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author:("giese, D.")
1.  A Preliminary Study of Clinical Abbreviation Disambiguation in Real Time 
Applied Clinical Informatics  2015;6(2):364-374.
To save time, healthcare providers frequently use abbreviations while authoring clinical documents. Nevertheless, abbreviations that authors deem unambiguous often confuse other readers, including clinicians, patients, and natural language processing (NLP) systems. Most current clinical NLP systems “post-process” notes long after clinicians enter them into electronic health record systems (EHRs). Such post-processing cannot guarantee 100% accuracy in abbreviation identification and disambiguation, since multiple alternative interpretations exist.
Authors describe a prototype system for real-time Clinical Abbreviation Recognition and Disambiguation (rCARD) – i.e., a system that interacts with authors during note generation to verify correct abbreviation senses. The rCARD system design anticipates future integration with web-based clinical documentation systems to improve quality of healthcare records. When clinicians enter documents, rCARD will automatically recognize each abbreviation. For abbreviations with multiple possible senses, rCARD will show a ranked list of possible meanings with the best predicted sense at the top. The prototype application embodies three word sense disambiguation (WSD) methods to predict the correct senses of abbreviations. We then conducted three experments to evaluate rCARD, including 1) a performance evaluation of different WSD methods; 2) a time evaluation of real-time WSD methods; and 3) a user study of typing clinical sentences with abbreviations using rCARD.
Using 4,721 sentences containing 25 commonly observed, highly ambiguous clinical abbreviations, our evaluation showed that the best profile-based method implemented in rCARD achieved a reasonable WSD accuracy of 88.8% (comparable to SVM – 89.5%) and the cost of time for the different WSD methods are also acceptable (ranging from 0.630 to 1.649 milliseconds within the same network). The preliminary user study also showed that the extra time costs by rCARD were about 5% of total document entry time and users did not feel a significant delay when using rCARD for clinical document entry.
The study indicates that it is feasible to integrate a real-time, NLP-enabled abbreviation recognition and disambiguation module with clinical documentation systems.
PMCID: PMC4493336  PMID: 26171081
Clinical abbreviation; machine learning; clinical documentation system
2.  Generating Clinical Notes for Electronic Health Record Systems 
Applied Clinical Informatics  2010;1(3):232-243.
Clinical notes summarize interactions that occur between patients and healthcare providers. With adoption of electronic health record (EHR) and computer-based documentation (CBD) systems, there is a growing emphasis on structuring clinical notes to support reusing data for subsequent tasks. However, clinical documentation remains one of the most challenging areas for EHR system development and adoption. The current manuscript describes the Vanderbilt experience with implementing clinical documentation with an EHR system. Based on their experience rolling out an EHR system that supports multiple methods for clinical documentation, the authors recommend that documentation method selection be made on the basis of clinical workflow, note content standards and usability considerations, rather than on a theoretical need for structured data.
PMCID: PMC2963994  PMID: 21031148
Computer based documentation; electronic health records; medical informatics applications; computerized medical records systems; user-computer interface
3.  Implementation of organizational practices to protect information in health organizations. 
In March of 1997, the National Research Council (NRC) of the National Academy of Sciences issued the report, "For the Record: Protecting Electronic Health Information." In its report, the Council recommended both technical and organizational practices to protect electronic health information. At the time the report was issued, Vanderbilt University Medical Center was deeply immersed in the development of organizational practices consistent with the Council's recommendations. We agreed that the recommended technical and organizational practices are important for protecting other information types in addition to health information, and that they suggest appropriate practices for non-electronic information, as well. In this paper, we focus on our process for developing and implementing the seven organizational practices recommended for immediate implementation.
PMCID: PMC2232171  PMID: 9929244
4.  The Vanderbilt University fast track to IAIMS: transition from planning to implementation. 
Vanderbilt University Medical Center is implementing an Integrated Advanced Information Management System (IAIMS) using a fast-track approach. The elapsed time between start-up and completion of implementation will be 7.5 years. The Start-Up and Planning phases of the project are complete. The Implementation phase asks one question: How does an organization create an environment that redirects and coordinates a variety of individual activities so that they come together to provide an IAIMS? Four answers to this question are being tested. First, design resources to be "scalable"--i.e., capable of supporting enterprise-wide use. Second, provide information technology planning activities as ongoing core functions that direct local efforts. Third, design core infrastructure resources to be both reusable and expandable at the local level. Fourth, use milestones to measure progress toward selected endpoints to permit early refinement of plans and strategies.
PMCID: PMC116315  PMID: 8880678
5.  Cross-institutional reuse of a problem statement knowledge base. 
This article describes client and server applications for a problem statement knowledge base derived from a large corpus of provider entered terminology. The current status and potential for integration of the server into the Vanderbilt University Medical Center computing environment are discussed. Finally, an experiment in multiple dimensions of reuse for problem list terms is introduced, and possible strategies to mediate between free text and coded data are examined.
PMCID: PMC2233559  PMID: 9357607
6.  Integrating health sciences librarians into biomedicine. 
Vanderbilt University Medical Center (VUMC) developed a model training program to prepare current and future health sciences librarians for roles that are integrated into the diverse fabric of the health care professions. As a complement to the traditional and theoretical aspects of a librarian's education, this mixture of supplemental coursework and intensive practical training emphasizes active management of information, problem-solving skills, learning in context, and direct participation in research, while providing the opportunity for advanced academic pursuits. The practical training will take place under the auspices of an established Integrated Advanced Information Management Systems (IAIMS) library that is fully integrated with the Health Center Information Management Unit and Academic Biomedical Informatics Unit. During the planning phase, investigators are analyzing the model's aims and requirements, concentrating on (a) refining the current understanding of the roles health sciences librarians occupy; (b) developing educational strategies that prepare librarians to fulfill expanded roles; and (c) planning for an evaluation process that will support iterative revision and refinement of the model.
PMCID: PMC226193  PMID: 8913556
7.  Evaluation of long-term maintenance of a large medical knowledge base. 
OBJECTIVE: Evaluate the effects of long-term maintenance activities on existing portions of a large internal medicine knowledge base. DESIGN: Five physicians who were not among the original developers of the knowledge base independently updated a total of 15 QMR disease profiles; each updated submission was modified by a review of group serving as the "gold standard, " and the pre- and post-study versions of each updated disease profile were compared. MEASUREMENTS: Numbers and types of changes, defined as any difference between the original version and the final version of a disease profile; reason for each change; and bibliographic references cited by the physicians as supporting evidence. RESULTS: A total of 16% of all entries were modified by the updating process; up to 95% of the entries in a disease profile were affected. The two most common modifications were changes to the frequency of an entry, and creation of a new entry. Laboratory findings were affected much more often than were history, symptom, or physical exam findings. The dominant reason for changes was appearance of new evidence in the medical literature. The literature cited ranged from 1944 to the present. CONCLUSIONS: This study provides an evaluation of the rate of change within the QMR medical knowledge base due to long-term maintenance. The results show that this is a demanding activity that may profoundly affect certain portions of a knowledge base, and that different types of knowledge (e.g., simple laboratory vs expensive or invasive laboratory findings) are affected by the process in different ways.
PMCID: PMC116270  PMID: 7496879
8.  Increasing the availability of the computerized patient record. 
The MARS clinical repository, originally developed at the University of Pittsburgh, provides electronic access to the patient record at Vanderbilt University Medical Center. The original client interface we developed runs on all standard clinical workstations in the medical center, but is operating-system dependent. Porting and maintaining it on the variety of hardware- and software combinations found on VUMC personal computers would be fairly costly. To broaden the availability of the system to faculty and health care providers in all areas, and to support future access from Vanderbilt-affiliated providers outside the main campus, we are developing a new Web-based client. The new client provides good functionality and performance, and will be a strategic asset in our long-term commitment to making relevant clinical information immediately available to authorized health care providers.
PMCID: PMC2232918  PMID: 8947743
9.  Information needs of health care professionals in an AIDS outpatient clinic as determined by chart review. 
OBJECTIVE: To examine the information needs of health care professionals in HIV-related clinical encounters, and to determine the suitability of existing information sources to address those needs. SETTING: HIV outpatient clinic. PARTICIPANTS: Seven health care professionals with diverse training and patient care involvement. METHODS: Based on patient charts describing 120 patient encounters, participants generated 266 clinical questions. Printed and on-line information sources were used to answer questions in two phases: using commonly available sources and using all available medical library sources. MEASUREMENTS: The questions were divided into 16 categories by subject. The number of questions answered, their categories, the information source(s) providing answers, and the time required to answer questions were recorded for each phase. RESULTS: Each participant generated an average of 3.8 clinical questions per chart. Five categories accounted for almost 75% of all questions; the treatment protocols/regimens category was most frequent (24%). A total of 245 questions (92%) were answered, requiring an average of 15 minutes per question. Most (87%) of the questions were answered via electronic sources, even though paper sources were consulted first. CONCLUSIONS: The participating professionals showed considerable information needs. A combination of on-line and paper sources was necessary to provide the answers. The study suggests that present-day information sources are not entirely satisfactory for answering clinical questions generated by examining charts of HIV-infected patients.
PMCID: PMC116221  PMID: 7850563
10.  LabTalk/2: a middleware approach to HIS integration. 
LabTalk/2 is an intelligent interface between a legacy order-entry system and a legacy laboratory information system. Unlike other interfaces, LabTalk/2 does more than just transform data from one format to another; it transforms the manner in which data is processed. Utilizing the "middleware" concept, it sits independently between the two systems, decoupling their maintenance needs. Implementation has been successful.
PMCID: PMC2579068  PMID: 8563250
11.  Comparing contents of a knowledge base to traditional information sources. 
Physicians rely on the medical literature as a major source of medical knowledge and data. The medical literature, however, is continually evolving and represents different sources at different levels of coverage and detail. The recent development of computerized medical knowledge bases has added a new form of information that can potentially be used to address the practicing physician's information needs. To understand how the information from various sources differs, we compared the description of a disease found in the QMR knowledge base to those found in two general internal medicine textbooks and two specialized nephrology textbooks. The study shows both differences in coverage and differences in the level of detail. Textbooks contain information about pathophysiology and therapy that is not present in the diagnostic knowledge base. The knowledge base contains a more detailed description of the associated findings, more quantitative information, and a greater number of references to peer-reviewed medical articles. The study demonstrates that computerized knowledge bases, if properly constructed, may be able to provide clinicians with a useful new source of medical knowledge that is complementary to existing sources.
PMCID: PMC2850652  PMID: 8130550
12.  A tool for the computer-assisted creation of QMR medical knowledge base disease profiles. 
QMR-KAT is a computer-based tool which assists physicians in the construction of the QMR medical knowledge base. Each QMR disease profile results from an in-depth analysis of the published medical literature, and from consultations with expert clinicians. QMR-KAT is an interactive knowledge acquisition program which facilitates the creation of new disease profiles, records the supporting evidence for each disease profile entry, and enforces consistency with the existing knowledge base. The program has been used in the creation of all new QMR disease profiles over the past two years. It has also been used to support a study on the reproducibility of knowledge base construction.
PMCID: PMC2247698  PMID: 1807775

Results 1-12 (12)