| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
Journal of the American Medical Informatics Association, Vol 1, 161-174, Copyright © 1994 by American Medical Informatics Association
ARTICLES |
C Friedman, PO Alderson, JH Austin, JJ Cimino and SB Johnson
Columbia University, New York, NY, USA.
OBJECTIVE: Development of a general natural-language processor that identifies clinical information in narrative reports and maps that information into a structured representation containing clinical terms. DESIGN: The natural-language processor provides three phases of processing, all of which are driven by different knowledge sources. The first phase performs the parsing. It identifies the structure of the text through use of a grammar that defines semantic patterns and a target form. The second phase, regularization, standardizes the terms in the initial target structure via a compositional mapping of multi- word phrases. The third phase, encoding, maps the terms to a controlled vocabulary. Radiology is the test domain for the processor and the target structure is a formal model for representing clinical information in that domain. MEASUREMENTS: The impression sections of 230 radiology reports were encoded by the processor. Results of an automated query of the resultant database for the occurrences of four diseases were compared with the analysis of a panel of three physicians to determine recall and precision. RESULTS: Without training specific to the four diseases, recall and precision of the system (combined effect of the processor and query generator) were 70% and 87%. Training of the query component increased recall to 85% without changing precision.
This article has been cited by other articles:
 |
|
 |
|
  H. Xu, P. D. Stetson, and C. Friedman Methods for Building Sense Inventories of Abbreviations in Clinical Notes J. Am. Med. Inform. Assoc., January 1, 2009; 16(1): 103 - 108. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Uzuner, X. Zhang, and T. Sibanda Machine Learning and Rule-based Approaches to Assertion Classification J. Am. Med. Inform. Assoc., January 1, 2009; 16(1): 109 - 115. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Rodriguez-Esteban, P. M. Roberts, and M. E. Crawford Identifying and classifying biomedical perturbations in text Nucleic Acids Res., December 12, 2008; (2008) gkn986v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. J. Friedlin and C. J. McDonald A Software Tool for Removing Patient Identifying Information from Clinical Documents J. Am. Med. Inform. Assoc., September 1, 2008; 15(5): 601 - 610. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. A. Dang, M. K. Kalra, M. A. Blake, T. J. Schultz, E. F. Halpern, and K. J. Dreyer Extraction of Recommendation Features in Radiology with Natural Language Processing: Exploratory Study Am. J. Roentgenol., August 1, 2008; 191(2): 313 - 320. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. W. D'Avolio and A. A.T. Bui The Clinical Outcomes Assessment Toolkit: A Framework to Support Automated Clinical Records-based Outcomes Assessment and Performance Measurement Research J. Am. Med. Inform. Assoc., May 1, 2008; 15(3): 333 - 340. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. W. D'Avolio, M. S. Litwin, S. O. Rogers Jr., and A. A.T. Bui Facilitating Clinical Outcomes Assessment through the Automated Identification of Quality Measures for Prostate Cancer Surgery J. Am. Med. Inform. Assoc., May 1, 2008; 15(3): 341 - 348. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. S. Chen, G. Hripcsak, H. Xu, M. Markatou, and C. Friedman Automated Acquisition of Disease Drug Knowledge from Biomedical and Clinical Documents: An Initial Study J. Am. Med. Inform. Assoc., January 1, 2008; 15(1): 87 - 98. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Uzuner, I. Goldstein, Y. Luo, and I. Kohane Identifying Patient Smoking Status from Medical Discharge Records J. Am. Med. Inform. Assoc., January 1, 2008; 15(1): 14 - 24. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Zhou, S. Parsons, and G. Hripcsak The Evaluation of a Temporal Reasoning System in Processing Clinical Discharge Summaries J. Am. Med. Inform. Assoc., January 1, 2008; 15(1): 99 - 106. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Huang and H. J. Lowe A Novel Hybrid Approach to Automated Negation Detection in Clinical Radiology Reports J. Am. Med. Inform. Assoc., May 1, 2007; 14(3): 304 - 311. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Friedman, T. Borlawsky, L. Shagina, H. R. Xing, and Y. A. Lussier Bio-Ontology and text: bridging the modeling gap Bioinformatics, October 1, 2006; 22(19): 2421 - 2429. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. V.S. Pakhomov, J. D. Buntrock, and C. G. Chute Automating the Assignment of Diagnosis Codes to Patient Encounters Using Example-based and Machine Learning Techniques J. Am. Med. Inform. Assoc., September 1, 2006; 13(5): 516 - 525. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Kukafka, M. E. Bales, A. Burkhardt, and C. Friedman Human and Automated Coding of Rehabilitation Discharge Summaries According to the International Classification of Functioning, Disability, and Health J. Am. Med. Inform. Assoc., September 1, 2006; 13(5): 508 - 515. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Y. Sun and Y. Sun A System for Automated Lexical Mapping J. Am. Med. Inform. Assoc., May 1, 2006; 13(3): 334 - 343. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Hazlehurst, H. R. Frost, D. F. Sittig, and V. J. Stevens MediClass: A System for Detecting and Classifying Encounter-based Clinical Events in Any Electronic Medical Record J. Am. Med. Inform. Assoc., September 1, 2005; 12(5): 517 - 529. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. B. Melton and G. Hripcsak Automated Detection of Adverse Events Using Natural Language Processing of Discharge Summaries J. Am. Med. Inform. Assoc., July 1, 2005; 12(4): 448 - 457. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Huang, H. J. Lowe, D. Klein, and R. J. Cucina Improved Identification of Noun Phrases in Clinical Radiology Reports Using a High-Performance Statistical Natural Language Parser Augmented with the UMLS Specialist Lexicon J. Am. Med. Inform. Assoc., May 1, 2005; 12(3): 275 - 285. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Tao, C. Friedman, and Y. A. Lussier Visualizing information across multidimensional post-genomic structured and textual databases Bioinformatics, April 15, 2005; 21(8): 1659 - 1667. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. J. Thomas, H. Ouellette, E. F. Halpern, and D. I. Rosenthal Automated Computer-Assisted Categorization of Radiology Reports Am. J. Roentgenol., February 1, 2005; 184(2): 687 - 690. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. J. Dreyer, M. K. Kalra, M. M. Maher, A. M. Hurier, B. A. Asfaw, T. Schultz, E. F. Halpern, and J. H. Thrall Application of Recently Developed Computer Algorithm for Automatic Classification of Unstructured Radiology Reports: Validation Study Radiology, February 1, 2005; 234(2): 323 - 329. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Chen, H. Liu, and C. Friedman Gene name ambiguity of eukaryotic nomenclatures Bioinformatics, January 15, 2005; 21(2): 248 - 256. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Friedman, L. Shagina, Y. Lussier, and G. Hripcsak Automated Encoding of Clinical Documents Based on Natural Language Processing J. Am. Med. Inform. Assoc., September 1, 2004; 11(5): 392 - 402. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Huang, H. J. Lowe, and W. R. Hersh A Pilot Study of Contextual UMLS Indexing to Improve the Precision of Concept-based Representation in XML-structured Clinical Radiology Reports J. Am. Med. Inform. Assoc., November 1, 2003; 10(6): 580 - 587. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. B. Wilcox and G. Hripcsak The Role of Domain Knowledge in Automating Medical Text Report Classification J. Am. Med. Inform. Assoc., July 1, 2003; 10(4): 330 - 338. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. G. Mutalik, A. Deshpande, and P. M. Nadkarni Use of General-purpose Negation Detection to Augment Concept Indexing of Medical Documents: A Quantitative Study Using the UMLS J. Am. Med. Inform. Assoc., November 1, 2001; 8(6): 598 - 609. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. K. Taira, S. G. Soderland, and R. M. Jakobovits Automatic Structuring of Radiology Free-Text Reports RadioGraphics, January 1, 2001; 21(1): 237 - 245. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Fiszman, W. W. Chapman, D. Aronsky, R. S. Evans, and P. J. Haug Automatic Detection of Acute Bacterial Pneumonia from Chest X-ray Reports J. Am. Med. Inform. Assoc., November 1, 2000; 7(6): 593 - 604. [Abstract] [Full Text]
|
|
|
|
|
|
S. B. Johnson A Semantic Lexicon for Medical Language Processing J. Am. Med. Inform. Assoc., May 1, 1999; 6(3): 205 - 218. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Friedman, G. Hripcsak, L. Shagina, and H. Liu Representing Information in Patient Reports Using Natural Language Processing and the Extensible Markup Language J. Am. Med. Inform. Assoc., January 1, 1999; 6(1): 76 - 87. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. F. Cooper and R. A. Miller An Experiment Comparing Lexical and Statistical Methods for Extracting MeSH Terms from Clinical Free Text J. Am. Med. Inform. Assoc., January 1, 1998; 5(1): 62 - 75. [Abstract] [Full Text]
|
|
|
|
|
|
P. L. Miller Aspects of IAIMS Implementation That Require Further Research J. Am. Med. Inform. Assoc., April 1, 1997; 4(2): S52 - S61. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
