Advertisement

Towards Automatic Patient Eligibility Assessment: From Free-Text Criteria to Queries

  • Krystyna Milian
  • Annette ten Teije
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7885)

Abstract

The presented work contributes to bridging the representation of clinical trials and patient data. Our ultimate goal is to support the trial recruitment, by automating the process of formalizing eligibility criteria of clinical trials, starting from free text of criteria and leading to a computable representation. This paper discusses the final step in the pipeline i.e. generating queries from the structured representation consisting of detected patterns and semantic entities. The queries allow to evaluate patient eligibility for a given trial. To enable easy incorporation of semantic reasoning using medical ontologies, we built the queries in SPARQL and use the OWL representation of one the standards for patient data storage - openEHR archetypes and NCI ontology. The available public repository of archetypes and the expressivity of SPARQL allow to create template queries for the majority of patterns.

Keywords

query generation semantic reasoning clinical trials medical ontologies patient data representation 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Milian, K., Bucur, A., ten Teije, A.: Formalization of clinical trial eligibility criteria: Evaluation of a pattern-based approach. In: BIBM (2012)Google Scholar
  2. 2.
    Milian, K., Bucur, A., van Harmelen, F.: Building a Library of Eligibility Criteria to Support Design of Clinical Trials. In: ten Teije, A., Völker, J., Handschuh, S., Stuckenschmidt, H., d’Acquin, M., Nikolov, A., Aussenac-Gilles, N., Hernandez, N. (eds.) EKAW 2012. LNCS, vol. 7603, pp. 327–336. Springer, Heidelberg (2012)CrossRefGoogle Scholar
  3. 3.
    Cunningham, H., Maynard, D., Bontcheva, K., Tablan, V., Aswani, N., Roberts, I., Gorrell, G., Funk, A., Roberts, A., Damljanovic, D., Heitz, T., Greenwood, M.A., Saggion, H., Petrak, J., Li, Y., Peters, W.: Text Processing with GATE (2011)Google Scholar
  4. 4.
    Aronson, A.R.: MetaMap: Mapping Text to the UMLS Metathesaurus. In: AMIA, pp. 17–21 (2001)Google Scholar
  5. 5.
    Lezcano, L., Sicilia, M.-A., Rodríguez-Solano, C.: Integrating reasoning and clinical archetypes using OWL ontologies and SWRL rules. JBI 44(2), 343–353 (2011)Google Scholar
  6. 6.
    Dentler, K., ten Teije, A., Cornet, R., de Keizer, N.: Semantic Integration of Patient Data and Quality Indicators Based on openEHR Archetypes. In: Lenz, R., Miksch, S., Peleg, M., Reichert, M., Riaño, D., ten Teije, A. (eds.) ProHealth 2012/KR4HC 2012. LNCS, vol. 7738, pp. 85–97. Springer, Heidelberg (2013)CrossRefGoogle Scholar
  7. 7.
    Milian, K., Bucur, A., van Harmelen, F., ten Teije, A.: Identifying most relevant concepts to describe clinical trial eligibility criteria. Health Inf. (2013)Google Scholar
  8. 8.
    Weng, C., Wu, X., Luo, Z., Boland, M.R., Theodoratos, D., Johnson, S.B.: EliXR: An Approach to Eligibility Criteria Extraction and Representation. JAMIAGoogle Scholar
  9. 9.
    Boland, M., Tu, S., Carini, S., Sim, I., Weng, C.: EliXR-TIME: A Temporal Knowledge Representation for Clinical Research Eligibility Criteria. In: AMIA (2012)Google Scholar
  10. 10.
    Tu, S.W., Peleg, M., Carini, S., Bobak, M., Ross, J., Rubin, D., Sim, I.: A practical method for transforming free-text eligibility criteria into computable criteria. JBI 44(2), 239–250 (2011)Google Scholar
  11. 11.
    Besana, P., Cuggia, M., Zekri, O., Bourde, A., Burgun, A.: Using semantic web technologies for clinical trial recruitment. In: Patel-Schneider, P.F., Pan, Y., Hitzler, P., Mika, P., Zhang, L., Pan, J.Z., Horrocks, I., Glimm, B., et al. (eds.) ISWC 2010, Part II. LNCS, vol. 6497, pp. 34–49. Springer, Heidelberg (2010)CrossRefGoogle Scholar
  12. 12.
    Patel, C., Cimino, J., Dolby, J., Fokoue, A., Kalyanpur, A., Kershenbaum, A., Ma, L., Schonberg, E., Srinivas, K.: Matching patient records to clinical trials using ontologies. In: Aberer, K., et al. (eds.) ISWC/ASWC 2007. LNCS, vol. 4825, pp. 816–829. Springer, Heidelberg (2007)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Krystyna Milian
    • 1
  • Annette ten Teije
    • 1
  1. 1.VU University Amsterdamthe Netherlands

Personalised recommendations