Skip to main content
SpringerLink
Log in
SpringerLink
Log in

Using Semantic Web Technologies to Underpin the SNOMED CT Query Language

  • Conference paper
  • First Online:
Artificial Intelligence XXXIV (SGAI 2017)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 10630))

Abstract

SNOMED International is working on a query language specification for SNOMED CT, which we call here SCTQL. SNOMED CT is the leading terminology for use in Electronic Health Records (EHRs). SCTQL can contribute to effective retrieval and reuse of clinical information within EHRs. This paper analyses the functional capabilities needed for SCTQL and proposes two implementations that rely on ontological representations of SNOMED CT: one based on the W3C SPARQL 1.1 query language and another based on the OWL API. The paper reports the performance and correctness of both implementations as well as highlights their benefits and drawbacks.

D. Tsarkov—Now at Google International GmbH, Brandschenkestrasse 110, 8002 Zürich, Switzerland.

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

References

  1. SNOMED International. http://www.snomed.org

  2. Wardle, M., Spencer, A.: Implementation of SNOMED CT in an online clinical database. Future Hosp. J. 4, 126–130 (2017)

    Google Scholar 

  3. NLM Tools for EHR Certification and Meaningful Use. http://www.nlm.nih.gov/healthit/meaningful_use.html

  4. Lee, D., Cornet, R., Lau, F., de Keizer, N.: A survey of SNOMED CT implementations. J. Biomed. Inform. 46, 87–96 (2013)

    Article  Google Scholar 

  5. SNOMED CT Worldwide. http://www.snomed.org/snomed-ct/snomed-ct-worldwide

  6. Lee, D.H., Lau, F.Y., Quan, H.: A method for encoding clinical datasets with SNOMED CT. BMC Med. Inf. Decis. Making 10, 53 (2010)

    Article  Google Scholar 

  7. Clinical Observations Recording and Encoding (CORE) Problem List Subset of SNOMED CT. http://www.nlm.nih.gov/research/umls/Snomed/core_subset.html

  8. SNOMED CT Nursing Problem List Subset. http://www.nlm.nih.gov/research/umls/Snomed/nursing_problemlist_subset.html

  9. Veterans Health Administration and Kaiser Permanente (VA/KP) Problem List subset. http://www.nlm.nih.gov/research/umls/Snomed/snomed_problem_list.html

  10. UK SNOMED CT subsets. http://isd.digital.nhs.uk/trud3/user/guest/group/0/pack/40

  11. Hansen, D.P., Giermanski, M., Dujmovic, M., Passenger, J., Lawley, M.J.: Building SNOMED CT reference sets for use as interface terminologies. Electron. J. Health Inf. 6, 1 (2011)

    Article  Google Scholar 

  12. SNOMED Technical Implementation Guide. http://confluence.ihtsdotools.org/display/DOCTIG/Technical+Implementation+Guide

  13. Data Analytics with SNOMED CT. http://snomed.org/analytics

  14. Raghupathi, W., Raghupathi, V.: Big data analytics in healthcare: promise and potential. Health Inf. Sci. Syst. 2, 3 (2014)

    Article  Google Scholar 

  15. SNOMED CT Query Language. http://confluence.ihtsdotools.org/display/SLPG/SNOMED+CT+Query+Language

  16. SNOMED CT Expression Constraint Language. http://confluence.ihtsdotools.org/display/DOCECL/Expression+Constraint+Language+-+Specification+and+Guide

  17. SNOMED CT Query Language Specification version 0.8 draft. http://www.cs.man.ac.uk/~rector/temp/SNOMED_TQL_for_comment.doc

  18. SNOMED CT Query Service. http://github.com/IHTSDO/snomed-query-service

  19. OWL 2. http://www.w3.org/TR/owl2-overview/

  20. SPARQL 1.1 query language. http://www.w3.org/TR/sparql11-query/

  21. Horridge, M., Bechhofer, S.: The OWL API: A Java API for OWL ontologies. Seman. Web 2, 11–21 (2011)

    Google Scholar 

  22. Schulz, S., Jansen, L.: Formal ontologies in biomedical knowledge representation. Yearb Med Inform 8, 132–146 (2013)

    Google Scholar 

  23. Baader, F., Horrocks, I., Sattler, U.: Description logics as ontology languages for the semantic web. In: Hutter, D., Stephan, W. (eds.) Mechanizing Mathematical Reasoning. LNCS, vol. 2605, pp. 228–248. Springer, Heidelberg (2005). https://doi.org/10.1007/978-3-540-32254-2_14

    Chapter  Google Scholar 

  24. Berners-Lee, T., Hendler, J., Lassila, O.: The semantic web. Sci. Am. 284, 28–37 (2001)

    Article  Google Scholar 

  25. Antoniou, G., Van Harmelen, F.: A Semantic Web Primer. MIT Press, Cambridge (2004)

    Google Scholar 

  26. Baader, F., Horrocks, I., Lutz, C., Sattler, U.: An Introduction to Description Logic. Cambridge University Press, Cambridge (2017)

    Book  MATH  Google Scholar 

  27. Krötzsch, M.: OWL 2 profiles: an introduction to lightweight ontology languages. In: Eiter, T., Krennwallner, T. (eds.) Reasoning Web 2012. LNCS, vol. 7487, pp. 112–183. Springer, Heidelberg (2012). https://doi.org/10.1007/978-3-642-33158-9_4

    Chapter  Google Scholar 

  28. Wang, Y., Halper, M., Wei, D., Gu, H., Perl, Y., Xu, J., Elhanan, G., Chen, Y., Spackman, K.A., Case, J.T., Hripcsak, G.: Auditing complex concepts of SNOMED using a refined hierarchical abstraction network. J. Biomed. Inform. 45, 1–14 (2012)

    Article  Google Scholar 

  29. Jiang, G., Chute, C.G.: Auditing the semantic completeness of SNOMED CT using formal concept analysis. J. Am. Med. Inform. Assoc. 16, 89–102 (2009)

    Article  Google Scholar 

  30. Horridge, M., Drummond, N., Goodwin, J., Rector, A.L., Stevens, R., Wang, H.: The manchester OWL syntax. In: OWLed, vol. 216 (2006)

    Google Scholar 

  31. Hartel, F.W., de Coronado, S., Dionne, R., Fragoso, G., Golbeck, J.: Modeling a description logic vocabulary for cancer research. J. Biomed. Inform. 38, 114–129 (2005)

    Article  Google Scholar 

  32. Jena ARQ. http://jena.apache.org/documentation/query/

  33. SPARQL 1.1 Entailment Regimes. http://www.w3.org/TR/sparql11-entailment/

  34. Zhang, G.-Q., Bodenreider, O.: Using SPARQL to test for lattices: application to quality assurance in biomedical ontologies. In: Patel-Schneider, P.F., Pan, Y., Hitzler, P., Mika, P., Zhang, L., Pan, J.Z., Horrocks, I., Glimm, B. (eds.) ISWC 2010. LNCS, vol. 6497, pp. 273–288. Springer, Heidelberg (2010). https://doi.org/10.1007/978-3-642-17749-1_18

    Chapter  Google Scholar 

  35. FaCT++. http://owl.man.ac.uk/factplusplus/

  36. ELK. http://www.cs.ox.ac.uk/isg/tools/ELK/

  37. Kim, J.D., Cohen, K.B.: Natural language query processing for SPARQL generation: a prototype system for SNOMED CT. In: BioLINK, pp. 32–38 (2013)

    Google Scholar 

  38. Alonso-Calvo, R., Paraiso-Medina, S., Perez-Rey, D., Alonso-Oset, E., van Stiphout, R., Yu, S., Taylor, M., Buffa, F., Fernandez-Lozano, C., Pazos, A., Maojo, V.: A semantic interoperability approach to support integration of gene expression and clinical data in breast cancer. Comput. Biol. Med. (2017)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Computer Science, The University of Manchester, Manchester, UK

    Mercedes Arguello Casteleiro, Dmitry Tsarkov, Bijan Parsia & Ulrike Sattler

Authors
  1. Mercedes Arguello Casteleiro
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dmitry Tsarkov
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bijan Parsia
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ulrike Sattler
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mercedes Arguello Casteleiro .

Editor information

Editors and Affiliations

  1. University of Portsmouth, Portsmouth, United Kingdom

    Max Bramer

  2. Middlesex University , London, United Kingdom

    Miltos Petridis

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Casteleiro, M.A., Tsarkov, D., Parsia, B., Sattler, U. (2017). Using Semantic Web Technologies to Underpin the SNOMED CT Query Language. In: Bramer, M., Petridis, M. (eds) Artificial Intelligence XXXIV. SGAI 2017. Lecture Notes in Computer Science(), vol 10630. Springer, Cham. https://doi.org/10.1007/978-3-319-71078-5_20

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-71078-5_20

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-71077-8

  • Online ISBN: 978-3-319-71078-5

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation