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At least 991 records · Page 55Linked to original sources
PubMed2001

A Java viewer to publish Digital Imaging and Communications in Medicine (DICOM) radiologic images on the World Wide Web.

The world wide web is an exciting service that allows one to publish electronic documents made of text and images on the internet. Client software called a web browser can access these documents, and display and print them. The most popular browsers are currently Microsoft Internet Explorer (Microsoft, Redmond, WA) and Netscape Communicator (Netscape Communications, Mountain View, CA). These browsers can display text in hypertext markup language (HTML) format and images in Joint Photographic Expert Group (JPEG) and Graphic Interchange Format (GIF). Currently, neither browser can display radiologic images in native Digital Imaging and Communications in Medicine (DICOM) format. With the aim to publish radiologic images on the internet, we wrote a dedicated Java applet. Our software can display radiologic and histologic images in DICOM, JPEG, and GIF formats, and provides a a number of functions like windowing and magnification lens. The applet is compatible with some web browsers, even the older versions. The software is free and available from the author.

Humans↗
PubMed2006

CellML2SBML: conversion of CellML into SBML.

UNLABELLED: CellML and SBML are XML-based languages for storage and exchange of molecular biological and physiological reaction models. They use very similar subsets of MathML to specify the mathematical aspects of the models. CellML2SBML is implemented as a suite of XSLT stylesheets that, when applied consecutively, convert models expressed in CellML into SBML without significant loss of information. The converter is based on the most recent stable versions of the languages (CellML version 1.1; SBML Level 2 Version 1), and the XSLT used in the stylesheets adheres to the XSLT version 1.0 specification. Of all 306 models in the CellML repository in April 2005, CellML2SBML converted 91% automatically into SBML. Minor manual changes to the unit definitions in the originals raised the percentage of successful conversions to 96%. AVAILABILITY: http://sbml.org/software/cellml2sbml/. SUPPLEMENTARY INFORMATION: Instructions for use and further documentation available on http://sbml.org/software/cellml2sbml/

Cell Physiological Phenomena↗
PubMed1992

Text-interpreter language for flexible generation of patient notes and instructions.

An interpreted computer language has been developed along with a windowed user interface and multi-printer-support formatter to allow preparation of documentation of patient visits, including progress notes, prescriptions, excuses for work/school, outpatient laboratory requisitions, and patient instructions. Input is by trackball or mouse with little or no keyboard skill required. For clinical problems with specific protocols, the clinician can be prompted with problem-specific items of history, exam, and lab data to be gathered and documented. The language implements a number of text-related commands as well as branching logic and arithmetic commands. In addition to generating text, it is simple to implement arithmetic calculations such as weight-specific drug dosages; multiple branching decision-support protocols for paramedical personnel (or physicians); and calculation of clinical scores (e.g., coma or trauma scores) while simultaneously documenting the status of each component of the score. ASCII text files produced by the interpreter are available for computerized quality audit. Interpreter instructions are contained in text files users can customize with any text editor.

Computers↗
PubMed2002

Structured reporting in neuroradiology.

We have developed a system to structure free-text neuroradiology reports using a natural language processing program and formatted the output into the digital image and communication in medicine (DICOM) standard for structured reporting (SR). DICOM SR formats the correspondence of pertinent diagnostic images to the radiologist's dictated report of clinical findings. In addition, DICOM SR allows the information to be organized into a tree structure. Individual nodes of the tree can contain individual items or lists. Structuring the content of free-text information allows the creation of hierarchies with defined relationships between the concepts contained within the report.

Brain↗
PubMed1998

Information frames: a new multimedia approach to Web-based learning of biology and medicine.

Presentation of content in hyperlinked multimedia formats for teaching has failed using the computer's power of navigation through rich visual and auditory information. We have developed "Information Frames", an authoring tool in hypertext markup language (html) format, that allows easy utilization by technology-challenged teachers and professors, and attracts students because of interactive, design-based learning. An Information Frame contains a definition, explanation and illustration of a single concept. Topics are provided with hyperlinks to other Information Frames having related concepts that may provide prerequisite knowledge, or may raise the concept to a more integrative level. A graphical view of the linked-Information Frames presents a Concept Map of the overall topic.

Computer Communication Networks↗
PubMed2001

Presentation of problem-specific, text-based medical knowledge: XML and related technologies.

Systematic reviews of the impact of clinical decision support systems on provider behavior and patient outcome have shown evidence of benefit. Knowledge-based functions for decision support or monitoring that are integrated in clinical information systems are a potentially effective way. But these concepts are restricted by the efforts required for development and maintenance of the information systems and the limited number of implemented medical rules. Physicians are familiar to get their information from text-based sources. It seems to be straight-forward to rely on a document-based solution in order to present problem-specific information at the point of care. We have developed a concept for context-sensitive retrieving and presentation of text-based medical knowledge (textbook of internal medicine) using the eXtensible Markup Language (XML) and related technologies. This concept can facilitate the electronic query and presentation of this resource. XML may replace narrative text as a storage format and allows to structure the data in a stepwise fashion. On the basis of structured data we are able to improve the search quality for clinical information and its presentation which forms a crucial pre-requisite for the use of the information and the implementation of evidence-based care in the clinical routine.

Decision Support Systems, Clinical↗
PubMed1998

Intention-based critiquing of guideline-oriented medical care.

We present a methodology and tool for providing retrospective review and critiquing of guideline-based medical care given to patients. We show how our guideline representation language, Asbru, which supports the use of physicians intentions in addition to physician's actions, allows us to compare the care given to a patient at the level of the intention to treat in addition to the more detailed plan carried out. We have developed an algorithm based on this representation for retrospective quality assessment of guideline-based care. Our method takes the physician's and institution's preferences and policies into account in explaining or justifying physician deviations from the recommendations of a guideline.

Algorithms↗
PubMed2002

Combining diagnosis and treatment using ASBRU.

Traditionally, diagnosis and treatment have been seen as two distinct tasks. Consequently, most approaches to computer supported health care focus on one of the two-mostly on diagnosis or rather on the interpretation of measurements which is much better understood and formalised. However, in practice diagnosis and treatment overlap and influence each other in many ways. Combinations range from repeatedly going through the diagnosis-treatment loop over a period of time to permanent monitoring of the patients' health condition as it is done in intensive care units. In this article we describe how to model these combinations using the clinical protocol-representation language ASBRU. It implements treatment steps in a hierarchy of skeletal, time-oriented plans. Diagnosis can either be described in a declarative way in the conditions, under which treatment steps are taken or it can be modelled explicitly as plans of their own right. We demonstrate our approach using examples taken from the American Association of Paediatricians' guideline for the treatment of hyperbilirubinemia in the new-born.

Clinical Protocols↗
PubMed2001

IML: An image markup language.

Image Markup Language is an extensible markup language (XML) schema used to describe both image metadata and annotations. It describes both data pertaining to an entire image, and data that are tied to specific regions or features of the image. Developed for a specific domain in Medical Education, this pa-per describes extensions to take advantage of the Dublin Core metadata standard, and of an XML schema for vector graphics representation. We have developed a prototype system of open source tools implementing an authoring system, a client system, and an image annotation database which can be queried though the Web.

Diagnostic Imaging↗
PubMed2001

Sharable representation of clinical guidelines in GLIF: relationship to the Arden Syntax.

Clinical guidelines are intended to improve the quality and cost effectiveness of patient care. Integration of guidelines into electronic medical records and order-entry systems, in a way that enables delivery of patient-specific advice at the point of care, is likely to encourage guidelines acceptance and effectiveness. Among the methodologies for modeling guidelines and medical decision rules, the Arden Syntax for Medical Logic Modules and the GuideLine Interchange Format version 3 (GLIF3) emphasize the importance of sharing encoded logic across different medical institutions and implementation platforms. These two methodologies have similarities and differences; in this paper we clarify their roles. Both methods can be used to support sharing of medical knowledge, but they do so in complementary situations. The Arden Syntax is suitable for representing individual decision rules in self-contained units called Medical Logic Modules (MLMs), which are usually implemented as event-driven alerts or reminders. In contrast, GLIF3 is designed for encoding complex multistep guidelines that unfold over time. As a consequence, GLIF3 has several mechanisms for complexity management and additional constructs that may require overhead unnecessary for expressing simple alerts and reminders. Unlike the Arden Syntax, GLIF3 encourages a top-down process of guideline modeling consisting of three levels that are created in order: Level 1 comprises a human-readable flowchart of clinical decisions and actions. Level 2 comprises a computable specification that can be verified for logical consistency and completeness; and Level 3 comprises an implementable specification that includes information required for local adaptation of guideline logic as well as for mapping guideline variables onto institutional medical records. A major emphasis of the current GLIF3 development process has been to create the computable specification that formally represents medical decision and eligibility criteria. We based GLIF3's formal expression language on the Arden Syntax's logic grammar, making the necessary extensions to the Arden Syntax's data structures and operators to support GLIF3's object-oriented data model. We discuss why the process of generating a set of MLMs from a GLIF-encoded guideline cannot be automated, why it can result in information loss, and why simple medical rules are best represented as individual MLMs. We thus show that the Arden Syntax and GLIF3 play complementary roles in representing medical knowledge for clinical decision support.

Computer Simulation↗
PubMed1997

Standard generalized mark-up language: should it have a role in clinical records?

Standard generalized mark-up language (SGML) could have a role as one of the information management tools available to system developers and users because it has unique features that can help solve some of the current problems in clinical informatics. SGML allows the logical structure of multimedia documents to be described in a way that is independent of the hardware or software platform. This offers considerable advantages for purchasers of systems because it gives an opportunity to develop records that can be readily authored and read by a variety of systems, offering a route to effective communication of electronic clinical information.

England↗
PubMed2003

Adapting current Arden Syntax knowledge for an object oriented event monitor.

Arden Syntax for Medical Logic Module (MLM)1 was designed for writing and sharing task-specific health knowledge in 1989. Several researchers have developed frameworks to improve the sharability and adaptability of Arden Syntax MLMs, an issue known as "curly braces" problem. Karadimas et al proposed an Arden Syntax MLM-based decision support system that uses an object oriented model and the dynamic linking features of the Java platform.2 Peleg et al proposed creating a Guideline Expression Language (GEL) based on Arden Syntax's logic grammar.3 The New York Presbyterian Hospital (NYPH) has a collection of about 200 MLMs. In a process of adapting the current MLMs for an object-oriented event monitor, we identified two problems that may influence the "curly braces" one: (1) the query expressions within the curly braces of Arden Syntax used in our institution are cryptic to the physicians, institutional dependent and written ineffectively (unpublished results), and (2) the events are coded individually within a curly braces, resulting sometimes in a large number of events - up to 200.

Decision Support Systems, Clinical↗
PubMed2003

XML as standard for communicating in a document-based electronic patient record: a 3 years experiment.

During the past few years, the eXtensible Markup Language (XML) has progressively become a gold standard for accessing, representing and exchanging information, especially in the health care environment. This paper presents an implementation of the use of XML for the electronic patient record (EPR) and discusses more specifically its growing use in two areas of the EPR: first, as a format for the exchange of structured messages, and second, as a comprehensible way of representing patient documents. These statements rely on a 3 years experiment conducted at the Geneva University Hospital as part of its document-centered EPR.

Delivery of Health Care↗
PubMed1997

Virtual reality publication of spiral ct-derived three-dimensional models: or, creation of spiral, CT-derived, three-dimensional VRML objects.

Three-dimensional models can be generated from slice images, such as those obtained from computed tomography (CT) and magnetic resonance imaging (MRI) using a variety of techniques. A popular method for rendering 3D anatomical models is the creation of polygonal mesh surfaces representing the boundary between tissues. Mesh surfaces can be rendered extremely quickly using conventional personal computers, without recourse to more expensive graphic workstations. The dissemination of three-dimensional (3D) models across the Internet has been made significantly easier by the definition of the Virtual Reality Markup Language (VRML) format. The VRML definition allows the parameters and relationships of 3D objects to be described in a text format. The text file can be transfered from a host computer to a remote client computer through the World Wide Web and viewed using readily available software (See Appendix). VRML is based on the definition of primitive 3D objects such as polygons and spheres. Consequently, the transition from a mesh surface derived from a clinical image data set to a VRML object is relatively simple, allowing for convenient and cost-effective dissemination of 3D clinical models across the internet.

Bronchi↗
PubMed1994

Finding temporal patterns--a set-based approach.

We created an inference engine and query language for expressing temporal patterns in data. The patterns are represented by using temporally-ordered sets of data objects. Patterns are elaborated by reference to new objects inferred from original data, and by interlocking temporal and other relationships among sets of these objects. We found the tools well-suited to define scenarios of events that are evidence of inappropriate use of prescription drugs, using Medicaid administrative data that describe medical events. The tools' usefulness in research might be considerably more general.

Artificial Intelligence↗
PubMed2002

Indexing of Internet resources in order to improve the provision of problem-relevant medical information.

Due to the information overload and the unstructured access to (medical) information of the internet, it isn't hardly possible to find problem-relevant medical information in an appropriate time (e.g. during a consultation). The web offers a mixture of web pages, forums, newsgroups and databases. The search for problem-relevant information for a certain knowledge area encounters on two basic problems. On the one hand, you have to find in the jungle of the information, relevant resources for your individual clinical case (treatment, diagnosis, therapeutic option etc..). The second problem consists of being able to judge the quality of individual contents of inteernet pages. On the basis of the different informational needs of health care professionals and patients a catalog with inteernet resources was created to tumor diseases such as lung cancer (small cell and non-small cell carcinoma), colorectal cancer and thyroid cancer. Explicit and implicit metainformation, if available, such as the title of the document, language, date or keywords are stored in the database. The database entries are editorially revised, so that further specific metainformation is available for the information retrieval. Our pragmatic approach of searching, editing, and archiving of internet content is still necessary since most of the web documents are based on HTML, which doesn't allow for structuring (medical) information and assigning metainformation sufficiently. The use of specific metainformation is crucial in order to improve the recall and precision of internet searches. In the future, XML and related technologies (RDF) will meet these requirements.

Abstracting and Indexing↗
PubMed2006

SemBiosphere: a semantic web approach to recommending microarray clustering services.

Clustering is a popular method for analyzing microarray data. Given the large number of clustering algorithms being available, it is difficult to identify the most suitable ones for a particular task. It is also difficult to locate, download, install and run the algorithms. This paper describes a matchmaking system, SemBiosphere, which solves both problems. It recommends clustering algorithms based on some minimal user requirement inputs and the data properties. An ontology was developed in OWL, an expressive ontological language, for describing what the algorithms are and how they perform, in addition to how they can be invoked. This allows machines to "understand" the algorithms and make the recommendations. The algorithm can be implemented by different groups and in different languages, and run on different platforms at geographically distributed sites. Through the use of XML-based web services, they can all be invoked in the same standard way. The current clustering services were transformed from the non-semantic web services of the Biosphere system, which includes a variety of algorithms that have been applied to microarray gene expression data analysis. New algorithms can be incorporated into the system without too much effort. The SemBiosphere system and the complete clustering ontology can be accessed at http://yeasthub2.gersteinlab. org/sembiosphere/.

Algorithms↗
PubMed2005

Designing and implementing health data and information providers.

OBJECTIVES: To model and implement web portals providing access to certified and high-quality information in the domain of health. MATERIAL AND METHODS: The Unified Medical Language System (UMLS) knowledge sources of the U.S. National Library of Medicine and principles of implementation resulting from the previous ARIANE project are described. The XML technology that allows files transformations by the means of XSLT is briefly presented. RESULTS: The design and implementation of software modules that exploit knowledge sources, operate the translation of a user's query to selected information sources, and wrap obtained results are detailed. Querying documentary and factual medical databases are presented. DISCUSSION: Current implementation and wrapping perspectives are discussed in terms of integration and interoperability of health information and data resources.

France↗