Evaluation of Clinical Text Segmentation to Facilitate Cohort Retrieval

Tracy Edinger, Dina Demner-Fushman, Aaron M. Cohen, Steven Bedrick, William Hersh

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


Objective: Secondary use of electronic health record (EHR) data is enabled by accurate and complete retrieval of the relevant patient cohort, which requires searching both structured and unstructured data. Clinical text poses difficulties to searching, although chart notes incorporate structure that may facilitate accurate retrieval. Methods: We developed rules identifying clinical document sections, which can be indexed in search engines that allow faceted searches, such as Lucene or Essie, an NLM search engine. We developed 22 clinical cohorts and two queries for each cohort, one utilizing section headings and the other searching the whole document. We manually evaluated a subset of retrieved documents to compare query performance. Results: Querying by section had lower recall than whole-document queries (0.83 vs 0.95), higher precision (0.73 vs 0.54), and higher F1 (0.78 vs 0.69). Conclusion: This evaluation suggests that searching specific sections may improve precision under certain conditions and often with loss of recall.

Original languageEnglish (US)
Pages (from-to)660-669
Number of pages10
JournalAMIA ... Annual Symposium proceedings. AMIA Symposium
StatePublished - 2017

ASJC Scopus subject areas

  • Medicine(all)


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