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A Methodology for Biomedical Ontology Reuse

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Natural Language Processing and Information Systems (NLDB 2016)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 9612))

Abstract

The abundance of biomedical ontologies is beneficial to the development of biomedical related systems. However, existing biomedical ontologies such as the National Cancer Institute Thesaurus (NCIT), Foundational Model of Anatomy (FMA) and Systematized Nomenclature of Medicine-Clinical Terms (SNOMED CT) are often too large to be implemented in a particular system and cause unnecessary high usage of memory and slow down the system’s processing time. Developing a new ontology from scratch just for the use of a particular system is deemed as inefficient since it requires additional time and causes redundancy. Thus, a potentially better method is by reusing existing ontologies. However, currently there are no specific methods or tools for reusing ontologies. This paper aims to provide readers with a step by step method in reusing ontologies together with the tools that can be used to ease the process.

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Notes

  1. 1.

    http://www.nactem.ac.uk/software/termine.

  2. 2.

    http://tubo.lirmm.fr/biotex/.

  3. 3.

    http://bioportal.bioontology.org.

References

  1. Alani, H.: Position paper: ontology construction from online ontologies. In: Proceedings of the 15th International Conference on World Wide Web, WWW 2006, pp. 491–495. ACM, New York (2006)

    Google Scholar 

  2. Boland, G.: Enhancing the radiology product: the value of voice-recognition technology. Clin. Radiol. 62(11), 1127 (2007)

    Article  Google Scholar 

  3. Bontas, E.P., Mochol, M., Tolksdorf, R.: Case studies on ontology reuse. In: Proceedings of the 5th International Conference on Knowledge Management IKNOW 2005 (2005)

    Google Scholar 

  4. Caldarola, E.G., Picariello, A., Rinaldi, A.M.: An approach to ontology integration for ontology reuse in knowledge based digital ecosystems. In: Proceedings of the 7th International Conference on Management of Computational and Collective IntElligence in Digital EcoSystems, pp. 1–8. ACM (2015)

    Google Scholar 

  5. Capellades, M.A.: Assessment of reusability of ontologies: a practical example. In: Proceedings of AAAI 1999 Workshop on Ontology Management, pp. 74–79. AAAI Press (1999)

    Google Scholar 

  6. Jonquet, C., Musen, M.A., Shah, N.H.: Building a biomedical ontology recommender web service. J. Biomed. Semant. 1(S1), 1 (2010)

    Article  Google Scholar 

  7. Lossio-Ventura, J.A., Jonquet, C., Roche, M., Teisseire, M.: Biotex: a system for biomedical terminology extraction, ranking, and validation. In: 13th International Semantic Web Conference (2014)

    Google Scholar 

  8. Maedche, A., Motik, B., Stojanovic, L., Studer, R., Volz, R.: An infrastructure for searching, reusing and evolving distributed ontologies. In: Proceedings of the 12th International Conference on World Wide Web, WWW 2003, pp. 439–448. ACM, New York (2003)

    Google Scholar 

  9. Mejino Jr., J.L., Rubin, D.L., Brinkley, J.F.: FMA-RadLex: an application ontology of radiological anatomy derived from the foundational model of anatomy reference ontology. In: AMIA Annual Symposium Proceedings, vol. 2008, p. 465. American Medical Informatics Association (2008)

    Google Scholar 

  10. Noy, N.F., Shah, N.H., Whetzel, P.L., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D.L., Storey, M.-A., Chute, C.G., et al.: Bioportal: ontologies and integrated data resources at the click of a mouse. Nucleic acids research, pp. W170–W173 (2009)

    Google Scholar 

  11. Russ, T., Valente, A., MacGregor, R., Swartout, W.: Practical experiences in trading off ontology usability and reusability. In: Proceedings of the 12th Workshop on Knowledge Acquisition, Modeling and Management (KAW 1999), pp. 16–21 (1999)

    Google Scholar 

  12. Shah, T., Rabhi, F., Ray, P.: OSHCO: a cross-domain ontology for semantic interoperability across medical and oral health domains. In: 2013 IEEE 15th International Conference on e-Health Networking, Applications Services (Healthcom), pp. 460–464, October 2013

    Google Scholar 

  13. Shah, T., Rabhi, F., Ray, P., Taylor, K.: A guiding framework for ontology reuse in the biomedical domain. In: 2014 47th Hawaii International Conference on System Sciences (HICSS), pp. 2878–2887. IEEE (2014)

    Google Scholar 

  14. Simperl, E.: Reusing ontologies on the semantic web: a feasibility study. Data knowl. Eng. 68(10), 905–925 (2009)

    Article  Google Scholar 

  15. Uschold, M., Clark, P., Healy, M., Williamson, K., Woods, S.: An experiment in ontology reuse. In: Proceedings of the 11th Knowledge Acquisition Workshop (1998)

    Google Scholar 

  16. Zulkarnain, N.Z., Crofts, G., Meziane, F.: An architecture to support ultrasound report generation and standardisation. In: Proceedings of the International Conference on Health Informatics, pp. 508–513 (2015)

    Google Scholar 

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Author information

Authors and Affiliations

  1. School of Computing, Science and Engineering, Informatics Research Centre, University of Salford, Salford, M5 4WT, UK

    Nur Zareen Zulkarnain & Farid Meziane

  2. School of Health Science, University of Salford, Salford, M6 6PU, UK

    Gillian Crofts

Authors
  1. Nur Zareen Zulkarnain
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  2. Farid Meziane
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  3. Gillian Crofts
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Corresponding author

Correspondence to Nur Zareen Zulkarnain .

Editor information

Editors and Affiliations

  1. ConservatoireNational desArts et Métiers, Paris, France

    Elisabeth Métais

  2. University of Salford, Salford, United Kingdom

    Farid Meziane

  3. University of Salford, Salford, United Kingdom

    Mohamad Saraee

  4. Oakland University, Rochester, Michigan, USA

    Vijayan Sugumaran

  5. University of Salford, Salford, United Kingdom

    Sunil Vadera

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© 2016 Springer International Publishing Switzerland

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Zulkarnain, N.Z., Meziane, F., Crofts, G. (2016). A Methodology for Biomedical Ontology Reuse. In: Métais, E., Meziane, F., Saraee, M., Sugumaran, V., Vadera, S. (eds) Natural Language Processing and Information Systems. NLDB 2016. Lecture Notes in Computer Science(), vol 9612. Springer, Cham. https://doi.org/10.1007/978-3-319-41754-7_1

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  • DOI: https://doi.org/10.1007/978-3-319-41754-7_1

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-41753-0

  • Online ISBN: 978-3-319-41754-7

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