Natural language processing in biomedicine: a unified system architecture overview.

TitleNatural language processing in biomedicine: a unified system architecture overview.
Publication TypeJournal Article
Year of Publication2014
AuthorsDoan, S, Conway, M, Phuong, TMinh, Ohno-Machado, L
JournalMethods Mol Biol
Date Published2014
iDASH CategoryNatural Language Processing
Abstract<p>In contemporary electronic medical records much of the clinically important data-signs and symptoms, symptom severity, disease status, etc.-are not provided in structured data fields but rather are encoded in clinician-generated narrative text. Natural language processing (NLP) provides a means of unlocking this important data source for applications in clinical decision support, quality assurance, and public health. This chapter provides an overview of representative NLP systems in biomedicine based on a unified architectural view. A general architecture in an NLP system consists of two main components: background knowledge that includes biomedical knowledge resources and a framework that integrates NLP tools to process text. Systems differ in both components, which we review briefly. Additionally, the challenge facing current research efforts in biomedical NLP includes the paucity of large, publicly available annotated corpora, although initiatives that facilitate data sharing, system evaluation, and collaborative work between researchers in clinical NLP are starting to emerge.</p>
Alternate JournalMethods Mol. Biol.
PubMed ID24870142
Grant ListU54HL108460 / HL / NHLBI NIH HHS / United States
UH3HL108785 / HL / NHLBI NIH HHS / United States