Skip to main content
SpringerLink
Log in

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

  • Conference paper
Artificial Intelligence in Medicine (AIME 2013)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 7885))

Included in the following conference series:

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.

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 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  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. 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)

    Chapter  Google Scholar 

  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. Aronson, A.R.: MetaMap: Mapping Text to the UMLS Metathesaurus. In: AMIA, pp. 17–21 (2001)

    Google Scholar 

  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. 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)

    Chapter  Google Scholar 

  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. Weng, C., Wu, X., Luo, Z., Boland, M.R., Theodoratos, D., Johnson, S.B.: EliXR: An Approach to Eligibility Criteria Extraction and Representation. JAMIA

    Google Scholar 

  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. 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. 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)

    Chapter  Google Scholar 

  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)

    Chapter  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. VU University Amsterdam, the Netherlands

    Krystyna Milian & Annette ten Teije

Authors
  1. Krystyna Milian
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Annette ten Teije
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Academic Medical Center, Dept. of Medical Informatics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands

    Niels Peek

  2. Dept. of Information Egineering and Communications, University of Murcia, Campus de Espinardo, 30100, Espinardo, Murcia, Spain

    Roque Marín Morales

  3. Department of Information Systems, University of Haifa, Rabin Bldg, Haifa, Israel

    Mor Peleg

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Milian, K., ten Teije, A. (2013). Towards Automatic Patient Eligibility Assessment: From Free-Text Criteria to Queries. In: Peek, N., Marín Morales, R., Peleg, M. (eds) Artificial Intelligence in Medicine. AIME 2013. Lecture Notes in Computer Science(), vol 7885. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38326-7_12

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-38326-7_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-38325-0

  • Online ISBN: 978-3-642-38326-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation