Skip to main content
SpringerLink
Log in

Automatic Maintenance of Semantic Annotations

  • Conference paper
  • First Online:
Knowledge Engineering and Knowledge Management (EKAW 2016)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 10180))

Included in the following conference series:

Abstract

Biomedical Knowledge Organization Systems (KOS) play a key role in enriching information in order to make them machine understandable. This is done through semantic annotation which consists in the association of concept labels taken from KOS with pieces of digital information taken from the source to annotate. However, the dynamic nature of these KOS directly impacts on the annotations, creating a mismatch between the enriched data and the concept labels. This PhD study addresses the evolution of semantic annotations due to the evolution of KOS and aims at proposing an approach to automatize the maintenance of semantic annotations.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    W3C Web Annotation Data Model.

  2. 2.

    LIFE project.

  3. 3.

    Memento protocol.

References

  1. Arnold, P., Rahm, E.: Semantic enrichment of ontology mappings: a linguistic-based approach. In: Catania, B., Guerrini, G., Pokorný, J. (eds.) ADBIS 2013. LNCS, vol. 8133, pp. 42–55. Springer, Heidelberg (2013). doi:10.1007/978-3-642-40683-6_4

    Chapter  Google Scholar 

  2. Cardoso, S.D., Pruski, C., Silveira, M., Lin, Y.-C., Groß, A., Rahm, E., Reynaud-Delaître, C.: Leveraging the impact of ontology evolution on semantic annotations. In: Blomqvist, E., Ciancarini, P., Poggi, F., Vitali, F. (eds.) EKAW 2016. LNCS, vol. 10024, pp. 68–82. Springer, Cham (2016). doi:10.1007/978-3-319-49004-5_5

    Chapter  Google Scholar 

  3. Da Silveira, M., Dos Reis, J.C., Pruski, C.: Management of dynamic biomedical terminologies: current status and future challenges. Yearb. Med. Inform. 10(1), 125–133 (2015)

    Article  Google Scholar 

  4. Dos Reis, J.C., Pruski, C., Da Silveira, M., Reynaud-Delaître, C.: Dykosmap: a framework for mapping adaptation between biomedical knowledge organization systems. J. Biomed. Inform. 55, 153–173 (2015)

    Article  Google Scholar 

  5. Eilbeck, K., Moore, B., Holt, C., Yandell, M.: Quantitative measures for the management and comparison of annotated genomes. BMC Bioinform. 10(1), 67 (2009)

    Article  Google Scholar 

  6. Frost, H.R., Moore, J.H.: Optimization of gene set annotations via entropy minimization over variable clusters (emvc). Bioinformatics 30(12), 1698–1706 (2014). (Oxford, England)

    Article  Google Scholar 

  7. Funk, C., Baumgartner, W., Garcia, B., Roeder, C., Bada, M., Cohen, K.B., Hunter, L.E., Verspoor, K.: Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinform. 15(1), 1–29 (2014)

    Article  Google Scholar 

  8. Groß, A., Hartung, M., Prüfer, K., Kelso, J., Rahm, E.: Impact of ontology evolution on functional analyses. Bioinformatics 28(20), 2671–2677 (2012)

    Article  Google Scholar 

  9. Hartung, M., Gross, A., Rahm, E.: Conto-diff: generation of complex evolution mappings for life science ontologies. J. Biomed. Inform. 46, 15–32 (2013)

    Article  Google Scholar 

  10. Hodge, G.: Systems of knowledge organization for digital libraries: beyond traditional authority files. Reports - Descriptive (2000)

    Google Scholar 

  11. Lowe, H.J., Barnett, G.O.: Understanding and using the medical subject headings (mesh) vocabulary to perform literature searches. JAMA 271(14), 1103–1108 (1994)

    Article  Google Scholar 

  12. Luong, P.H., Dieng-Kuntz, R.: A rule-based approach for semantic annotation evolution in the CoSWEM system. In: Koné, M., Lemire, D. (eds.) Canadian Semantic Web. Semantic Web and Beyond, pp. 103–120. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  13. Mowery, D.L., Jordan, P.W., Wiebe, J., Harkema, H., Chapman, W.W.: Semantic annotation of clinical events for generating a problem list. In: AMIA Annual Symposium proceedings/AMIA Symposium, AMIA Symposium 2013, pp. 1032–1041 (2013)

    Google Scholar 

  14. Park, Y.R., Kim, J.J.H., Lee, H.W., Yoon, Y.J.: GOChase-II: correcting semantic inconsistencies from gene ontology-based annotations for gene products. BMC Bioinform. 12(Suppl 1), S40 (2011)

    Google Scholar 

  15. Traverso-Ribón, I., Vidal, M.-E., Palma, G.: AnnEvol: an evolutionary framework to description ontology-based annotations. In: Ashish, N., Ambite, J.-L. (eds.) DILS 2015. LNCS, vol. 9162, pp. 87–103. Springer, Cham (2015). doi:10.1007/978-3-319-21843-4_7

    Chapter  Google Scholar 

  16. Uren, V., Cimiano, P., Iria, J., Handschuh, S., Vargas-Vera, M., Motta, E., Ciravegna, F.: Semantic annotation for knowledge management: requirements and a survey of the state of the art. Web Semant. Sci. Serv. Agents World Wide Web 4(1), 14–28 (2006)

    Article  Google Scholar 

Download references

Acknowledgment

The author would like to thank both National Research Fund (FNR), who supported this work, and his advisors: Cédric Pruski, Marcos Da Silveira and Chantal Reynaud-Delaître.

Author information

Authors and Affiliations

  1. LIST, Luxembourg Institute of Science and Technology, 5, avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg

    Silvio Domingos Cardoso

  2. LRI, Univ. Paris-Sud, CNRS, Université Paris-Saclay, Orsay, France

    Silvio Domingos Cardoso

Authors
  1. Silvio Domingos Cardoso
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Silvio Domingos Cardoso .

Editor information

Editors and Affiliations

  1. University of Bologna , Bologna, Italy

    Paolo Ciancarini

  2. University of Bologna , Bologna, Italy

    Francesco Poggi

  3. Stanford University , Palo Alto, California, USA

    Matthew Horridge

  4. Lancaster University , Lancaster, United Kingdom

    Jun Zhao

  5. Garvan Institute of Medical Research , Darlinghurst, New South Wales, Australia

    Tudor Groza

  6. Universidad Politecnica de Madrid , Boadilla del Monte, Spain

    Mari Carmen Suarez-Figueroa

  7. The Open University , Milton Keynes, United Kingdom

    Mathieu d'Aquin

  8. STLab ISTC-CNR , Rome, Italy

    Valentina Presutti

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this paper

Cite this paper

Cardoso, S.D. (2017). Automatic Maintenance of Semantic Annotations. In: Ciancarini, P., et al. Knowledge Engineering and Knowledge Management. EKAW 2016. Lecture Notes in Computer Science(), vol 10180. Springer, Cham. https://doi.org/10.1007/978-3-319-58694-6_33

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-58694-6_33

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-58693-9

  • Online ISBN: 978-3-319-58694-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation