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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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
Staab S, Studer R (eds) (2009) Handbook on ontologies, 2nd edn. Series: International handbooks on information systems, Springer, Heidelberg
Gruber TR (1993) A translation approach to portable ontology specifications. Knowl Acquis 5:199–220
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
The Generalized Upper Model. http://www.fb10.uni-bremen.de/anglistik/langpro/webspace/jb/gum/index.htm. Accessed 26 Aug 2011
Sensus ontology. http://www.isi.edu/natural-language/projects/ONTOLOGIES.html. Accessed 21 Aug 2011
Penman Upper Model. http://www.fb10.uni-bremen.de/anglistik/langpro/kpml/um89/um89-root.htm. Accessed 26 Aug 2011
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: 187–205
Frame ontology. http://www-ksl.stanford.edu/knowledge-sharing/ontologies/html/frame-ontology/index.html. Accessed 21 Aug 2011
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, Deventer
Uschold M, Gruninger M (1996) Ontologies: principles, methods and applications. Knowl Eng Rev 11(2):93–137
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):89–123
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, 2004
Web Ontology Language (OWL). http://www.w3.org/TR/owl-features/. Accessed 10 Aug 2011
Resource Description Framework (RDF). http://en.wikipedia.org/wiki/Resource_Description_Framework. Accessed 10 Aug 2011
DIG Interface. http://dig.sourceforge.net/. Accessed 10 Aug 2011
RacerPro. http://www.racer-systems.com/. Accessed 10 Aug 2011
FaCT++. http://owl.cs.manchester.ac.uk/fact++/. Accessed 10 Aug 2011
KAON2. http://kaon2.semanticweb.org/. Accessed 10 Aug 2011
Jena. http://jena.sourceforge.net/. Accessed 15 July 2011
Kalyanpur A, Parsia B, Sirin E, Cuenca-Grau B, Hendler J (2005) SWOOP, a web ontology editing browser. J Web Semantics 4(2):144–153
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 982
Gangemi A, Pisanelli DM, Geri S (1999) An overview of the ONIONS project: applying ontologies to the integration of medical terminologies. Data Knowl Eng 31:183–220
http://lhncbc.nlm.nih.gov/cgsb_site/servlet/Turbine/template/research%2Cmedterm%2COntology.vm. Accessed 15 July 2011
The Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29
The Gene Ontology Consortium (2001) Creating the gene ontology resource: design and implementation. Genome Res 11(8):1425–1433
Rosse C, Mejino JLV (2003) A reference ontology for bioinformatics: the foundational model of anatomy. J Biomed Inform 36:478–500
Topic Maps. http://www.topicmaps.org/. Accessed 15 July 2011
XTM syntax. http://www.topicmaps.org/xtm/. Accessed 20 July 2011
LTM. http://www.ontopia.net/download/ltm.html. Accessed 20 July 2011
AsTMa. http://astma.it.bond.edu.au/. Accessed 20 July 2011
Omigator. http://www.ontopia.net/solutions/omnigator.html. Accessed 20 July 2011
Empolis K42. http://notendur.hi.is/joner/eaps/cs_empo.htm. Accessed 20 July 2011
TM4L. http://compsci.wssu.edu/iis/nsdl/. Accessed 29 Aug 2011
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 171–184
http://www.nlm.nih.gov/mesh/2010/mesh_browser/MeSHtree.html. Accessed 20 Aug 2011
http://www.nlm.nih.gov/mesh/filelist.html. Accessed 20 Aug 2011
TMNav. http://tm4j.org/tmnav.html. Accessed 20 Aug 2011
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Stanescu, L., Burdescu, D.D., Brezovan, M., Mihai, C.G. (2012). Ontologies. In: Creating New Medical Ontologies for Image Annotation. SpringerBriefs in Electrical and Computer Engineering(). Springer, New York, NY. https://doi.org/10.1007/978-1-4614-1909-9_4
Download citation
DOI: https://doi.org/10.1007/978-1-4614-1909-9_4
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4614-1908-2
Online ISBN: 978-1-4614-1909-9
eBook Packages: EngineeringEngineering (R0)