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Natural Language Processing in Biomedicine: A Unified System Architecture Overview

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Clinical Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1168))

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.

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Abbreviations

BNF:

Backus–Naur form

cTAKES:

Clinical Text Analysis and Knowledge Extraction System

EMR:

Electronic medical record

GATE:

General Architecture for Text Engineering

LSP:

Linguistic String Project

MedLee:

Medical Language Extraction and Encoding System

MLP:

Medical language processor

NER:

Named entity recognition

NLP:

Natural language processing

POS:

Part of speech

UIMA:

Unstructured Information Management Architecture

UMLS:

Unified Medical Language System

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Acknowledgements

S.D. and L.O.M. were funded in part by NIH grants U54HL108460 and UH3HL108785.

Author information

Authors and Affiliations

  1. Division of Biomedical Informatics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA

    Son Doan & Lucila Ohno-Machado

  2. Division of Behavioral Medicine, University of California, San Diego, La Jolla, CA, USA

    Mike Conway

  3. Department of Computer Science, Posts and Telecommunications Institute of Technology, Hanoi, Vietnam

    Tu Minh Phuong

Authors
  1. Son Doan
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  2. Mike Conway
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  3. Tu Minh Phuong
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  4. Lucila Ohno-Machado
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Corresponding author

Correspondence to Son Doan .

Editor information

Editors and Affiliations

  1. Department of Medical Genomics, Royal Prince Alfred Hospital and Sydney Medical School, University of Sydney, Camperdown, Australia

    Ronald Trent

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Doan, S., Conway, M., Phuong, T.M., Ohno-Machado, L. (2014). Natural Language Processing in Biomedicine: A Unified System Architecture Overview. In: Trent, R. (eds) Clinical Bioinformatics. Methods in Molecular Biology, vol 1168. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0847-9_16

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  • DOI: https://doi.org/10.1007/978-1-4939-0847-9_16

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0846-2

  • Online ISBN: 978-1-4939-0847-9

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