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PubMedDate not supplied

[CISMeF: catalog and index of French-speaking medical sites].

The Internet has now become a major source of health information. The aim of CISMeF is to catalogue and index the main French-speaking sites and documents concerning health. This project was initiated by Rouen University Hospital. Its URL is http://www.chu-rouen.fr/cismef. CISMeF covers all areas of health care and medical sciences, and is indexed both alphabetically and according to subject. It was set up on a Sun workstation under the Sun UNIX operating system and is entirely based on static HTML. By May 1999, the number of sites and documents indexed was already over 6,500, with a mean of 75 new sites added each week. CISMeF is updated via a five-step process: resource collection, filtering, description, classification, and indexing. The Net Scoring criteria are used to assess the quality of health information on the Internet. These criteria concern eight categories: credibility, content, links, design, interactivity, quantitative aspects, ethics and accessibility. CISMeF uses two standard tools to organize information: the MeSH (medical subject heading) thesaurus from the Medline reference database (National Library of Medicine, USA) and the Dublin core metadata format. The sites and documents included in CISMeF are described using the following elements from the Dublin core project: title, author or creator, subject and keywords, description, publisher, date, resource type, format, identifier, and language.

Abstracting and Indexing↗
PubMed2004

TimeWrap--a method for automatic transformation of structured guideline components into formal process-representations.

Guideline and protocol representation languages have reached a level of complexity where auxiliary methods are needed to support the authoring of protocols in the particular language. Several approaches and methods exist that claim high knowledge about both, the medical context and the formal requirements. Therefore, we need knowledge-based methods to facilitate the human plan designer and create the protocols of the particular language as automated as possible. We present a three-step wrapper method, called TimeWrap, to extract information, in particular temporal issues, out of semistructured data and integrate it in a formal representation. We illustrate our approach using the guideline-representation language Asbru and examples from guidelines to treat conjunctivitis.

Conjunctivitis↗
PubMed1993

Grammatical formalization of metabolic processes.

In the field of biotechnology and medicine it is of interest to model and simulate metabolic processes. The usual methods to model metabolic pathways are chemical descriptions and differential equations. Moreover, the graph theoretical aspect is discussed and the development of expert systems is in process. In this paper we present the formalization of metabolic processes. Our formalization is based on the theory of formal languages. This formalization is called genetic grammar and represents an expansion of the Semi-Thue-System.

Computer Simulation↗
PubMed1996

Implications of the Java language on computer-based patient records.

The growth of the utilization of the World Wide Web (WWW) as a medium for the delivery of computer-based patient records (CBPR) has created a new paradigm in which clinical information may be delivered. Until recently the authoring tools and environment for application development on the WWW have been limited to Hyper Text Markup Language (HTML) utilizing common gateway interface scripts. While, at times, this provides an effective medium for the delivery of CBPR, it is a less than optimal solution. The server-centric dynamics and low levels of interactivity do not provide for a robust application which is required in a clinical environment. The emergence of Sun Microsystems' Java language is a solution to the problem. In this paper we examine the Java language and its implications to the CBPR. A quantitative and qualitative assessment was performed. The Java environment is compared to HTML and Telnet CBPR environments. Qualitative comparisons include level of interactivity, server load, client load, ease of use, and application capabilities. Quantitative comparisons include data transfer time delays. The Java language has demonstrated promise for delivering CBPRs.

Computer Communication Networks↗
PubMed1978

Computer-assisted analysis of written language: assessing the written language of deaf children.

Methods for assessing the written language of deaf students are reviewed. The merits and shortcomings of various objective indicators that have traditionally been used are discussed. These include various measures of total output, such as total number of words or sentences, and simple measures of diversity of usage such as the type-token ratio. There have been several attempts in recent years to include objective measures of syntactic complexity as part of an overall language assessment program. The use of a computer to assist teachers in the derivation of such syntactic measures is described. Two illustrative examples are provided. The first shows how the computer system performs a detailed syntactic analysis on a typical sentence taken from the written language of a deaf child. The second example shows how the system provides a summary analysis of several sentences in a theme. A statistical count of the syntactic forms used in the written language sample is provided at the end of the analysis.

Adolescent↗
PubMed2006

The Surgical Simulation and Training Markup Language (SSTML): an XML-based language for medical simulation.

Under contract with the Telemedicine & Advanced Technology Research Center (TATRC), Energid Technologies is developing a new XML-based language for describing surgical training exercises, the Surgical Simulation and Training Markup Language (SSTML). SSTML must represent everything from organ models (including tissue properties) to surgical procedures. SSTML is an open language (i.e., freely downloadable) that defines surgical training data through an XML schema. This article focuses on the data representation of the surgical procedures and organ modeling, as they highlight the need for a standard language and illustrate the features of SSTML. Integration of SSTML with software is also discussed.

Computer Simulation↗
PubMed1998

The globalization of crystallographic knowledge.

The rapid growth of the World Wide Web provides major new opportunities for distributed databases, especially in macromolecular science. A new generation of technology, based on structured documents (SD), is being developed which will integrate documents and data in a seamless manner. This offers experimentalists the chance to publish and archive high-quality data from any discipline. Data and documents from different disciplines can be combined and searched using technology such as eXtensible Markup Language (XML) and its associated support for hypermedia (XLL), metadata (RDF) and stylesheets (XSL). Opportunities in crystallography and related disciplines are described.

Crystallography↗
PubMed1996

The "SentiWeb" method for exploring a database on the Net.

Return of information is one of the main goals of any public health information system. About 25,000 maps and 10,000 graphs may be obtained from the time-series collected in the database of the French Communicable Diseases Network (FCDN). Furthermore, this huge epidemiological atlas is updated each week. What is the optimal way of returning such information? This report discloses the strategies used for enhancing the access facilities to the FCDN database for any users, particularly those without specific training in epidemiology or database query language. The technical options implemented in the SentiWeb server (http:/(/)www.b3e.jussieu.fr) are discussed.

Communicable Diseases↗
PubMed2006

Web-based diagnostic imaging service using XML forms.

Traditionally, radiology has been conceived as a support department providing patient scanning services to the other clinical departments in a hospital. However, recent advancements in networking technology and related information systems such as picture archiving and communication system (PACS) and radiology information system (RIS) provide new opportunities for inventing different types of diagnostic imaging businesses such as teleradiology. In this article, we examined the business processes of currently operating imaging centers and proposed a prototype of an information system that can facilitate their workflows in a more efficient way. The principal component of our proposed system is a report management module built on extensible markup language (XML) technologies that allows much flexibility and convenience for both imaging technicians and radiologists.

Ambulatory Care Facilities↗
PubMed2006

Automated identification of adverse events related to central venous catheters.

Methods for surveillance of adverse events (AEs) in clinical settings are limited by cost, technology, and appropriate data availability. In this study, two methods for semi-automated review of text records within the Veterans Administration database are utilized to identify AEs related to the placement of central venous catheters (CVCs): a Natural Language Processing program and a phrase-matching algorithm. A sample of manually reviewed records were then compared to the results of both methods to assess sensitivity and specificity. The phrase-matching algorithm was found to be a sensitive but relatively non-specific method, whereas a natural language processing system was significantly more specific but less sensitive. Positive predictive values for each method estimated the CVC-associated AE rate at this institution to be 6.4 and 6.2%, respectively. Using both methods together results in acceptable sensitivity and specificity (72.0 and 80.1%, respectively). All methods including manual chart review are limited by incomplete or inaccurate clinician documentation. A secondary finding was related to the completeness of administrative data (ICD-9 and CPT codes) used to identify intensive care unit patients in whom a CVC was placed. Administrative data identified less than 11% of patients who had a CVC placed. This suggests that other methods, including automated methods such as phrase matching, may be more sensitive than administrative data in identifying patients with devices. Considerable potential exists for the use of such methods for the identification of patients at risk, AE surveillance, and prevention of AEs through decision support technologies.

Artificial Intelligence↗
PubMedDate not supplied

Computer languages and operating systems. What they are and how they work.

Programs (software) make a computer's circuits (hardware) perform useful work. This article reviews briefly how computers are programmed, beginning with the storage of data and program instructions. A simple description of how a computer executes a sequence of instructions (program) is followed by the basic concepts of machine-language and assembly-language programming. An overview of higher-level computer languages and a description of the distinction between systems and applications programs are also included.

Computers↗
PubMed2003

Metric-space indexes as a basis for scalable biological databases.

Biochemical databases will be best served by the development of new specialized database management systems whose storage managers are based on metric-space indexing techniques and the development a database query languages that embody semantics derived from biochemical models of similarity and evolution. Important biochemical data types cannot be effectively mapped to low dimensional coordinate systems on which O(log n) indexing methods rely. It is clear from an abundance of bioinformatic discoveries that biochemical data is not random and exhibits interesting structure with respect to clustering. Metric-space indexing exploits a data set's intrinsic clustering to speed the execution of similarity queries, even when the data cannot be mapped to a coordinate system. Database management systems that seamlessly integrate semantically rich query languages with a metric-storage and retrieval mechanism will allow biologists to simply and concisely develop informatic studies that have traditionally been large and labor intensive.

Computational Biology↗
PubMed2002

The Bio* toolkits--a brief overview.

Bioinformatics research is often difficult to do with commercial software. The Open Source BioPerl, BioPython and Biojava projects provide toolkits with multiple functionality that make it easier to create customised pipelines or analysis. This review briefly compares the quirks of the underlying languages and the functionality, documentation, utility and relative advantages of the Bio counterparts, particularly from the point of view of the beginning biologist programmer.

Computational Biology↗
PubMed2004

MuSiC: a tool for multiple sequence alignment with constraints.

SUMMARY: MuSiC is a web server to perform the constrained alignment of a set of sequences, such that the user-specified residues/nucleotides are aligned with each other. The input of the MuSiC system consists of a set of protein/DNA/RNA sequences and a set of user-specified constraints, each with a fragment of residue/nucleotide that (approximately) appears in all input sequences. The output of MuSiC is a constrained multiple sequence alignment in which the fragments of the input sequences whose residues/nucleotides exhibit a given degree of similarity to a constraint are aligned together. The current MuSiC system is implemented in Java language and can be accessed via a simple web interface. AVAILABILITY: http://genome.life.nctu.edu.tw/MUSIC

Algorithms↗