title: Natural language processing in biomedicine: a unified system architecture overview.
abstract: 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.
authors.affiliation: Division of Biomedical Informatics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA, sodoan@ucsd.edu.
authors.forename: Son
authors.initials: S
authors.lastname: Doan
authors.forename: Mike
authors.initials: M
authors.lastname: Conway
authors.forename: Tu Minh
authors.initials: TM
authors.lastname: Phuong
authors.forename: Lucila
authors.initials: L
authors.lastname: Ohno-Machado
mesh_terms: D020811:Biomedical Technology; D057286:Electronic Health Records; D006801:Humans; D009323:Natural Language Processing