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At least 343 records · Page 19Linked to original sources
PubMed1991

VIDEOFAR: an epidemiologic tool for drug utilization studies.

VIDEOFAR is a computerized drug prescription monitoring system oriented to gain an epidemiological insight into the phenomenon of "drug prescription". The set of activities carried out within the VIDEOFAR project were focused to: define methods of analysis of prescription data, which could be transferred to the peripherical operating settings of the National Health Service (Local Health Units, Epidemiologic Observatories, Regional Pharmaceutical Services, etc.); implement a Drug Data Base to allow a flexible utilization of information; implement software systems in different computer environments.

Data Collection↗
PubMed2004

The intelligent data management system for toxicogenomics.

Toxicogenomics is now emerging as one of the most important genomic application because the toxicity test based on gene expression profiles is expected to be more precise and efficient than current histopathological approaches in a pre-clinical phase. One of the challenging issues in toxicogenomics is the construction of intelligent database management system which can deal with heterogeneous and complex data from many different experimental and information sources. TEST(Toxicogenomics for Efficient Safety Test) database is especially focused on the connectivity of heterogeneous data and the intelligent query system which enable users to obtain relevant useful information from the complex data sets. The database deals with four kinds of information; compound, histopathology, gene expression, and annotation information. Currently, TEST database maintains toxicogenomics information for 16 compounds, 45 microarrays, 190 animal experiments, and customized 4.8 K rat clone set. Our presented system is expected to be a good information source for studying of toxicology mechanism in the genome-wide level and can also be applied to the designing toxicity test chip.

Animals↗
PubMed2005

[Health surveys in Europe. Overview and activities to harmonize the methods and instruments for comparing the data].

In almost every European country health surveys are conducted in order to describe the health status of the population and to use these data for planning health services and preventive activities. In the last 10-15 years the availability and quality of data from population-based health surveys in Europe have greatly improved, particularly in the countries of Central and Eastern Europe. Nevertheless the design, quality of data and the comparability across countries, nations and cultures remain a challenge. Therefore WHO and EU have started various activities to harmonize the methods and instruments in health surveys. These activities are described in this contribution.

Database Management Systems↗
PubMed2005

Design and development of a web-based application for diabetes patient data management.

A web-based database management system developed for collecting, managing and analysing information of diabetes patients is described here. It is a searchable, client-server, relational database application, developed on the Windows platform using Oracle, Active Server Pages (ASP), Visual Basic Script (VB Script) and Java Script. The software is menu-driven and allows authorized healthcare providers to access, enter, update and analyse patient information. Graphical representation of data can be generated by the system using bar charts and pie charts. An interactive web interface allows users to query the database and generate reports. Alpha- and beta-testing of the system was carried out and the system at present holds records of 500 diabetes patients and is found useful in diagnosis and treatment. In addition to providing patient data on a continuous basis in a simple format, the system is used in population and comparative analysis. It has proved to be of significant advantage to the healthcare provider as compared to the paper-based system.

Diabetes Mellitus↗
PubMed2003

A pesticide runoff model for simulating runoff losses of pesticides from agricultural lands.

An integrated modeling system was developed to predict runoff losses of pesticides from agricultural lands. The system is an integration of a mathematical model, a database system, and a geographic information system. Information on soil type, land use, land slope, watershed boundaries, precipitation, pesticide usage, as well as physical and chemical properties of pesticides have been input to a GIS, managed through a database, and used for further modeling studies. The modeling outputs were in turn put into the database, such that runoff patterns along with pesticides losses could be further simulated by using a database management system. The final results could then be visualized through GIS. The developed modeling system was applied to the Kintore Creek Watershed, Ontario, Canada, for simulating losses of atrazine from agricultural lands. A water quality monitoring project was carried out from 1988 to 1992 in the watershed to detect conditions of surface water pollution due to the use of pesticides. The modeling outputs were verified through the monitoring data, demonstrating reasonable prediction accuracy. The result indicated that the model provides an effective means for forecasting pesticide runoff from agriculture lands.

Agriculture↗
PubMed2006

TMABoost: an integrated system for comprehensive management of tissue microarray data.

In the last decade, high-throughput technologies such as DNA and tissue microarrays (TMAs) have become a means of large-scale investigation of gene expression, providing a plethora of new biomedical data in a relatively short time. Data collection and organization are critical aspects in this process to ensure the quality and reliability of future data interpretation. In this work, we propose a comprehensive approach to handle TMA data with the aim of supporting and promoting biomarker development. We describe a web-based system for the complete management of tissue microarray data in the field of pathology. The system has been in use since June, 2003. Our approach includes automatic localization and identification of tissue microarray samples, and quantitative image analysis that allows high-throughput screening of TMAs by ensuring nonsubjective measures and novel prognosis associations. In this paper, we present the architecture and the components of this system.

Algorithms↗
PubMed2006

SmiNet-2: Description of an internet-based surveillance system for communicable diseases in Sweden.

Electronic systems for communicable diseases surveillance enhance quality by simplifying reporting, improving completeness, and increasing timeliness. In this article we outline the ideas and technologies behind SmiNet-2, a new comprehensive regional/national system for communicable disease surveillance in Sweden. The system allows for reporting from physicians (web form) and laboratories (direct from lab data system) over the internet. Using a unique personal identification number, SmiNet-2 automatically merges clinical and laboratory notifications to case records. Privileged users, at national and county level, work against a common central server containing all notifications and case records. In addition, SmiNet-2 has separate county servers with tools for outbreak investigations, contact tracing and case management. SmiNet-2 was first used in September 2004. Individual counties receive up to 90% of all notifications electronically. In its first year, SmiNet-2 received 54 980 clinical notifications and 32,765 laboratory notifications, which generated 58,891 case records. Since most clinicians in Sweden have easy access to the internet, a general web-based reporting has been feasible, and it is anticipated that within a few years all reporting to SmiNet-2 will be over the internet. In this context, some of the major advantages of SmiNet-2 when compared with other systems are timeliness in the dataflow (up to national level), the full integration of clinical and laboratory notifications, and the capability to handle more than 50 diseases with tailor-made notification forms within one single system.

Communicable Diseases↗
PubMed2001

Heterogeneous database integration in biomedicine.

The rapid expansion of biomedical knowledge, reduction in computing costs, and spread of internet access have created an ocean of electronic data. The decentralized nature of our scientific community and healthcare system, however, has resulted in a patchwork of diverse, or heterogeneous, database implementations, making access to and aggregation of data across databases very difficult. The database heterogeneity problem applies equally to clinical data describing individual patients and biological data characterizing our genome. Specifically, databases are highly heterogeneous with respect to the data models they employ, the data schemas they specify, the query languages they support, and the terminologies they recognize. Heterogeneous database systems attempt to unify disparate databases by providing uniform conceptual schemas that resolve representational heterogeneities, and by providing querying capabilities that aggregate and integrate distributed data. Research in this area has applied a variety of database and knowledge-based techniques, including semantic data modeling, ontology definition, query translation, query optimization, and terminology mapping. Existing systems have addressed heterogeneous database integration in the realms of molecular biology, hospital information systems, and application portability.

Computational Biology↗
PubMed2003

TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts.

TRAIT is a knowledgebase integrating information on transcripts with related data from genome, proteins, ortholog genes and diseases. It was initially built as a system to manage an EST-based gene discovery project on human skeletal muscle, which yielded over 4500 independent sequence clusters. Transcripts are annotated using automatic as well as manual procedures, linking known transcripts to public databases and unknown transcripts to tables of predicted features. Data are stored in a MySQL database. Complex queries are automatically built by means of a user-friendly web interface that allows the concurrent selection of many fields such as ontology, expression level, map position and protein domains. The results are parsed by the system and returned in a ranked order, in respect to the number of satisfied criteria.

Database Management Systems↗
PubMed2006

SPLASH: systematic proteomics laboratory analysis and storage hub.

In the field of proteomics, the increasing difficulty to unify the data format, due to the different platforms/instrumentation and laboratory documentation systems, greatly hinders experimental data verification, exchange, and comparison. Therefore, it is essential to establish standard formats for every necessary aspect of proteomics data. One of the recently published data models is the proteomics experiment data repository [Taylor, C. F., Paton, N. W., Garwood, K. L., Kirby, P. D. et al., Nat. Biotechnol. 2003, 21, 247-254]. Compliant with this format, we developed the systematic proteomics laboratory analysis and storage hub (SPLASH) database system as an informatics infrastructure to support proteomics studies. It consists of three modules and provides proteomics researchers a common platform to store, manage, search, analyze, and exchange their data. (i) Data maintenance includes experimental data entry and update, uploading of experimental results in batch mode, and data exchange in the original PEDRo format. (ii) The data search module provides several means to search the database, to view either the protein information or the differential expression display by clicking on a gel image. (iii) The data mining module contains tools that perform biochemical pathway, statistics-associated gene ontology, and other comparative analyses for all the sample sets to interpret its biological meaning. These features make SPLASH a practical and powerful tool for the proteomics community.

Database Management Systems↗
PubMed2002

IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database.

Recent advances in electron cryomicroscopy instrumentation and single particle reconstruction have created opportunities for high-throughput and high-resolution three-dimensional (3D) structure determination of macromolecular complexes. However, it has become impractical and inefficient to rely on conventional text file data management and command-line programs to organize and process the increasing numbers of image data required in high-resolution studies. Here, we present a distributed relational database for managing complex datasets and its integration into our high-resolution software package IMIRS (Image Management and Icosahedral Reconstruction System). IMIRS consists of a complete set of modular programs for icosahedral reconstruction organized under a graphical user interface and provides options for user-friendly, step-by-step data processing as well as automatic reconstruction. We show that the integration of data management with processing in IMIRS automates the tedious tasks of data management, enables data coherence, and facilitates information sharing in a distributed computer and user environment without significantly increasing the time of program execution. We demonstrate the applicability of IMIRS in icosahedral reconstruction toward high resolution by using it to obtain an 8-A 3D structure of an intermediate-sized dsRNA virus.

Animals↗
PubMed1986

Microcomputer use in an oral biopsy service.

The need for rapid and accurate retrieval of the data generated by an oral biopsy service and the adjacent medical center was met with the purchase and programming of a microcomputer and hard disk drive. The planning phase involved an assessment of the needs of the department, creation of an ideal form to be displayed on the video screen that can be easily used to enter the information, selection of coding systems, and selection of compatible hardware and software. Customized in-house programming using a commercially available database management system has created an entry form and menu-driven information retrieval system tailored to the needs of the department.

Biopsy↗
PubMed2000

EcoGene: a genome sequence database for Escherichia coli K-12.

The EcoGene database provides a set of gene and protein sequences derived from the genome sequence of Escherichia coli K-12. EcoGene is a source of re-annotated sequences for the SWISS-PROT and Colibri databases. EcoGene is used for genetic and physical map compilations in collaboration with the Coli Genetic Stock Center. The EcoGene12 release includes 4293 genes. EcoGene12 differs from the GenBank annotation of the complete genome sequence in several ways, including (i) the revision of 706 predicted or confirmed gene start sites, (ii) the correction or hypothetical reconstruction of 61 frame-shifts caused by either sequence error or mutation, (iii) the reconstruction of 14 protein sequences interrupted by the insertion of IS elements, and (iv) pre-dictions that 92 genes are partially deleted gene fragments. A literature survey identified 717 proteins whose N-terminal amino acids have been verified by sequencing. 12 446 cross-references to 6835 literature citations and s are provided. EcoGene is accessible at a new website: http://bmb.med.miami.edu/EcoGene/EcoWeb. Users can search and retrieve individual EcoGene GenePages or they can download large datasets for incorporation into database management systems, facilitating various genome-scale computational and functional analyses.

Databases, Factual↗
PubMed2005

Database design and implementation for quantitative image analysis research.

Quantitative image analysis (QIA) goes beyond subjective visual assessment to provide computer measurements of the image content, typically following image segmentation to identify anatomical regions of interest (ROIs). Commercially available picture archiving and communication systems focus on storage of image data. They are not well suited to efficient storage and mining of new types of quantitative data. In this paper, we present a system that integrates image segmentation, quantitation, and characterization with database and data mining facilities. The paper includes generic process and data models for QIA in medicine and describes their practical use. The data model is based upon the Digital Imaging and Communications in Medicine (DICOM) data hierarchy, which is augmented with tables to store segmentation results (ROIs) and quantitative data from multiple experiments. Data mining for statistical analysis of the quantitative data is described along with example queries. The database is implemented in PostgreSQL on a UNIX server. Database requirements and capabilities are illustrated through two quantitative imaging experiments related to lung cancer screening and assessment of emphysema lung disease. The system can manage the large amounts of quantitative data necessary for research, development, and deployment of computer-aided diagnosis tools.

Algorithms↗
PubMed1998

Adoption of security and confidentiality features in an operational community health information network: the Comox Valley experience--case example.

Since 1993, a budding community health information network (CHIN) has been in operation in the Comox Valley in Canada. A general hospital and three multi-doctor clinics are linked electronically. The clinics operate without paper charts using a comprehensive clinic information system. The link is provided by RSALink, a commercial message exchange service, based on Health Link, a system developed at the University of Victoria (McDaniel et al., Can. Med. Inform. 1 (1994) 40-41; McDaniel, Dissertation, University of Victoria, Canada, 1994). Health Link is a highly adaptable message exchange service with rich functionality. Despite this, the system is used exclusively to receive laboratory results transmitted by the hospital's laboratory system (RSAStat). The results are deposited in the patient data base of a commercial clinic information system (CliniCare). This case is instructive because the users' selection of services available through Health Link allows us to observe the preferences in this informational sophisticated environment. Laboratory data transmission is appreciated as highly beneficial. The reliability, security and ample privacy protection and authentication features of Health Link, in contrast, are used in a black box mode and are not consciously exploited. This is consistent with our experience of the use of other systems which have operated for a substantial time, essentially without serious protection features. Our experience suggests that security and confidentiality features are exploited only to the extent that they do not require additional effort or conscientious intervention. This puts the system provider in the difficult position of either offering interactive systems that nobody will use, or providing automated features that nobody is aware of and that are therefore not used to full advantage--if at all.

British Columbia↗
PubMed2006

SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.

Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at http://www.evolvingcode.net/codon/sgdb/index.php, or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at http://www.evolvingcode.net/codon/sgdb/aligner.php, and discuss questions, findings and related information on an associated e-forum at http://www.evolvingcode.net/forum/viewforum.php?f=27.

Databases, Nucleic Acid↗