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PubMed2004

SignalML: metaformat for description of biomedical time series.

This paper introduces a complete and elegant solution to the problem of inherent incompatibility of different formats used for digital storage of biomedical time series (in particular EEG) and their annotations. We define a simple XML-based language, in which information on the structure of binary data files can be simply and efficiently coded. In most cases, description of an existing format takes relatively few lines of XML code. Once written, this information can be used by any software, which, owing to this meta-description, may read the original data files, thus eliminating the need for conversions and duplication of data. This proposition is hereby submitted to an open discussion within the community involved in relevant research, clinical and commercial applications. Links to the current version of the XML Schema defining the language and pilot implementation of a compliant viewer/annotator are located at http://eeg.pl/SignalML/.

Database Management Systems↗
PubMed1997

The GRAIL concept modelling language for medical terminology.

The GALEN representation and integration language (GRAIL) has been developed to support effective clinical user interfaces and extensible re-usable models of medical terminology. It has been used successfully to develop the prototype GALEN common reference (CORE) model for medical terminology and for a series of projects in clinical user interfaces within the GALEN and PEN&PAD projects. GRAIL is a description logic or frame language with novel features to support part-whole and other transitive relations and to support the GALEN modelling style aimed at re-use and application independence. GRAIL began as an experimental language. However, it has clarified many requirements for an effective knowledge representation language for clinical concepts. It still has numerous limitations despite its practical successes. The GRAIL experience is expected to form the basis for future languages which meet the same requirements but have greater expressiveness and more soundly based semantics. This paper provides a description and motivation for the GRAIL language and gives examples of the modelling paradigm which it supports.

Artificial Intelligence↗
PubMed2001

Numeric simulation of plant signaling networks.

Plants have evolved an intricate signaling apparatus that integrates relevant information and allows an optimal response to environmental conditions. For instance, the coordination of defense responses against pathogens involves sophisticated molecular detection and communication systems. Multiple protection strategies may be deployed differentially by the plant according to the nature of the invading organism. These responses are also influenced by the environment, metabolism, and developmental stage of the plant. Though the cellular signaling processes traditionally have been described as linear sequences of events, it is now evident that they may be represented more accurately as network-like structures. The emerging paradigm can be represented readily with the use of Boolean language. This digital (numeric) formalism allows an accurate qualitative description of the signal transduction processes, and a dynamic representation through computer simulation. Moreover, it provides the required power to process the increasing amount of information emerging from the fields of genomics and proteomics, and from the use of new technologies such as microarray analysis. In this review, we have used the Boolean language to represent and analyze part of the signaling network of disease resistance in Arabidopsis.

Algorithms↗
PubMed2004

BIRD: Bio-Image Referral Database. Design and implementation of a new web based and patient multimedia data focused system for effective medical diagnosis and therapy.

This paper presents a low cost software platform prototype supporting health care personnel in retrieving patient referral multimedia data. These information are centralized in a server machine and structured by using a flexible eXtensible Markup Language (XML) Bio-Image Referral Database (BIRD). Data are distributed on demand to requesting client in an Intranet network and transformed via eXtensible Stylesheet Language (XSL) to be visualized in an uniform way on market browsers. The core server operation software has been developed in PHP Hypertext Preprocessor scripting language, which is very versatile and useful for crafting a dynamic Web environment.

Database Management Systems↗
PubMed2000

A language for generating tomographic images of mathematical phantoms.

A computer language is presented that can be used to generate image files, as if the images are created with a CT or a MR scanner. The language defines objects in the "scanner's" coordinate system, as sets of quadratic inequalities. Each of these objects, e.g., an ellipsoid or a half-plane or a cylinder, has its own density. Objects can be superimposed and collections of objects are allowed to translate and rotate. The language allows for a concise way of describing complex objects with precisely defined geometries and densities. An implementation of the language can be used for testing, developing, and analyzing diagnostic software, treatment planning systems, etc. A software module that is based on the language can be made available. The utility of the module for acceptance testing of radiation therapy treatment planning systems is described.

Algorithms↗
PubMed2003

The InterMed approach to sharable computer-interpretable guidelines: a review.

InterMed is a collaboration among research groups from Stanford, Harvard, and Columbia Universities. The primary goal of InterMed has been to develop a sharable language that could serve as a standard for modeling computer-interpretable guidelines (CIGs). This language, called GuideLine Interchange Format (GLIF), has been developed in a collaborative manner and in an open process that has welcomed input from the larger community. The goals and experiences of the InterMed project and lessons that the authors have learned may contribute to the work of other researchers who are developing medical knowledge-based tools. The lessons described include (1) a work process for multi-institutional research and development that considers different viewpoints, (2) an evolutionary lifecycle process for developing medical knowledge representation formats, (3) the role of cognitive methodology to evaluate and assist in the evolutionary development process, (4) development of an architecture and (5) design principles for sharable medical knowledge representation formats, and (6) a process for standardization of a CIG modeling language.

Computer Systems↗
PubMed2003

A meta-data-based learning resource server for medicine.

The World Wide Web (WWW) promises many advantages in the distribution and presentation of electronic learning modules for medical education. However, there is a well-known obstacle: finding the right offers on demand. We developed a solution based on international standards called Learning Resource Server Medicine (LRSMed), which provides a meta-data collection of electronic learning modules. Based on the meta-data, LRSMed offers a service for the learners to retrieve WWW resources at the time of learning. We used the IMS Learning Resource Meta-data Information Model as suitable meta-data specification, the eXtensible Markup Language (XML) as syntax for interfaces and the Oracle suite for implementation. LRSMed is available at http://mmedia.medizin.uni-essen.de/portal/. More than 260 learning resources are currently registered and described. So far a user-interface has been implemented which allows searching, commenting and editing. In the next future we will add an application programming interface (API) for the integration of LRSMed in portals, learning platforms and information systems of hospitals, medical practices or healthcare networks.

Internet↗
PubMed2005

PAT: a protein analysis toolkit for integrated biocomputing on the web.

PAT, for Protein Analysis Toolkit, is an integrated biocomputing server. The main goal of its design was to facilitate the combination of different processing tools for complex protein analyses and to simplify the automation of repetitive tasks. The PAT server provides a standardized web interface to a wide range of protein analysis tools. It is designed as a streamlined analysis environment that implements many features which strongly simplify studies dealing with protein sequences and structures and improve productivity. PAT is able to read and write data in many bioinformatics formats and to create any desired pipeline by seamlessly sending the output of a tool to the input of another tool. PAT can retrieve protein entries from identifier-based queries by using pre-computed database indexes. Users can easily formulate complex queries combining different analysis tools with few mouse clicks, or via a dedicated macro language, and a web session manager provides direct access to any temporary file generated during the user session. PAT is freely accessible on the Internet at http://pat.cbs.cnrs.fr.

Computational Biology↗
PubMedDate not supplied

Comprehensive treatment of children with recurrent serous otitis media.

Myringotomy and tube procedures provide effective relief in the majority of cases of serous otitis media, but at least 14% of children are estimated to have recurrence. These children may be at risk for language delays that have been suspected of causing later language problems. After three months' duration of serous otitis, a language evaluation should be given the infant or child. Any language delay should be promptly treated with a home language stimulation program and, in more extreme cases, there should be a consideration of hearing aid use.

Age Factors↗
PubMed2006

Longitudinal research to promote effective refugee resettlement.

Canada's relative generosity in admitting refugees and fairness in considering refugee claims has earned this country an enviable reputation. However, having opened its doors to those selected, Canada's resettlement policies and programs fail to provide for their needs, and to promote their optimal adaptation. Based on a decade-long investigation of the resettlement of more than 1300 Southeast Asian refugee--'Boat People'--the current report examines how research concerning (a) the impact of pre-migration trauma; (b) the mental health impact of social resources such as the like-ethnic community, refugee sponsorship programs, and language training; and (c) individual coping strategies such as suppressing the past, can contribute both to theory and to improving policy and practice. The presentation acknowledges the contributions of Dr. Alexander H. Leighton by demonstrating the importance of his insistence on the need for a longitudinal perspective both for conducting research and for planning programs and services.

Adaptation, Psychological↗
PubMed2006

Using the open-source statistical language R to analyze the dichotomous Rasch model.

R, an open-source statistical language and data analysis tool, is gaining popularity among psychologists currently teaching statistics. R is especially suitable for teaching advanced topics, such as fitting the dichotomous Rasch model--a topic that involves transforming complicated mathematical formulas into statistical computations. This article describes R's use as a teaching tool and a data analysis software program in the analysis of the Rasch model in item response theory. It also explains thetheory behind, as well as an educator's goals for, fitting the Rasch model with joint maximum likelihood estimation. This article also summarizes the R syntax for parameter estimation and the calculation of fit statistics. The results produced by R is compared with the results obtained from MINISTEP and the output of a conditional logit model. The use of R is encouraged because it is free, supported by a network of peer researchers, and covers both basic and advanced topics in statistics frequently used by psychologists.

Algorithms↗
PubMed2003

Representation of relationships between data in healthcare documents.

In healthcare data are to a large extent represented in narrative textual documents. The analysis of narrative text has not been solved successfully up to now. The results of natural language processing or fully indexing systems have not been completely satisfying. It is in particular difficult to detect and describe reliably relationships between data items in narrative text. The eXtensible Markup Language XML has opened new and very promising perspectives in this environment which could improve the storage, processing and analysis of narrative textual documents in particular in healthcare.

Germany↗
PubMedDate not supplied

Operating experience with the relational patient database.

Our three years of experience in the routine use of a relational database for patient admissions is discussed. Following a brief summary of the principles and structures of the patient database, the problems of relational data manipulation languages (DML) and query languages are discussed in more detail. Experience with the physical representation of the data base is discussed. Our experience shows that a relational database, due to its structural clarity, offers clear advantages: data independence from user applications is achieved with a relational DML. The descriptive query language has end user acceptance problems. Possible reasons for these acceptance problems are analysed in more detail.

Database Management Systems↗
PubMed2002

BioDataServer: a SQL-based service for the online integration of life science data.

Regarding molecular biology, we see an exponential growth of data and knowledge. Among others, this fact is reflected in more than 300 molecular databases which are readily available on the Internet. The usage of these data requires integration tools capable of complex information fusion processes. This paper will present a novel concept for user specific integration of life science data. Our approach is based on a mediator architecture in conjunction with freely adjustable data schemes. The implemented prototype is called BioDataServer and can be accessed on the Internet: http://integration.genophen.de. To realize a comfortable usage of the resulted data sets of the integration process, a SQL-based query language and a XML data format were developed and implemented.

Computational Biology↗
PubMed2005

Building an internationalized content delivery architecture: lessons learned.

Increasingly, small development teams are building internationalized architectures for delivering large amounts of content. The AIM e-Learning project is one such example: in 2 years, 4 people built a system which currently delivers the print equivalent of 1500 pages of text, in 4 languages, to users in over 140 countries world wide. Here we discuss the lessons we have learned through development, including issues surrounding staffing, process, technologies and next steps.

Education, Distance↗
PubMedDate not supplied

Standard Generalized Markup Language for self-defining structured reports.

Structured reporting is the process of using standardized data elements and predetermined data-entry formats to record observations. The Standard Generalized Markup Language (SGML; International Standards Organization (ISO) 8879:1986)--an open, internationally accepted standard for document interchange was used to encode medical observations acquired in an Internet-based structured reporting system. The resulting report is self-documenting: it includes a definition of its allowable data fields and values encoded as a report-specific SGML document type definition (DTD). The data-entry forms, DTD, and report document instances are based on report specifications written in a simple, SGML-based language designed for that purpose. Reporting concepts can be linked with those of external vocabularies such as the Unified Medical Language System (UMLS) Metathesaurus. The use of open standards such as SGML is an important step in the creation of open, universally comprehensible structured reports.

Information Storage and Retrieval↗
PubMed1998

A hypermedia-based medical records management system.

This article presents a new way to manage computerized medical records, based on a totally-hypermedia system. As a matter of fact, the classical use of a database limits the necessary variability of the medical record, in function of both the patient profile and the care practitioner habits. The system we propose is based on a hospital Intranet, and on the XML language. This language allows the definition of semantic tags in hyperdocuments, and thus information retrieval is ensured through semantic tags indexation.

Computer Communication Networks↗