Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Oct;51:272-9.
doi: 10.1016/j.jbi.2014.06.006. Epub 2014 Jun 26.

Complex Epilepsy Phenotype Extraction From Narrative Clinical Discharge Summaries

Affiliations
Free PMC article

Complex Epilepsy Phenotype Extraction From Narrative Clinical Discharge Summaries

Licong Cui et al. J Biomed Inform. .
Free PMC article

Abstract

Epilepsy is a common serious neurological disorder with a complex set of possible phenotypes ranging from pathologic abnormalities to variations in electroencephalogram. This paper presents a system called Phenotype Exaction in Epilepsy (PEEP) for extracting complex epilepsy phenotypes and their correlated anatomical locations from clinical discharge summaries, a primary data source for this purpose. PEEP generates candidate phenotype and anatomical location pairs by embedding a named entity recognition method, based on the Epilepsy and Seizure Ontology, into the National Library of Medicine's MetaMap program. Such candidate pairs are further processed using a correlation algorithm. The derived phenotypes and correlated locations have been used for cohort identification with an integrated ontology-driven visual query interface. To evaluate the performance of PEEP, 400 de-identified discharge summaries were used for development and an additional 262 were used as test data. PEEP achieved a micro-averaged precision of 0.924, recall of 0.931, and F1-measure of 0.927 for extracting epilepsy phenotypes. The performance on the extraction of correlated phenotypes and anatomical locations shows a micro-averaged F1-measure of 0.856 (Precision: 0.852, Recall: 0.859). The evaluation demonstrates that PEEP is an effective approach to extracting complex epilepsy phenotypes for cohort identification.

Keywords: Cohort identification; Epilepsy; Information extraction.

Figures

Figure 1
Figure 1
Epileptogenic Zone, Seizure Semiology, Lateralizing Sign captured in an orignal discharge summary.
Figure 2
Figure 2
Interictal and Ictal EEG findings captured in a source discharge summary.
Figure 3
Figure 3
Pipeline of the Phenotype Exaction in Epilepsy (PEEP) system.
Figure 4
Figure 4
Baseline MetaMapRENER to generate phenotype and anatomical location candidate pairs.
Figure 5
Figure 5
Correlation algorithm to identify pairs of phenotypes and anatomical locations for a document.

Similar articles

See all similar articles

Cited by 9 articles

See all "Cited by" articles

Publication types

Feedback