.fb10.uni-bremen.de/anglistik/langpro/webspace/jb/gum/index.htm. Accessed 26 Aug 2011
  6. 6.
  7. 7.
  8. 8.
    Van Der P, Vet EP, Speel P, Mars NJI (1994) The Plinius ontology of ceramic materials. Workshop notes ECAI’94 workshop comparison of implemented ontologies: 187–205Google Scholar
  9. 9.
  10. 10.
    Thomas RG (1993) Toward principles for the design of ontologies used for knowledge sharing. In: Guarino N, Poli R (eds) Formal ontology in conceptual analysis and knowledge representation. Kluwer Academic, DeventerGoogle Scholar
  11. 11.
    Uschold M, Gruninger M (1996) Ontologies: principles, methods and applications. Knowl Eng Rev 11(2):93–137CrossRefGoogle Scholar
  12. 12.
    Gennari J, Musen MA, Fergerson RW, Grosso WE, Crubezy M, Eriksson H, Noy NF, Tu SW (2003) The evolution of Protégé: an environment for knowledge-based systems development. Int J Hum Comp Stud 58(1):89–123CrossRefGoogle Scholar
  13. 13.
    Knublauch H, Fergerson RW, Noy NF, Musen MA (2004) The Protégé OWL plugin: an open development environment for semantic web applications. In: 3rd international semantic web conference, Hiroshima, 2004Google Scholar
  14. 14.
    Web Ontology Language (OWL). http://www.w3.org/TR/owl-features/. Accessed 10 Aug 2011
  15. 15.
    Resource Description Framework (RDF). http://en.wikipedia.org/wiki/Resource_Description_Framework. Accessed 10 Aug 2011
  16. 16.
    DIG Interface. http://dig.sourceforge.net/. Accessed 10 Aug 2011
  17. 17.
    RacerPro. http://www.racer-systems.com/. Accessed 10 Aug 2011
  18. 18.
    FaCT++. http://owl.cs.manchester.ac.uk/fact++/. Accessed 10 Aug 2011
  19. 19.
    KAON2. http://kaon2.semanticweb.org/. Accessed 10 Aug 2011
  20. 20.
    Jena. http://jena.sourceforge.net/. Accessed 15 July 2011
  21. 21.
    Kalyanpur A, Parsia B, Sirin E, Cuenca-Grau B, Hendler J (2005) SWOOP, a web ontology editing browser. J Web Semantics 4(2):144–153CrossRefGoogle Scholar
  22. 22.
    Rector AL, Rogers JE, Zanstra PE, Van Der Haring E. OpenGALEN: open source medical terminology and tools. In: Proceedings of the AMIA Symposium, Washington DC, 2003, p 982Google Scholar
  23. 23.
    Gangemi A, Pisanelli DM, Geri S (1999) An overview of the ONIONS project: applying ontologies to the integration of medical terminologies. Data Knowl Eng 31:183–220MATHCrossRefGoogle Scholar
  24. 24.
  25. 25.
    The Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29CrossRefGoogle Scholar
  26. 26.
    The Gene Ontology Consortium (2001) Creating the gene ontology resource: design and implementation. Genome Res 11(8):1425–1433CrossRefGoogle Scholar
  27. 27.
    Rosse C, Mejino JLV (2003) A reference ontology for bioinformatics: the foundational model of anatomy. J Biomed Inform 36:478–500CrossRefGoogle Scholar
  28. 28.
    Topic Maps. http://www.topicmaps.org/. Accessed 15 July 2011
  29. 29.
    XTM syntax. http://www.topicmaps.org/xtm/. Accessed 20 July 2011
  30. 30.
    LTM. http://www.ontopia.net/download/ltm.html. Accessed 20 July 2011
  31. 31.
    AsTMa. http://astma.it.bond.edu.au/. Accessed 20 July 2011
  32. 32.
    Omigator. http://www.ontopia.net/solutions/omnigator.html. Accessed 20 July 2011
  33. 33.
    Empolis K42. http://notendur.hi.is/joner/eaps/cs_empo.htm. Accessed 20 July 2011
  34. 34.
    TM4L. http://compsci.wssu.edu/iis/nsdl/. Accessed 29 Aug 2011
  35. 35.
    Nelson SJ, Johnston D, Humphreys BL (2001) Relationships in medical subject headings. In: Bean CA, Green R (eds) Relationships in the organization of knowledge. Kluwer, Dordrecht, pp 171–184Google Scholar
  36. 36.
  37. 37.
  38. 38.
    TMNav. http://tm4j.org/tmnav.html. Accessed 20 Aug 2011

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Liana Stanescu
    • 1
  • Dumitru Dan Burdescu
    • 1
  • Marius Brezovan
    • 1
  • Cristian Gabriel Mihai
    • 1
  1. 1.Department of Software EngineeringUniversity of CraiovaCraiovaRomania

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