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Extracting COVID-19 diagnoses and symptoms from clinical text: A new annotated corpus and neural event extraction framework

, Mari Ostendorf, Matthew Thompson, Meliha Yetisgen
Published: 1 May 2021
Journal of Biomedical Informatics , Volume 117, pp 103761-103761; doi:10.1016/j.jbi.2021.103761

Abstract: Coronavirus disease 2019 (COVID-19) is a global pandemic. Although much has been learned about the novel coronavirus since its emergence, there are many open questions related to tracking its spread, describing symptomology, predicting the severity of infection, and forecasting healthcare utilization. Free-text clinical notes contain critical information for resolving these questions. Data-driven, automatic information extraction models are needed to use this text-encoded information in large-scale studies. This work presents a new clinical corpus, referred to as the COVID-19 Annotated Clinical Text (CACT) Corpus, which comprises 1,472 notes with detailed annotations characterizing COVID-19 diagnoses, testing, and clinical presentation. We introduce a span-based event extraction model that jointly extracts all annotated phenomena, achieving high performance in identifying COVID-19 and symptom events with associated assertion values (0.83–0.97 F1 for events and 0.73–0.79 F1 for assertions). Our span-based event extraction model outperforms an extractor built on MetaMapLite for the identification of symptoms with assertion values. In a secondary use application, we predicted COVID-19 test results using structured patient data (e.g. vital signs and laboratory results) and automatically extracted symptom information, to explore the clinical presentation of COVID-19. Automatically extracted symptoms improve COVID-19 prediction performance, beyond structured data alone.
Keywords: COVID-19 / Coronavirus / Machine learning / Natural language processing / Information extraction

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