TY - JOUR
T1 - Evaluation of Clinical Text Segmentation to Facilitate Cohort Retrieval
AU - Edinger, Tracy
AU - Demner-Fushman, Dina
AU - Cohen, Aaron M.
AU - Bedrick, Steven
AU - Hersh, William
PY - 2017
Y1 - 2017
N2 - 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.
AB - 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.
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M3 - Article
C2 - 29854131
AN - SCOPUS:85058764771
SN - 1559-4076
VL - 2017
SP - 660
EP - 669
JO - AMIA ... Annual Symposium proceedings. AMIA Symposium
JF - AMIA ... Annual Symposium proceedings. AMIA Symposium
ER -