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PubMedDate not supplied

Technical implementation of an Internet address database with online maintenance module.

The article describes the technical implementation and management of the Internet address database of the center for ZMK (University of Münster, Dental School) Münster, which is integrated in the "ZMK-Web" website. The editorially maintained system guarantees its topicality primarily due to the electronically organized division of work with the aid of an online maintenance module programmed in JavaScript/PHP, as well as a database-related feedback function for the visitor to the website through configuration-independent direct mail windows programmed in JavaScript/PHP.

Database Management Systems↗
PubMed2002

[The computer aided-therapy system of tumor thermal-treatment instrument using HIFU technology].

Tumor thermal-treatment instrument is a newly developed medical instrument using HIFU technology. On the basis of a brief introduction of the system structure, this paper emphasizes the computer aided-therapy system applying a lot of computer technologies such as digital signal processing, digital signal communication computer aided design, artificial intelligence and database management system. Finally a concise therapy process using computer aided-therapy system is also introduced.

Artificial Intelligence↗
PubMed2004

PaVESy: Pathway Visualization and Editing System.

UNLABELLED: A data managing system for editing and visualization of biological pathways is presented. The main component of PaVESy (Pathway Visualization and Editing System) is a relational SQL database system. The database design allows storage of biological objects, such as metabolites, proteins, genes and respective relations, which are required to assemble metabolic and regulatory biological interactions. The database model accommodates highly flexible annotation of biological objects by user-defined attributes. In addition, specific roles of objects are derived from these attributes in the context of user-defined interactions, e.g. in the course of pathway generation or during editing of the database content. Furthermore, the user may organize and arrange the database content within a folder structure and is free to group and annotate database objects of interest within customizable subsets. Thus, we allow an individualized view on the database content and facilitate user customization. A JAVA-based class library was developed, which serves as the database programming interface to PaVESy. This API provides classes, which implement the concepts of object persistence in SQL databases, such as entries, interactions, annotations, folders and subsets. We created editing and visualization tools for navigation in and visualization of the database content. User approved pathway assemblies are stored and may be retrieved for continued modification, annotation and export. Data export is interfaced with a range of network visualization programs, such as Pajek or other software allowing import of SBML or GML data format. AVAILABILITY: http://pavsey.mpimp-golm.mpg.de

Database Management Systems↗
PubMed2005

Overview of BioCreAtIvE: critical assessment of information extraction for biology.

BACKGROUND: The goal of the first BioCreAtIvE challenge (Critical Assessment of Information Extraction in Biology) was to provide a set of common evaluation tasks to assess the state of the art for text mining applied to biological problems. The results were presented in a workshop held in Granada, Spain March 28-31, 2004. The articles collected in this BMC Bioinformatics supplement entitled "A critical assessment of text mining methods in molecular biology" describe the BioCreAtIvE tasks, systems, results and their independent evaluation. RESULTS: BioCreAtIvE focused on two tasks. The first dealt with extraction of gene or protein names from text, and their mapping into standardized gene identifiers for three model organism databases (fly, mouse, yeast). The second task addressed issues of functional annotation, requiring systems to identify specific text passages that supported Gene Ontology annotations for specific proteins, given full text articles. CONCLUSION: The first BioCreAtIvE assessment achieved a high level of international participation (27 groups from 10 countries). The assessment provided state-of-the-art performance results for a basic task (gene name finding and normalization), where the best systems achieved a balanced 80% precision / recall or better, which potentially makes them suitable for real applications in biology. The results for the advanced task (functional annotation from free text) were significantly lower, demonstrating the current limitations of text-mining approaches where knowledge extrapolation and interpretation are required. In addition, an important contribution of BioCreAtIvE has been the creation and release of training and test data sets for both tasks. There are 22 articles in this special issue, including six that provide analyses of results or data quality for the data sets, including a novel inter-annotator consistency assessment for the test set used in task 2.

Computational Biology↗
PubMed1998

aCHEdb: the database system for ESTHER, the alpha/beta fold family of proteins and the Cholinesterase gene server.

Acetylcholinesterase belongs to a family of proteins, the alpha/beta hydrolase fold family, whose constituents evolutionarily diverged from a common ancestor and share a similar structure of a central beta sheet surrounded by alpha helices. These proteins fulfil a wide range of physiological functions (hydrolases, adhesion molecules, hormone precursors) [Krejci,E., Duval,N., Chatonnet,A., Vincens,P. and Massoulié,J. (1991) Proc. Natl. Acad. Sci. USA , 88, 6647-6651]. ESTHER (for esterases, alpha/beta hydrolase enzymes and relatives) is a database aimed at collecting in one information system, sequence data together with biological annotations and experimental biochemical results related to the structure-function analysis of the enzymes of the family. The major upgrade of the database comes from the use of a new database management system: aCHEdb which uses the ACeDB program designed by Richard Durbin and Jean Thierry-Mieg. It can be found at http://www.ensam.inra.fr/cholinesterase

Animals↗
PubMed1995

CQL: a database in smart card for health care applications.

The CQL-Card is the first smart card in the world to use Database Management Systems (DBMS) concepts. The CQL-Card is particularly suited to a portable file in health applications where the information is required by many different partners, such as health insurance organizations, emergency services, and General Practitioners. All the information required by these different partners can be shared with independent security mechanisms. Database engine functions are carried out by the card, which manages tables, views, and dictionaries. Medical Information is stored in tables and views are logical and dynamic subsets of tables. For owner-partners like MIS (Medical Information System), it is possible to grant privileges (select, insert, update, and delete on table or view) to other partners. Furthermore, dictionaries are structures that contain requested descriptions and which allow adaptation to computer environments. Health information held in the CQL-Card is accessed using CQL (Card Query Language), a high level database query language which is a subset of the standard SQL (Structured Query Language). With this language, CQL-Card can be easily integrated into Medical Information Systems.

France↗
PubMed2002

euGenes: a eukaryote genome information system.

euGenes is a genome information system and database that provides a common summary of eukaryote genes and genomes, at http://iubio.bio.indiana.edu/eugenes/. Seven popular genomes are included: human, mouse, fruitfly, Caenorhabditis elegans worm, Saccharomyces yeast, Arabidopsis mustard weed and zebrafish, with more planned. This information, automatically extracted and updated from several source databases, offers features not readily available through other genome databases to bioscientists looking for gene relationships across organisms. The database describes 150 000 known, predicted and orphan genes, using consistent gene names along with their homologies and associations with a standard vocabulary of molecular functions, cell locations and biological processes. Usable whole-genome maps including features, chromosome locations and molecular data integration are available, as are options to retrieve sequences from these genomes. Search and retrieval methods for these data are easy to use and efficient, allowing one to ask combined questions of sequence features, protein functions and other gene attributes, and fetch results in reports, computable tabular outputs or bulk database forms. These summarized data are useful for integration in other projects, such as gene expression databases. euGenes provides an extensible, flexible genome information system for many organisms.

Animals↗
PubMedDate not supplied

Clinical data repositories: an overview.

Clinical data repositories are becoming mandatory for patient care providers so that the information demands of regulatory and reimbursement entities can be fulfilled. Clinicians who lack experience in the world of information technology are often the driving force behind the purchase of a clinical data repository. This document is intended to provide an understanding of data systems and data utility for those who must combine clinical and financial information to create the best possible patient care delivery system in accordance with stringent financial and regulatory guidelines.

Benchmarking↗
PubMed1996

[Criteria of good manufacturing practice conforming electronic data processing].

Good manufacturing practices (GMP) are not only supported by data management systems but also implicate that they must meet the supplier qualification criteria in terms of GMP. Elements which technically support a GMP-conformity are multiuser-operating systems, relational data bases, object-oriented languages and data parameters. The most important part is covered by human resources of a bloodbank, which starts with the definition and ends with validation tests. Only the required profile of the end-user makes the GMP-conformity of a data management system constructable and realizable. Competence in project-management and clearly structured projects let such systems perform as planned.

Blood Banks↗
PubMed2001

Update on the European database.

The European medical device Directives require the establishment of a centralised database for storing regulatory information and data on medical devices. The work to establish this system is progressing and the database may be operational within 18 to 24 months. This article discusses the work that has been done to establish the database, the types of data to be stored in it, and the current status of the project.

Database Management Systems↗
PubMedDate not supplied

Using a relational database to support nursing research.

Designing, implementing, and maintaining a relational database for a complex, longitudinal clinical research project can be the key to the success of a research project. Related issues of data entry, accuracy, confidentiality, security, data analysis, and evaluation of research activities are among the considerations that must be addressed. Our experience with designing a system that was effective and user-friendly to manage the data collected during a 6-year, National Institutes of Health-funded, nursing research project is highlighted. Nurses and other healthcare providers may find our experience with a relational database helpful and applicable to similar clinical research projects.

Clinical Nursing Research↗
PubMed2000

A methodology for development of configurable remote access measurement system

A configurable remote access measurement system (CRAMS) is designed using an object oriented methodology (OOM) and implemented using the integration of an object oriented language, JAVA, a relational database management system, MS-ACCESS, and an instrumentation software package (LabVIEW). OOM is a powerful technique that is used to manage the complexity of large systems. It allows for easy maintenance and upgrading of the developed systems. The main focus of this paper is to present a detailed procedure for the analysis, design and implementation of CRAMS. The functionality of CRAMS is demonstrated by creating a remotely accessible laboratory environment using a set of programmable and virtual instruments connected to a PC server.

Journal Article↗
PubMed1993

Data management in multi-center clinical trials and the role of a nation-wide computer network. A 5 year evaluation.

Multidisciplinary collaboration in multi-center trials needs a formalized data management structure to ensure true progress monitoring and high quality research data. Cadans, a customized facility for data management, related to the Interuniversity Cardiology Institute of the Netherlands, designed a computer-based data management system for multidisciplinary multi-center collaborative research projects. In this paper we describe the system and the role of integrated access to research databases on a data network. Areas of concern are also discussed.

Cardiology↗
PubMed2006

Properties of a federated epidemiology query system.

PURPOSE: The purpose of the study was to establish knowledge about how online access to epidemiological data from general practitioners (GPs) electronic health record (EHR) system should be provided. Before such systems are developed and deployed a decision about the appropriate system architecture must be made. Such a decision should ideally be based on knowledge about the properties of different system architectures. This choice is important because the system architecture may affect the willingness of GPs to participate in providing epidemiological data from their EHR system. METHOD: Verifying the performance and properties of an architectural approach by implementing and deploying a system on a trans-institutional level and performing evaluations studies is a very resource demanding method to establish a foundation for the decision of appropriate system architecture. Instead, we have tried to create this foundation by constructing a prototype system, establish knowledge about the properties of the system using experiments, and finally compare the properties of the federated approach to the properties of the centralised approach. By using this methodological approach we provide the best available knowledge, on this stage, for the appropriate system architecture to use for providing access to epidemiological data from the local population. RESULTS: Our experimental results show that it is possible to improve the timeliness and the temporal and spatial resolution of epidemiological data, compared to traditional centralised disease surveillance systems. Up-to-date epidemiological data from the local population may be provided directly from the source EHR system within 4s. The responsiveness of the system is minimally affected (0.1s) as the number of participating data providers grows from 1 to 49 data providers. The comparison of the federated approach to the centralised approach indicates that federated approaches avoid the privacy issues involved, as intended; it offers better scalability when computing speed is compared, and it provides better specificity because more data about the patient may be used. CONCLUSION: The conclusion from our study is that the federated approach to providing epidemiological data about the local population has many benefits over the traditional centralised approach. A federated approach to an epidemiology system may raise the GPs awareness of local disease outbreak because it is possible to share information about incidence rates of communicable diseases and use of laboratory requests in a geographical area that predates laboratory-based disease surveillance. The effects of the federated approach could be improved data quality in the EHR systems and improved representativeness of the epidemiological data for the areas covered by such systems.

Database Management Systems↗