Terminology model discovery using natural language processing and visualization techniques

Medical terminologies are important for unambiguous encoding and exchange of clinical information. The traditional manual method of developing terminology models is time-consuming and limited in the number of phrases that a human developer can examine. In this paper, we present an automated method for developing medical terminology models based on natural language processing (NLP) and information visualization techniques. Surgical pathology reports were selected as the testing corpus for developing a pathology procedure terminology model. The use of a general NLP processor for the medical domain, MedLEE, provides an automated method for acquiring semantic structures from a free text corpus and sheds light on a new high-throughput method of medical terminology model development. The use of an information visualization technique supports the summarization and visualization of the large quantity of semantic structures generated from medical documents. We believe that a general method based on NLP and information visualization will facilitate the modeling of medical terminologies.

[1]  Carol Friedman,et al.  Research Paper: A General Natural-language Text Processor for Clinical Radiology , 1994, J. Am. Medical Informatics Assoc..

[2]  W. DuMouchel,et al.  Unlocking Clinical Data from Narrative Reports: A Study of Natural Language Processing , 1995, Annals of Internal Medicine.

[3]  George Hripcsak,et al.  Research Paper: The Role of Domain Knowledge in Automating Medical Text Report Classification , 2003, J. Am. Medical Informatics Assoc..

[4]  Christian Lovis,et al.  A light knowledge model for linguistic applications , 2001, AMIA.

[5]  Carol Friedman,et al.  A Comparison of Semantic Categories of the ISO Reference Terminology Models for Nursing and the MedLEE Natural Language Processing System , 2004, MedInfo.

[6]  Robert H. Baud,et al.  GALEN: a third generation terminology tool to support a multipurpose national coding system for surgical procedures , 2000, Int. J. Medical Informatics.

[7]  Carol Friedman,et al.  Research Paper: The Canon Group's Effort: Working Toward a Merged Model , 1995, J. Am. Medical Informatics Assoc..

[8]  Kent A. Spackman,et al.  Role grouping as an extension to the description logic of Ontylog, motivated by concept modeling in SNOMED , 2002, AMIA.

[9]  Judy G. Ozbolt.  Terminology Standards for Nursing , 2000 .

[10]  George Hripcsak,et al.  Assessing explicit error reporting in the narrative electronic medical record using keyword searching , 2003, J. Biomed. Informatics.

[11]  J. Cimino.  Desiderata for Controlled Medical Vocabularies in the Twenty-First Century , 1998, Methods of Information in Medicine.

[12]  Carol Friedman,et al.  Extracting Information on Pneumonia in Infants Using Natural Language Processing of Radiology Reports , 2003, BioNLP@ACL.

[13]  Stanley M. Huff,et al.  Development of a Template Model to Represent the Information Content of Chest Radiology Reports , 2001, MedInfo.

[14]  Clement J. McDonald,et al.  Viewpoint: The Barriers to Electronic Medical Record Systems and How to Overcome Them , 1997, J. Am. Medical Informatics Assoc..

[15]  Robert A. Greenes,et al.  Research Paper: Experiments in Concept Modeling for Radiographic Image Reports , 1994, J. Am. Medical Informatics Assoc..

[16]  Werner Ceusters,et al.  Syntactic-semantic tagging as a mediator between linguistic representations and formal models: an exercise in linking SNOMED to GALEN , 1999, Artif. Intell. Medicine.

[17]  Keith E. Campbell,et al.  Challenges in the Development and Testing of a Reference Terminology Model for Nursing Interventions , 2001, MedInfo.

[18]  Carol Friedman,et al.  Facilitating Cancer Research using Natural Language Processing of Pathology Reports , 2004, MedInfo.

[19]  G Hripcsak,et al.  Natural language processing and its future in medicine. , 1999, Academic medicine : journal of the Association of American Medical Colleges.

[20]  A L Rector,et al.  The GALEN project. , 1994, Computer methods and programs in biomedicine.

[21]  J J Cimino,et al.  Terminology Tools: State of the Art and Practical Lessons , 2001, Methods of Information in Medicine.

[22]  Justin Starren,et al.  Expressiveness of the Breast Imaging Reporting and Database System (BI-RADS) , 1997, AMIA.

[23]  Judy G. Ozbolt.  White Paper: Terminology Standards for Nursing: Collaboration at the Summit , 2000, J. Am. Medical Informatics Assoc..

[24]  George Hripcsak,et al.  Automated detection of adverse events using natural language processing of discharge summaries. , 2005, Journal of the American Medical Informatics Association : JAMIA.

[25]  J. Austin,et al.  Use of natural language processing to translate clinical information from a database of 889,921 chest radiographic reports. , 2002, Radiology.

[26]  David Robinson,et al.  Clinical administration procedures in the Read Thesaurus: extending the ENV 1828 model to support regional terminology requirements , 1998, AMIA.

[27]  George Hripcsak,et al.  A comparison of the Charlson comorbidities derived from medical language processing and administrative data , 2002, AMIA.

[28]  Stanley M. Huff,et al.  Position Paper: Toward a Medical-concept Representation Language , 1994, J. Am. Medical Informatics Assoc..

[29]  Linda G. Shapiro,et al.  The digital anatomist foundational model: principles for defining and structuring its concept domain , 1998, AMIA.

[30]  A Rossi Mori,et al.  An ontological perspective on surgical procedures. , 1996, Proceedings : a conference of the American Medical Informatics Association. AMIA Fall Symposium.

[31]  Suzanne Bakken,et al.  An evaluation of the usefulness of two terminology models for integrating nursing diagnosis concepts into SNOMED Clinical Terms® , 2002, Int. J. Medical Informatics.

[32]  José L. V. Mejino,et al.  Representing Complexity in Part-Whole Relationships within the Foundational Model of Anatomy , 2003, AMIA.

[33]  George Hripcsak,et al.  Automated encoding of clinical documents based on natural language processing. , 2004, Journal of the American Medical Informatics Association : JAMIA.

[34]  Hongfang Liu,et al.  A vocabulary development and visualization tool based on natural language processing and the mining of textual patient reports , 2003, J. Biomed. Informatics.

[35]  Suzanne Bakken,et al.  An Evaluation of the Utility of the CEN Categorial Structure for Nursing Diagnoses as a Terminology Model for Integrating Nursing Diagnosis Concepts into SNOMED , 2001, Medinfo.

[36]  José L. V. Mejino,et al.  The role of definitions in biomedical concept representation , 2001, AMIA.

[37]  Robert H. Baud,et al.  Galen : a third generation terminology tool to support a multipurpose national coding system for surgical procedures , 1999, MIE.

[38]  Barry Smith,et al.  The Role of Foundational Relations in the Alignment of Biomedical Ontologies , 2004, MedInfo.

[39]  Philip J. B. Brown,et al.  Semantic based concept differential retrieval & equivalence detection in clinical terms version 3 (Read Codes) , 1999, AMIA.

[40]  Carol Friedman,et al.  Automating SNOMED coding using medical language understanding: a feasibility study , 2001, AMIA.

[41]  Carol Friedman,et al.  A broad-coverage natural language processing system , 2000, AMIA.

[42]  Carol Friedman,et al.  A schema for representing medical language applied to clinical radiology. , 1994, Journal of the American Medical Informatics Association : JAMIA.

[43]  Mark A. Musen,et al.  Research Paper: A Logical Foundation for Representation of Clinical Data , 1994, J. Am. Medical Informatics Assoc..

[44]  Roberto A. Rocha,et al.  Development of a compositional terminology model for nursing orders , 2004, Int. J. Medical Informatics.

[45]  Hongfang Liu,et al.  Representing information in patient reports using natural language processing and the extensible markup language. , 1999, Journal of the American Medical Informatics Association : JAMIA.

[46]  Judith C. Wagner,et al.  Natural language generation of surgical procedures , 1999, Int. J. Medical Informatics.

[47]  Hongfang Liu,et al.  A method for vocabulary development and visualization based on medical language processing and XML , 2000, AMIA.

[48]  José L. V. Mejino,et al.  A reference ontology for biomedical informatics: the Foundational Model of Anatomy , 2003, J. Biomed. Informatics.