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PubMed1987

Simplifying record linkage: software and strategy.

Although the methodology of record linkage is fairly well developed, there is a need for less expensive methods and simpler software to facilitate trying out different tactics to generate good linkages. The present work has built on a fourth generation language SAS (Statistical Analysis System) with accompanying macroprocessor, to develop a user-friendly and flexible system for both exact and probabilistic matching. The major features of the LINKS system are presented and illustrated using 1979-1984 information from the Manitoba Health Services Commission (MHSC) registry file with the Canadian Mortality Data Base. Initial runs with exact, then probabilistic, matching linked approximately 91% of the Vital Statistics records to corresponding MHSC records. Subsequent modification of parameters improved the linkage to 95%.

Database Management Systems↗
PubMed2002

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

During the past few years, the eXtensible Markup Language (XML) has experienced a growing use for accessing, representing and exchanging information, especially in the health care environment. This paper discusses the potentials of the use of XML for the electronic patient record (EPR) in two ways: 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 three years experiment conducted at the Geneva University Hospital as part of its document-centred EPR.

Medical Records Systems, Computerized↗
PubMed2004

The French language virtual medical university.

The work program of the French Language Virtual Medical University started about 2 years ago, and entered into a real active phase of development and implementation in 2002. Various national programs and organizational initiatives should accelerate and facilitate further appropriation of modem pedagogical approaches by knowledge providers and all users of the FSVMU, so as to advance on the way of virtual education. The French Language Virtual Medical University under the auspices of both the National Conference of Deans of Medical Schools and the International Conference of Deans of French-Speaking Medical Schools has been developed to create a major Internet portal for French-speaking distance medical learning and teaching. This construct should be representative of all medical schools in France and French-speaking countries. Contents will also be translated into English, Spanish and Arabic. All medical disciplines with their various levels of teaching are to be included. Cross-related fields are also going to be present in order to offer full range programs. The latter are intended to provide both initial and continuing education for medical students as well as all other categories of health professionals and medical and scientific research workers. To develop the appropriate technology and make such a portal, on one hand correspond to the specific educational requirements and proper training for health professionals, and on the other hand provide a general access to e-learning in all schools of medicine; in keeping with such goals, the following approaches should be stressed upon. To build a virtual space where individual patients, their families, patient associations as well as the general public, can obtain medical information of good quality for the purposes of both education and prevention. Providing such categories with reliable and validated sources of information, and offering an ethical basis for the increasing practice of e-medicine, represent in today's and tomorrow's world one of the great modern challenges for the medical community. Beyond the sole medical domain, the model offered by the FSVMU should be useful for the French-speaking Universities in all the fields of knowledge and training which are candidate to benefit from new educational means and methods.

Computer Simulation↗
PubMed2003

Standards for detailed clinical models as the basis for medical data exchange and decision support.

INTRODUCTION: Detailed clinical models are necessary to exchange medical data between heterogeneous computer systems and to maintain consistency in a longitudinal electronic medical record system. At Intermountain Health Care (IHC), we have a history of designing detailed clinical models. The purpose of this paper is to share our experience and the lessons we have learned over the last 5 years. DESIGN: IHC's newest model is implemented using eXtensible Markup Language (XML) Schema as the formalism, and conforms to the Health Level Seven (HL7) version 3 data types. The centerpiece of the new strategy is the Clinical Event Model, which is a flexible name-value pair data structure that is tightly linked to a coded terminology. DISCUSSION: We describe IHC's third-generation strategy for representing and implementing detailed clinical models, and discuss the reasons for this design.

Decision Support Systems, Clinical↗
PubMed2000

An evaluation of ontology exchange languages for bioinformatics.

Ontologies are specifications of the concepts in a given field, and of the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics. If the bioinformatics community is to share ontologies effectively, ontologies must be exchanged in a form that uses standardized syntax and semantics. This paper reports on an effort among the authors to evaluate alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community. The study selected a set of candidate languages, and defined a set of capabilities that the ideal ontology-exchange language should satisfy. The study scored the languages according to the degree to which they satisfied each capability. In addition, the authors performed several ontology-exchange experiments with the two languages that received the highest scores: OML and Ontolingua. The result of those experiments, and the main conclusion of this study, was that the frame-based semantic model of Ontolingua is preferable to the conceptual graph model of OML, but that the XML-based syntax of OML is preferable to the Lisp-based syntax of Ontolingua.

Computational Biology↗
PubMed2005

From XML to RDF: how semantic web technologies will change the design of 'omic' standards.

With the ongoing rapid increase in both volume and diversity of 'omic' data (genomics, transcriptomics, proteomics, and others), the development and adoption of data standards is of paramount importance to realize the promise of systems biology. A recent trend in data standard development has been to use extensible markup language (XML) as the preferred mechanism to define data representations. But as illustrated here with a few examples from proteomics data, the syntactic and document-centric XML cannot achieve the level of interoperability required by the highly dynamic and integrated bioinformatics applications. In the present article, we discuss why semantic web technologies, as recommended by the World Wide Web consortium (W3C), expand current data standard technology for biological data representation and management.

Algorithms↗
PubMed2002

Developing and integrating an adverse drug reaction reporting system with the hospital information system.

We have developed an adverse drug reaction (ADR) reporting system integrating it with Hospital Information System (HIS) of the University of Tokyo Hospital. Since this system is designed with JAVA, it is portable without re-compiling to any operating systems on which JAVA virtual machines work. In this system, we implemented an automatic data filling function using XML-based (extended Markup Language) files generated by HIS. This new specification would decrease the time needed for physicians and pharmacists to fill the spontaneous ADR reports. By clicking a button, the report is sent to the text database through Simple Mail Transfer Protocol (SMTP) electronic mails. The destination of the report mail can be changed arbitrarily by administrators, which adds this system more flexibility for practical operation. Although we tried our best to use the SGML-based (Standard Generalized Markup Language) ICH M2 guideline to follow the global standard of the case report, we eventually adopted XML as the output report format. This is because we found some problems in handling two bytes characters with ICH guideline and XML has a lot of useful features. According to our pilot survey conducted at the University of Tokyo Hospital, many physicians answered that our idea, integrating ADR reporting system to HIS, would increase the ADR reporting numbers.

Adverse Drug Reaction Reporting Systems↗
PubMed1995

A tool for provider interaction during patient care: G-CARE.

We have extended the CARE language to facilitate interaction with providers using the Medical Gopher order entry system during patient care to create G-CARE. We have used G-CARE in several randomized controlled trials and for routine clinical applications. The language has evolved and is now able to support nearly all of the decision support. Its flexibility allows G-CARE results to be used at many points throughout the patient care process. Based on actual use of G-CARE, we have found performance issues and lack of dynamically grouped order sets are limitations which need to be addressed.

Decision Making, Computer-Assisted↗
PubMed2003

Multiple metaphor environments: designing for diversity.

This paper advances a proposition for the engineering of interactive computer-based environments capable of exhibiting alternative interactive embodiments to cope with diversity in users, interaction platforms and usage contexts. Such systems are referred to as Multiple Metaphor Environments (MME). The theoretical underpinnings of an MME rely on a conception of HCI design as mapping functions in a machine-oriented language (target domain) to symbols in a user-oriented language (source domain), and vice versa. Such a conception, which is rooted in developments in communication theory and the philosophy of language, constitutes the baseline for formulating a proposal for the design of MME. The proposal comprises a set of engineering principles, process-oriented guidelines and design techniques intended to facilitate a detailed account of how interactive systems could be designed to cope with diversity. To aid the articulation of the various properties of MME, we refer to concrete case studies that provide exemplars of novel insights and promising design practices towards the specification of MME.

Artificial Intelligence↗
PubMed2004

A front-end automation tool supporting design, verification and reuse of SOC.

This paper describes an in-house developed language tool called VPerl used in developing a 250 MHz 32-bit high-performance low power embedded CPU core. The authors showed that use of this tool can compress the Verilog code by more than a factor of 5, increase the efficiency of the front-end design, reduce the bug rate significantly. This tool can be used to enhance the reusability of an intellectual property model, and facilitate porting design for different platforms.

Algorithms↗
PubMed2003

[Application of virtual reality modeling language in the fields of medical digital image].

This research aims at the process of three-dimensional(3D) reconstruction from medical body data using VRML and VC++, JavaScript language and focuses on the application of VRML for 3D reconstruction of medical digital images. The 2D medical digital images firstly are modified in VC++ language. Then, the images are manipulated by mould built in VRML and modified in JavaScript language. Finally, the 3D reconstruction of body internal organs can be formed in high quality near to those got in traditional methods. Furthermore, VRML browser can offer better windows of man-computer interaction in real time environment. As a new method and tool quite different from traditional ways of 3D reconstruction, VRML is useful for the visualization of medical 3D reconstruction based on 2D images and has a promising prospect in the field of medical image.

Image Processing, Computer-Assisted↗
PubMed2003

The UMLS knowledge source server: an object model for delivering UMLS data.

The Unified Medical Language System (UMLS), a project of the National Library of Medicine (NLM), regularly distributes a set of knowledge sources to the research community. These data are made available over the Internet through the UMLS Knowledge Source Server (UMLSKS). The new version of the UMLSKS is a complete redesign of the original system using Java and the Extensible Markup Language (XML) technologies to implement a fast, reliable, flexible, and extensible UMLS data retrieval system that includes an Application Programmer's Interface (API) and an Object Model of each of the Knowledge Sources: the UMLS Metathesaurus, the Semantic Network, and the SPECIALIST Lexicon. In this paper we present the design of the new system, outline each of the system design goals, the UMLS Object Model, and statistics showing the usage of the new UMLSKS and associated data. We conclude with implications for future work.

Information Storage and Retrieval↗
PubMed1999

Formal description of temporal knowledge in case reports.

Patient case analysis is an elementary and crucial process which clinicians are daily confronted with. The importance and complexity is reflected in the need to discuss cases in clinicopathological conferences and the documentation of more than 70,000 patient cases in MEDLINE. This paper introduces a generic patient case report language (PCRL) based on general medical temporal concepts to formalise temporal knowledge as present in case descriptions. The lack of such a generic technique is reflected by the fact that computers are very restrictive in accepting patient specific temporal information. Acceptance is almost always controlled and guided by specific predefined disease or treatment models. We strive for a case library consisting of unambiguous patient case descriptions formulated independent from future use.

Decision Making, Computer-Assisted↗
PubMed1999

Motif-based searching in TOPS protein topology databases.

MOTIVATION: TOPS cartoons are a schematic ion of protein three-dimensional structures in two dimensions, and are used for understanding and manual comparison of protein folds. Recently, an algorithm that produces the cartoons automatically from protein structures has been devised and cartoons have been generated to represent all the structures in the structural databank. There is now a need to be able to define target topological patterns and to search the database for matching domains. RESULTS: We have devised a formal language for describing TOPS diagrams and patterns, and have designed an efficient algorithm to match a pattern to a set of diagrams. A pattern-matching system has been implemented, and tested on a database derived from all the current entries in the Protein Data Bank (15,000 domains). Users can search on patterns selected from a library of motifs or, alternatively, they can define their own search patterns. AVAILABILITY: The system is accessible over the Web at http://tops.ebi.ac.uk/tops

Algorithms↗
PubMed2005

Design of a data model for developing laboratory information management and analysis systems for protein production.

Data management has emerged as one of the central issues in the high-throughput processes of taking a protein target sequence through to a protein sample. To simplify this task, and following extensive consultation with the international structural genomics community, we describe here a model of the data related to protein production. The model is suitable for both large and small facilities for use in tracking samples, experiments, and results through the many procedures involved. The model is described in Unified Modeling Language (UML). In addition, we present relational database schemas derived from the UML. These relational schemas are already in use in a number of data management projects.

Algorithms↗
PubMed2002

Biological data integration: wrapping data and tools.

Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat files, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an eXtensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.

Algorithms↗
PubMedDate not supplied

Comparing computer-interpretable guideline models: a case-study approach.

OBJECTIVES: Many groups are developing computer-interpretable clinical guidelines (CIGs) for use during clinical encounters. CIGs use "Task-Network Models" for representation but differ in their approaches to addressing particular modeling challenges. We have studied similarities and differences between CIGs in order to identify issues that must be resolved before a consensus on a set of common components can be developed. DESIGN: We compared six models: Asbru, EON, GLIF, GUIDE, PRODIGY, and PROforma. Collaborators from groups that created these models represented, in their own formalisms, portions of two guidelines: American College of Chest Physicians cough guidelines [correction] and the Sixth Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure. MEASUREMENTS: We compared the models according to eight components that capture the structure of CIGs. The components enable modelers to encode guidelines as plans that organize decision and action tasks in networks. They also enable the encoded guidelines to be linked with patient data-a key requirement for enabling patient-specific decision support. RESULTS: We found consensus on many components, including plan organization, expression language, conceptual medical record model, medical concept model, and data abstractions. Differences were most apparent in underlying decision models, goal representation, use of scenarios, and structured medical actions. CONCLUSION: We identified guideline components that the CIG community could adopt as standards. Some of the participants are pursuing standardization of these components under the auspices of HL7.

Decision Support Systems, Clinical↗
PubMed2001

Computerization of guidelines: towards a "guideline markup language".

Medical decision making is one of the most difficult daily tasks for physicians. Guidelines have been designed to reduce variance between physicians in daily practice, to improve patient outcomes and to control costs. In fact, few physicians use guidelines in daily practice. A way to ease the use of guidelines is to implement computerised guidelines (computer reminders). We present in this paper a method of computerising guidelines. Our objectives were: 1) to propose a generic model that can be instantiated for any specific guidelines; 2) to use eXtensible Markup Language (XML) as a guideline representation language to instantiate the generic model for a specific guideline. Our model is an object representation of a clinical algorithm, it has been validated by running two different guidelines issued by a French official Agency. In spite of some limitations, we found that this model is expressive enough to represent complex guidelines devoted to diabetes and hypertension management. We conclude that XML can be used as a description format to structure guidelines and as an interface between paper-based guidelines and computer applications.

Decision Making, Computer-Assisted↗