PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Database Management Systems”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources
PubMed1994

Audiometry database system using a local area network.

We linked several audiometers to a personal computer to implement a standard pure-tone audiometric database system using a local area network (LAN). The efficiency of data entry and retrieval was increased by taking advantage of a relational database. The following five programs were developed: automatic incorporation of hearing test data program, audiogram retrieval and display program, patient information incorporation program, data transmission program through LAN, and evaluation of results of tympanoplasty. Data obtained over ten years or more can be rapidly stored and retrieved in this system, making it easier to evaluate the patient's hearing after tympanoplasty.

Audiometry, Pure-Tone↗
PubMed2005

An agent-based system for re-annotation of genomes.

Genome annotation projects can produce incorrect results if they are based on obsolete data or inappropriate models. We have developed an automatic re-annotation system that uses agents to perform repetitive tasks and reports the results to the user. These tasks involve BLAST searches on biological databases (GenBank) and the use of detection tools (Genemark and Glimmer) to identify new open reading frames. Several agents execute these tools and combine their results to produce a list of open reading frames that is sent back to the user. Our goal was to reduce the manual work, executing most tasks automatically by computational tools. A prototype was implemented and validated using Mycoplasma pneumoniae and Haemophilus influenzae original annotated genomes. The results reported by the system identify most of new features present in the re-annotated versions of these genomes.

Computational Biology↗
PubMed2005

SPIN query tools for de-identified research on a humongous database.

The Shared Pathology Informatics Network (SPIN), a research initiative of the National Cancer Institute, will allow for the retrieval of more than 4 million pathology reports and specimens. In this paper, we describe the special query tool as developed for the Indianapolis/Regenstrief SPIN node, integrated into the ever-expanding Indiana Network for Patient care (INPC). This query tool allows for the retrieval of de-identified data sets using complex logic, auto-coded final diagnoses, and intrinsically supports multiple types of statistical analyses. The new SPIN/INPC database represents a new generation of the Regenstrief Medical Record system - a centralized, but federated system of repositories.

Confidentiality↗
PubMed2004

[Construction of directory for biomedical databases on INTERNET].

OBJECTIVE: To construct a global directory of biomedical databases(DBD), which can be used free of charge on INTERNET. It will be convenient for researchers to find out related databases quickly, easily and accurately by using DBD since there are not enough useful tools for database retrieval. Biomedical databases will be an accelerator in development of biomedicine with the help of DBD. METHODS: PubMed and Google were main tools for searching related databases. Proper search strategy with rigorous indexing rules helped us to filter databases. The database management system was Microsoft SQL-Server 2000. The web pages of DBD were designed with Macromedia Dreamwaver MX. ASP (active server pages) technology was used to deal with the key words and scores sent by users. RESULTS: There were 66 subjects and 1 258 databases in DBD at this time. We released the Chinese and English versions of DBD on the INTERNET at the same time http://cmbi.bjmu.edu.cn/DBList/index.htm http://cmbi.bjmu.edu.cn/DBList/index_en.htm . Score system was also established to evaluate the content of the indexed databases. Users can search DBD by subjects key words and alphabetic databases' names easily. CONCLUSION: DBD has laid the primary foundation for further core biomedical database evaluation system. DBD, as a useful tool for biomedical database retrieval, will be of great aid to users since databases have played a more and more important role in the biomedical research.

Databases as Topic↗
PubMed1993

Automated integration of external databases: a knowledge-based approach to enhancing rule-based expert systems.

Expert system applications in the biomedical domain have long been hampered by the difficulty inherent in maintaining and extending large knowledge bases. We have developed a knowledge-based method for automatically augmenting such knowledge bases. The method consists of automatically integrating data contained in commercially available, external, online databases with data contained in an expert system's knowledge base. We have built a prototype system, named DBX, using this technique to augment an expert system's knowledge base as a decision support aid and as a bibliographic retrieval tool. In this paper, we describe this prototype system in detail, illustrate its use, and discuss the lessons we have learned in its implementation.

Artificial Intelligence↗
PubMed2002

Ethical issues in public health informatics: implications for system design when sharing geographic information.

Public health programs today constitute a multi-professional inter-organizational environment, where both health service and other organizations are involved. Developing information systems, including the IT security measures needed to suit this complex context, is a challenge. To ensure that all involved organizations work together towards a common goal, i.e., promotion of health, an intuitive strategy would be to share information freely in these programs. However, in practice it is seldom possible to realize this ideal scenario. One reason may be that ethical issues are often ignored in the system development process. This investigation uses case study methods to explore ethical obstacles originating in the shared use of geographic health information in public health programs and how this affects the design of information systems. Concerns involving confidentiality caused by geographically referenced health information and influences of professional and organizational codes are discussed. The experience presented shows that disregard of ethical issues can result in a prolonged development process for public health information systems. Finally, a theoretical model of design issues based on the case study results is presented.

Computer Security↗
PubMed1986

Establishment of a large collection of extracted teeth for research.

A collection of over 14,000 teeth extracted at the Prince Philip Dental Hospital since 1982 has been organized and catalogued on a computerized database management system. The computer catalogue provides, for each tooth in the collection, information on the age and sex of the patient, and the date of extraction and condition of the tooth. The catalogue can be searched according to any combination of the descriptive variables in the database record. Researchers, including visiting scientists, can borrow teeth from the central "tooth library" on a temporary or permanent basis. Further information on particular teeth (e.g. patient's medical and dental histories, dental radiographs) can be obtained from patients' charts. Establishment of this collection has greatly facilitated the work of researchers in clinical dentistry, dental anatomy, and dental anthropology.

Humans↗
PubMed2004

Airborne gamma spectrometry--towards integration of European operational capability.

Airborne gamma spectrometry is an excellent tool for finding out in a timely manner the extent and magnitude of the dispersion of radioactive materials resulting from a nuclear disaster. To utilise existing European airborne monitoring capabilities for multilateral assistance in an accident is a complex administrative and technical matter. Several international exercises have been organised demonstrating the capability to cooperate. However, efficient mutual assistance between European countries requires conceptual work, standards and harmonisation of software. A unified radiological vocabulary and data exchange format in XML need to be developed. A comprehensive database is essential for data assimilation. An operations centre is needed for management and planning of surveys.

Aircraft↗
PubMed2006

WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks.

SUMMARY: WebCell is a web-based environment for managing quantitative and qualitative information on cellular networks and for interactively exploring their steady-state and dynamic behaviors in response to systemic perturbations. It is designed as a user-friendly web interface, allowing users to efficiently construct, visualize, analyze and store reaction network models, thereby facilitating kinetic modeling and in silico simulation of biological systems of interest. A collected model library is also available to provide comprehensive implications for cellular dynamics of the published models.

Cell Physiological Phenomena↗
PubMed2003

Metabolic database systems for the analysis of genome-wide function.

Genome sequencing projects provide an inventory of molecular components for a wide variety of organisms. Metabolic databases integrate these functional descriptions of individual modules into a higher-level characterization of cellular metabolism. This article reviews efforts related to the development of metabolic databases and discusses how such systems have aided the delineation of genome properties. We illustrate the design features of metabolic databases and discuss the challenges facing metabolic as well as databases of other functional type.

Database Management Systems↗
PubMed2002

SubtiList: the reference database for the Bacillus subtilis genome.

SubtiList is the reference database dedicated to the genome of Bacillus subtilis 168, the paradigm of Gram-positive endospore-forming bacteria. Developed in the framework of the B.subtilis genome project, SubtiList provides a curated dataset of DNA and protein sequences, combined with the relevant annotations and functional assignments. Information about gene functions and products is continuously updated by linking relevant bibliographic references. Recently, sequence corrections arising from both systematic verifications and submissions by individual scientists were included in the reference genome sequence. SubtiList is based on a generic relational data schema and a World Wide Web interface developed for the handling of bacterial genomes, called GenoList. The World Wide Web interface was designed to allow users to easily browse through genome data and retrieve information according to common biological queries. SubtiList also provides more elaborate tools, such as pattern searching, which are tightly connected to the overall browsing system. SubtiList is accessible at http://genolist.pasteur.fr/SubtiList/. Similar bacterial databases are accessible at http://genolist.pasteur.fr/.

Bacillus subtilis↗
PubMed2006

Status of clinical gene sequencing data reporting and associated risks for information loss.

Clinical gene sequencing is growing in importance and cost-effectiveness. In the past two years, the number of genes associated with disease has grown by roughly 25%. Knowledge of genetic variations will soon guide drug selection and dosages, predict risks from toxin exposures, and inform nutritional needs. Despite the significance of sequencing, methods for reporting results are problematic. Frequent use of paper and infrequent use of naming standards impede data exchange and make incorporation into the electronic medical record difficult. Reports often describe only variations found, rather than all data (all patient bases sequenced). Also, reports frequently do not describe reference data used to define variations. These practices create risks for loss of both data and information. Standardized electronic reporting of all data (all bases sequenced and all reference data) and electronic record systems capable of storing these results would both prevent data loss and simplify the preservation of information those data provide.

Computer Security↗
PubMed2003

Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.

The flood of data acquired from the increasing number of publicly available genomes has led to new demands for bioinformatics software. With the growing amount of information resulting from high throughput experiments new questions arise that often focus on the comparison of genes, genomes, and their expression profiles. Inferring new knowledge by combining different kinds of "post-genomics" data obviously necessitates the development of new approaches that allow the integration of variable data sources into a flexible framework. In this paper, we describe our concept for the integration of heterogeneous data into a platform for systems biology. We have implemented a Bioinformatics Resource for the Integration of heterogeneous Data from Genomic Explorations (BRIDGE) and illustrate the usability of our approach as a platform for systems biology for two sample applications.

Algorithms↗
PubMedDate not supplied

New role of a medical documentation system.

Architecture of a new medical documentation system (MDS) is proposed. First, we studied the traditional MDS in terms of organizational structure, main functions, means (resources) and personnel. Special emphasis is given to the information retrieval (IR) system which is the kernel of a MDS. Then, some achievements of information technology is summarized, and concept of a mixed IR system which is the kernel of the new system is presented. New architecture is then presented. Units which compose the entire system are: host documentation centre, local documentation centres, and documentation units. Eventually, objective and features of every part are discussed.

Database Management Systems↗
PubMed1993

A service-oriented information sources database for the biological sciences.

Researchers in the biological sciences require access to a variety of information sources located in various places on different computer networks. In order to satisfy the information needs of a researcher, appropriate information sources must be selected and access to these information sources and the computing services supporting them must be provided in a way that does not distract the researcher from problems of real interest. At the University of Missouri-Columbia a service-oriented information sources database is being developed as a key component of a layered-model design of an intelligent system which will provide a research environment appropriate to the needs of researchers in the biological sciences.

Artificial Intelligence↗
PubMed2005

Web services and workflow management for biological resources.

BACKGROUND: The completion of the Human Genome Project has resulted in large quantities of biological data which are proving difficult to manage and integrate effectively. There is a need for a system that is able to automate accesses to remote sites and to "understand" the information that it is managing in order to link data properly. Workflow management systems combined with Web Services are promising Information and Communication Technologies (ICT) tools. Some have already been proposed and are being increasingly applied to the biomedical domain, especially as many biology-related Web Services are now becoming available. Information on biological resources and on genomic sequences mutations are two examples of very specialized datasets that are useful for specific research domains. RESULTS: The architecture of a system that is able to access and execute predefined workflows is presented in this paper. Web Services allowing access to the IARC TP53 Mutation Database and CABRI catalogues of biological resources have been implemented and are available on-line. Example workflows which retrieve data from these Web Services have also been created and are available on-line. CONCLUSION: We present a general architecture and some building blocks for the implementation of a system that is able to remotely execute workflows of biomedical interest and show how this approach can effectively produce useful outputs. The further development and implementation of Web Services allowing access to an exhaustive set of biomedical databases and the creation of effective and useful workflows will improve the automation of in-silico analysis.

Animals↗
PubMed2006

Validation of the Provincial Transfer Authorization Centre database: a comprehensive database containing records of all inter-facility patient transfers in the province of Ontario.

BACKGROUND: The Provincial Transfer Authorization Centre (PTAC) was established as a part of the emergency response in Ontario, Canada to the Severe Acute Respiratory Syndrome (SARS) outbreak in 2003. Prior to 2003, data relating to inter-facility patient transfers were not collected in a systematic manner. Then, in an emergency setting, a comprehensive database with a complex data collection process was established. For the first time in Ontario, population-based data for patient movement between healthcare facilities for a population of twelve million are available. The PTAC database stores all patient transfer data in a large database. There are few population-based patient transfer databases and the PTAC database is believed to be the largest example to house this novel dataset. A patient transfer database has also never been validated. This paper presents the validation of the PTAC database. METHODS: A random sample of 100 patient inter-facility transfer records was compared to the corresponding institutional patient records from the sending healthcare facilities. Measures of agreement, including sensitivity, were calculated for the 12 common data variables. RESULTS: Of the 100 randomly selected patient transfer records, 95 (95%) of the corresponding institutional patient records were located. Data variables in the categories patient demographics, facility identification and timing of transfer and reason and urgency of transfer had strong agreement levels. The 10 most commonly used data variables had accuracy rates that ranged from 85.3% to 100% and error rates ranging from 0 to 12.6%. These same variables had sensitivity values ranging from 0.87 to 1.0. CONCLUSION: The very high level of agreement between institutional patient records and the PTAC data for fields compared in this study supports the validity of the PTAC database. For the first time, a population-based patient transfer database has been established. Although it was created during an emergency situation and data collection is dependent on front-line medical workers, the PTAC data has achieved a high level of validity, perhaps even higher than many purpose built databases created during non-emergency settings.

Database Management Systems↗