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PubMed2004

Implementation and evaluation of a negation tagger in a pipeline-based system for information extract from pathology reports.

We have developed a pipeline-based system for automated annotation of Surgical Pathology Reports with UMLS terms that builds on GATE--an open-source architecture for language engineering. The system includes a module for detecting and annotating negated concepts, which implements the NegEx algorithm--an algorithm originally described for use in discharge summaries and radiology reports. We describe the implementation of the system, and early evaluation of the Negation Tagger. Our results are encouraging. In the key Final Diagnosis section, with almost no modification of the algorithm or phrase lists, the system performs with precision of 0.84 and recall of 0.80 against a gold-standard corpus of negation annotations, created by modified Delphi technique by a panel of pathologists. Further work will focus on refining the Negation Tagger and UMLS Tagger and adding additional processing resources for annotating free-text pathology reports.

Algorithms↗
PubMed2006

[Design and implementation of a medical record management subsystem as a part of a telemedical system].

This paper introduces the work on the design and implementation of a medical record management subsystem, which is a part of a telemedicine system based on Microsoft .NET. First, an analysis is given on components and structure of medical record, together with an explanation for what is needed in a teleconsultation, how they should be organized and realized in a database, and how to deal with consultation data granularity using XML in combination with database; second, the work done during the realization stage is expatiated, including system analysis and design, database design, and system implementation.

Database Management Systems↗
PubMed1977

A system for coding the presenting requests of ambulatory patients.

Effective methods developed to review and study the care of patients in hospital have not been applicable to ambulatory care, in which definitive diagnosis is the exception rather than the rule. A reasonable alternative to using diagnosis as the basis for assessing ambulatory care is to use the problems or requests presented by the patients themselves. A system has been developed for classifying and coding this information for flexible computer retrieval. Testing indicates that the system is simple in design, easily mastered by nonphysicians and provides reliable, useful data at a low cost.

Ambulatory Care↗
PubMed1995

A model of clinical query management that supports integration of biomedical information over the World Wide Web.

A model of clinical query management is described that supports the integration of various types of biomedical information and the delivery of that information through a common interface. The model extends the architecture of the World Wide Web to include a Common Gateway Interface (CGI) mediator, which takes in user queries, performs syntactic and semantic processing to transform the input to a canonical form, selects the appropriate information sources to answer the query, translates the canonical query statement into a query of each information resource, queries the chosen information sources in parallel, and controls the analysis and display of results. We describe WebMedline, a CGI mediator that implements portions of this model, and discuss the benefits and limitations of this approach.

Computer Communication Networks↗
PubMed1998

Automated knowledge extraction from the UMLS.

This paper presents our work in extracting disease-chemical relationship knowledge from the UMLS Co-occurrence table (MRCOC) using an automated method. We evaluated the quality of the knowledge from UMLS MRCOC by comparing it with knowledge from other sources: For disease-lab chemical relationships, knowledge was obtained from a decision support system (DXplain) and our own knowledge base of medical terminology (MED) through automated processes. For disease-drug chemical relationships, knowledge was manually acquired from the medical literature. Evaluations showed that the UMLS MRCOC knowledge has good sensitivity, especially regarding disease-drug relationships. We are using this knowledge to produce disease-specific views of patients' electronic patient record.

Decision Support Systems, Clinical↗
PubMed1999

Electronic monitoring of clinical experience during undergraduate training in diagnostic radiography.

The clinical experience of a student radiographer has traditionally been recorded in a paper log book. Accurate maintenance of the book relied upon the student's diligence. The electronic logbook is a method of accurately recording the clinical experience of the student radiographer by retrieval of information from the database of a hospital information or radiology management system. The system requires minimal software modification in order to incorporate fields defining the ability of the student in association with the degree of infirmity of the patient. Retrieved information is processed by a specially designed software package at the Academic Centre and reports issued to Clinical Tutors. Benefits of the system include easy monitoring of student workload, ensuring that the student receives a wide and varied experience during training; improvement in student motivation; and use of a final report form in the student's portfolio.

Clinical Competence↗
PubMed1975

Natural language storage and retrieval of medical diagnostic information. Experience at the UCLA hospital and clinics over a 10-year period.

A natural language storage and retrieval system initially designed for pathology reports has been in operation for ten years at UCLA Hospital and Clinics. The original system has been improved to provide a thesaurus processor with added capabilities for expanding search request terms and a newly developed set of search programs with user options that make complex and more accurate retrievals possible. Summarized diagnostic statements or impressions from five specialities (Surgical Pathology, Bone Marrow, Autopsy, Nuclear Medicine, and Neuroradiology), are automatically encoded by referencing a master computer dictionary containing a unique numeric code for each English word. Input and retrievals are batch, off-line operations in free text, and are currently processed on the IBM 370/145. User acceptance is high, quality of retrievals improved, and cost is nominal. This paper describes an expanded natural language system which in now providing a viable form of information storage and retrieval for research, medical education, patient care, quality control, statistics and administrative purposes.

California↗
PubMed1995

The immune self: a selectionist theory of recognition, learning, and remembering within the immune system.

In this paper, I have briefly explored metaphors shared by the immune and nervous systems and shown that this exercise can lead to the elucidation of common principles of organization, as well as to predictions concerning how the immune system functions. Metaphor itself undoubtedly reflects the way in which we categorize and retrieve information 44], so it is not surprising that the deep processes of language tend to sample information from related data categories. Although the nervous and immune systems are obviously not the same and metaphors are indeed just that, my primary goal has been to suggest that by virtue of their having evolved in parallel over millions of years, the nervous and immune systems currently use the same archetypal principles and strategies to address related challenges in information processing and retrieval. Ultimately, nature is conservative. One need only look at a tree, a river, the airways, or the vascular bed in order to see how a fractal pattern of repetitive dichotomous branching has been used by each, in order to optimize the transport of fluids over large distances [45]. While each system has had to adopt different materials in order to solve the problem, the shape of their solutions is remarkably alike. In the immune and nervous systems, the elements used to produce optimal functional responses are also quite different, but again the solutions have been achieved by comparable strategies. I am certain that these two great systems of information processing, each responding with vastly different kinetics, will prove to be far more integrally interdependent than has been previously recognized. For example, should a swift response by the immune system be required in an overwhelming invasion by microbial pathogens, the immune system may be able to cooperate with the rapidly reacting nervous system to rid the host of the invaders. In this regard, we have shown that the beta-adrenergic hormone epinephrine rapidly increases the traffic of memory T-cells to mucosal sites, presumably representing an immune component of the fight-or-flight response [46]. Neural evolution appears to have as its goal the development of more efficient information processing systems that lead to higher levels of consciousness. However, in modern times, technologic advances in information processing have rapidly outstripped the slower adaptations that can be made by evolution. In order to satisfy his compulsive quest for information, man has recently developed and recruited the aid of computers.(ABSTRACT TRUNCATED AT 400 WORDS)

Association Learning↗
PubMed1993

A collaborative approach to standards, practices. Setting the stage for continuous quality improvement.

In retrospect, the most important thing we did was work together. We analyzed, refined, and validated our philosophical approach to patient care. We provided an information data base that is readily available for on-the-job reference and serves as a starting point for CQI activities. The very act of joint documentation of practices encourages open discussions about improvements to patient care. One physician states, We know that flaws in the process through which we produce care are everywhere--waste, duplication of effort, unnecessary complexity, and unpredictability . . . I believe that modern total quality management offers enormous hope to a medical care field that is rather desperate. . . . Collaborative practice and CQI activities are one hope. The scope of what nurses and physicians traditionally consider when discussing standards and practices must widen. We should no longer look only at patient care. We must simultaneously focus on how the management of total systems influences quality care for all patients. The CQI process, a proactive method, requires an accurate data base of information that is easily retrieved when looking for systems and individual patient care improvements. Our Computerized Collaborative Standards and Practices Manual is the reservoir for documenting practice plans developed and approved by all the disciplines involved. The process described here began with two closely knit operating room disciplines; this framework, however, offers the potential for expansion into a hospital-wide system of information organization and use.

Anesthesia Department, Hospital↗
PubMed2006

Benefits of the DICOM structured report.

Recently, the digital imaging and communications in medicine (DICOM) standard introduced rules for the encoding, transmission, and storage of the imaging diagnostic report. This medical document can be stored and communicated with the images in picture archiving and communication system (PACS). It is a structured document that contains text with links to other data such as images, waveforms, and spatial or temporal coordinates. Its structure, along with its wide use of coded information, enables the semantic understanding of the data that is essential for the Electronic Healthcare Record deployment. In this article, we present DICOM Structured Report (SR) and discuss its benefits. We show how SR enables efficient radiology workflow, improves patient care, optimizes reimbursement, and enhances the radiology ergonomic working conditions. As structured input significantly alters the interpretation process, understanding all its benefits is necessary to support the change.

Forms and Records Control↗
PubMed2005

Partitioning medical image databases for content-based queries on a Grid.

OBJECTIVES: In this paper we study the impact of executing a medical image database query application on the grid. For lowering the total computation time, the image database is partitioned into subsets to be processed on different grid nodes. METHODS: A theoretical model of the application complexity and estimates of the grid execution overhead are used to efficiently partition the database. RESULTS: We show results demonstrating that smart partitioning of the database can lead to significant improvements in terms of total computation time. CONCLUSIONS: Grids are promising for content-based image retrieval in medical databases.

Database Management Systems↗
PubMed2005

[Speech recognition: impact on workflow and report availability].

With ongoing technical refinements speech recognition systems (SRS) are becoming an increasingly attractive alternative to traditional methods of preparing and transcribing medical reports. The two main components of any SRS are the acoustic model and the language model. Features of modern SRS with continuous speech recognition are macros with individually definable texts and report templates as well as the option to navigate in a text or to control SRS or RIS functions by speech recognition. The best benefit from SRS can be obtained if it is integrated into a RIS/RIS-PACS installation. Report availability and time efficiency of the reporting process (related to recognition rate, time expenditure for editing and correcting a report) are the principal determinants of the clinical performance of any SRS. For practical purposes the recognition rate is estimated by the error rate (unit "word"). Error rates range from 4 to 28%. Roughly 20% of them are errors in the vocabulary which may result in clinically relevant misinterpretation. It is thus mandatory to thoroughly correct any transcribed text as well as to continuously train and adapt the SRS vocabulary. The implementation of SRS dramatically improves report availability. This is most pronounced for CT and CR. However, the individual time expenditure for (SRS-based) reporting increased by 20-25% (CR) and according to literature data there is an increase by 30% for CT and MRI. The extent to which the transcription staff profits from SRS depends largely on its qualification. Online dictation implies a workload shift from the transcription staff to the reporting radiologist.

Database Management Systems↗
PubMed2002

Manual semantic tagging to improve access to information in narrative electronic medical records.

OBJECTIVE: To assess effectiveness of information retrieval from narrative patient records utilizing manually supplied semantic tags. DESIGN: Retrospective evaluation of narrative electronic record notes with respect to consistency of manually supplied semantic tags. Assessment of retrieval effectiveness using string matching methods and methods based on structural characteristics of data. SETTING: Department of Neurology in a Norwegian university hospital using a document based electronic patient record system offering template assisted manual semantic indexing of textual record notes. MEASUREMENTS: Proportion of consistently tagged information. Retrieval effectiveness expressed as recall (sensitivity) and precision (positive predictive value). RESULTS: Seventy-five percent of the content was consistently tagged. Retrieval models based on simple string matching performed better than models based on semantic tags alone with respect to best mean recall and mean precision at high recall-levels. Models combining both simple string matching and semantic tagging performed better than separate models with respect to best mean recall (0.95) and mean precision at high levels of recall. CONCLUSION: Although template assisted semantic indexing of narrative electronic patient record notes showed suboptimal consistency, it significantly improved retrieval effectiveness with respect to best mean recall obtained by individual strategies and with respect to precision at any recall level.

Abstracting and Indexing↗
PubMed1984

A computerized database-management system for curriculum analysis.

This report describes a computerized database-management system designed to allow users to retrieve and report information on the curriculum of an undergraduate pathophysiology course. With the system the user can locate where and in what context a topic is covered in the course and can answer queries and prepare reports concerning, for example, format and duration of sessions, teaching aids used and instructors. The system is a unique tool that can be used to optimize course structure and content. It can easily be expanded to include other undergraduate medical courses, and the techniques can be applied to other disciplines.

Curriculum↗
PubMed2006

Use of personal digital assistant devices in order to access, consult and apply a corpus of clinical guidelines and decision-based support documentation like the Italian SPREAD Guidelines on stroke disease.

During the past few years, personal digital assistants (PDAs) have become widespread commodities, like computers and mobile phones. Many health-care providers, particularly physicians, routinely use PDAs in their everyday work. Accessing guidelines and clinical decision-based support tools, such as the downloadable version of the Italian SPREAD Guidelines represents one of the most important and common clinical applications. The current experience suggests that the need for best evidence models at the time of decision making is strong and that portable accessibility is critical: including just-in-time information systems that allow physicians to retrieve the best evidence at the point of care, and a standardized electronic health record (EHR) easily integrating into daily practice and is affordable to most family physicians.

Computers, Handheld↗