Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “database”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 253 records · Page 14Linked to original sources
PubMedDate not supplied

General database for ground water site information.

In most cases, analysis and modeling of flow and transport dynamics in ground water systems require long-term, high-quality, and multisource data sets. This paper discusses the structure of a multisite database (the H+ database) developed within the scope of the ERO program (French Environmental Research Observatory, http://www.ore.fr). The database provides an interface between field experimentalists and modelers, which can be used on a daily basis. The database structure enables the storage of a large number of data and data types collected from a given site or multiple-site network. The database is well suited to the integration, backup, and retrieval of data for flow and transport modeling in heterogeneous aquifers. It relies on the definition of standards and uses a templated structure, such that any type of geolocalized data obtained from wells, hydrological stations, and meteorological stations can be handled. New types of platforms other than wells, hydrological stations, and meteorological stations, and new types of experiments and/or parameters could easily be added without modifying the database structure. Thus, we propose that the database structure could be used as a template for designing databases for complex sites. An example application is the H+ database, which gathers data collected from a network of hydrogeological sites associated with the French Environmental Research Observatory.

Databases, Factual↗
PubMedDate not supplied

The validity of diagnosing chronic obstructive pulmonary disease from a large administrative database.

BACKGROUND: Health authorities create and maintain administrative databases. Despite the potential advantages of these databases, the validity of the information they include must be considered. OBJECTIVE: To examine the validity of diagnosing chronic obstructive pulmonary disease (COPD) from a large administrative database. METHODS: Physician services and prescription claims data related to COPD and asthma were extracted from the Quebec universal medical insurance register (Régie de l'assurance-maladie du Québec; RAMQ) from the period of April 1, 1994 to March 31, 1999. Before obtaining the data, criteria for the validity of the COPD diagnosis in the database were formulated based on the epidemiology of COPD in the province. The extent to which the database satisfied these criteria are described within the present paper. RESULTS: For patients aged 65 years or older, COPD was two times more prevalent in the RAMQ database than in the 1994/1995 National Population Health Survey. One in three patients with a RAMQ-diagnosis of COPD also had a RAMQ-diagnosis of asthma, and 47% of patients aged 65 years or older with a RAMQ-diagnosis of COPD did not fill any prescription for beta-2-agonists. In addition, 42% of patients with a RAMQ-diagnosis of COPD who never had a RAMQ-diagnosis of asthma appeared only once with that diagnosis in the database. Of all patients aged 65 years or older with a RAMQ-diagnosis of COPD, 37% and 23% met the operational definitions of 'possible COPD' and 'probable COPD', respectively. CONCLUSIONS: Most RAMQ-diagnoses of COPD lack validity; therefore, the validity of database diagnoses should be routinely ascertained before using administrative databases in clinical and health services research.

Adult↗
PubMed2006

CED: a conformational epitope database.

BACKGROUND: Antigen epitopes provide valuable information useful for disease prevention, diagnosis, and treatment. Recently, more and more databases focusing on different types of epitopes have become available. Conformational epitopes are an important form of epitope formed by residues that are sequentially discontinuous but close together in three-dimensional space. These epitopes have implicit structural information, making them attractive for both theoretical and applied biomedical research. However, most existing databases focus on linear rather than conformational epitopes. DESCRIPTION: We describe CED, a special database of well defined conformational epitopes. CED provides a collection of conformational epitopes and related information including the residue make up and location of the epitope, the immunological property of the epitope, the source antigen and corresponding antibody of the epitope. All entries in this database are manually curated from articles published in peer review journals. The database can be browsed or searched through a user-friendly web interface. Most epitopes in CED can also be viewed interactively in the context of their 3D structures. In addition, the entries are also hyperlinked to various databases such as Swiss-Prot, PDB, KEGG and PubMed, providing wide background information. CONCLUSION: A conformational epitope database called CED has been developed as an information resource for investigators involved in both theoretical and applied immunology research. It complements other existing specialised epitope databases. The database is freely available at http://web.kuicr.kyoto-u.ac.jp/~ced.

Animals↗
PubMed2000

A relational database for diagnosis of hematopoietic neoplasms using immunophenotyping by flow cytometry.

A relational database was developed to facilitate the diagnosis of hematopoietic neoplasms using results of immunophenotyping by flow cytometry. This database runs on personal computers and uses backward-chaining search to arrive at conclusions. Results of immunologic marker studies are processed by the database to obtain a set of differential diagnoses. The current version of this database includes diagnostic immunophenotyping pattern for 33 hematopoietic neoplasms. We tested this database using 92 clinical cases from 2 tertiary care medical centers. The database ranked the actual diagnosis as 1 of the top 5 differential diagnoses in 93% of the cases tested. The user can modify the database contents to suit individual needs. This database has been posted on the World Wide Web for direct access. We propose that this user-friendly database is a potential tool for computer-assisted diagnosis of hematopoietic neoplasms.

Antigens, CD↗
PubMed1997

Identifying the active general practice workforce in one division of general practice: the utility of public domain databases.

OBJECTIVE: To identify the non-specialist medical practitioner workforce engaged in active general practice in the region served by the Division of General Practice-Northern Tasmania and to determine the usefulness of public domain databases for enumeration of individual non-specialists providing general practice services. METHODS: A masterlist of the active general practice workforce was compiled by obtaining the names and addresses/postcodes of all non-specialist medical practitioners who were listed in at least one of nine public domain databases and who were confirmed by selected local medical practitioners to be in active general practice in the three months prior to 30 June 1994. This masterlist was used in calculating the sensitivity and positive predictive value (PPV) of each of the nine databases for enumerating non-specialist practitioners in active general practice. RESULTS: Combining the databases resulted in a list of 475 practitioners, which was refined to 139 practitioners who, by our criteria, were in active general practice. Databases had a range of sensitivities and PPVs, but those with high sensitivity tended to have low PPVs, and vice versa. The most useful database for enumerating these practitioners was the mailing list for Australian Family Physician (sensitivity, 94%; PPV, 0.79). CONCLUSIONS: When used alone, no single database had both high sensitivity and high positive predictive value for identifying the active general practice workforce. Combining multiple databases may improve precision. Developing methods to identify recent departures from local active practice has the potential to improve the PPV of existing highly sensitive databases.

Australia↗
PubMed1999

Comparison of literature searches on quality and costs for health technology assessment using the MEDLINE and EMBASE databases.

Biomedical databases are an important source of information for health technology assessment. However, there is considerable variation in the costs of accessing commercial databases. We sought to measure the quality, amount of overlap, and costs of information retrieved from two of the main database sources--MEDLINE and EMBASE. Librarians at two health technology assessment agencies ran a total of eight literature searches on various medical technologies, using both databases. All search results were independently reviewed by two researchers. The researchers were asked to identify relevant references and to rank each of these according to a level of evidence scale. The results were tabulated to show the number of references identified by each database, the number of relevant references ranked by level of evidence, and the number of these references that were unique to one or the other database. The cost of retrieving references from each source was also calculated. Each database contained relevant references not available in the other. Because of the longer time lag for indexing in MEDLINE, many of the references that originally appeared to be unique to EMBASE were subsequently available in MEDLINE as well. Since our study was conducted, MEDLINE has been made available worldwide, free of charge, via the Internet. Hence, the cost difference between the databases is now even greater. However, notwithstanding the costs, it appears that literature searches that rely on only one or the other database will inevitably miss pertinent information.

Abstracting and Indexing↗
PubMed2000

[The ZEBET database on alternative methods to animal experiments in the Internet--a concrete contribution to the protection of animals].

Up from February of the year 2000 ZEBET (German Centre for the Documentation and Validation of Alternative Methods) at the Federal Institute for Consumer Health Protection and Veterinary Medicine (BgVV) put the ZEBET-database on alternative methods to animal experiments on the Internet in English via DIMDI, the German Institute for Medical Documentation and Information (http://gripsdb.dimdi.de/engl/guieng.html). The access is free, moreover DIMDI's complete service is available to visitors of the ZEBET-database. The ZEBET database contains documents on alternatives to testing in animals, which have been carefully evaluated by ZEBET's staff according to the "3Rs"-concept established by Russel and Burch in 1959. Therefore, methods documented in the ZEBET database must meet at least one of the following criteria: "replacement" of an animal experiment by a non-animal method, "reduction" of the number of animals used, "refinement" of an experiment by minimising pain and suffering of animals. In addition, the ZEBET-database provides information on the current stage of development and validation of a method and on the acceptance for either scientific or regulatory purposes. Each document is characterised by the following criteria: the title of a method, keywords, assessment, summary and bibliographic references. To search DIMDI<<s-database and host-system the grips software has to be used. Examples are given for searching in the ZEBET-database. Currently 125 alternative methods are meeting the criteria of the ZEBET database. 50 of them are available online on the internet via DIMDI, the remaining 75 documents will be available by the end of the year 2000. International fellow organisations, e.g. FRAME (Fund for the Replacement of Animals in Medical Experiments) in the UK and CAAT (Johns Hopkins Center for Alternatives to Animal Testing) in the USA, have established links on their web sites to provide visitors free access to the ZEBET-database.

Animal Testing Alternatives↗
PubMed2001

Answering family physicians' clinical questions using electronic medical databases.

OBJECTIVE: We studied the ability of electronic medical databases to provide adequate answers to the clinical questions of family physicians. STUDY DESIGN: Two family physicians attempted to answer 20 questions with each of the databases evaluated. The adequacy of the answers was determined by the 2 physician searchers, and an arbitration panel of 3 family physicians was used if there was disagreement. DATA SOURCE: We identified 38 databases through nominations from national groups of family physicians, medical informaticians, and medical librarians; 14 met predetermined eligibility criteria. OUTCOMES MEASURED: The primary outcome was the proportion of questions adequately answered by each database and by combinations of databases. We also measured mean and median times to obtain adequate answers for individual databases. RESULTS: The agreement between family physician searchers regarding the adequacy of answers was excellent (k=0.94). Five individual databases (STAT!Ref, MDConsult, DynaMed, MAXX, and MDChoice.com) answered at least half of the clinical questions. Some combinations of databases answered 75% or more. The average time to obtain an adequate answer ranged from 2.4 to 6.5 minutes. CONCLUSION: Several current electronic medical databases could answer most of a group of 20 clinical questions derived from family physicians during office practice. However, point-of-care searching is not yet fast enough to address most clinical questions identified during routine clinical practice.

Clinical Competence↗
PubMed2002

Spanish personal name variations in national and international biomedical databases: implications for information retrieval and bibliometric studies.

OBJECTIVES: The study sought to investigate how Spanish names are handled by national and international databases and to identify mistakes that can undermine the usefulness of these databases for locating and retrieving works by Spanish authors. METHODS: The authors sampled 172 articles published by authors from the University of Granada Medical School between 1987 and 1996 and analyzed the variations in how each of their names was indexed in Science Citation Index (SCI), MEDLINE, and Indice Medico Español (IME). The number and types of variants that appeared for each author's name were recorded and compared across databases to identify inconsistencies in indexing practices. We analyzed the relationship between variability (number of variants of an author's name) and productivity (number of items the name was associated with as an author), the consequences for retrieval of information, and the most frequent indexing structures used for Spanish names. RESULTS: The proportion of authors who appeared under more then one name was 48.1% in SCI, 50.7% in MEDLINE, and 69.0% in IME. Productivity correlated directly with variability: more than 50% of the authors listed on five to ten items appeared under more than one name in any given database, and close to 100% of the authors listed on more than ten items appeared under two or more variants. Productivity correlated inversely with retrievability: as the number of variants for a name increased, the number of items retrieved under each variant decreased. For the most highly productive authors, the number of items retrieved under each variant tended toward one. The most frequent indexing methods varied between databases. In MEDLINE and IME, names were indexed correctly as "first surname second surname, first name initial middle name initial" (if present) in 41.7% and 49.5% of the records, respectively. However, in SCI, the most frequent method was "first surname, first name initial second name initial" (48.0% of the records) and first surname and second surname run together, first name initial (18.3%). CONCLUSIONS: Retrievability on the basis of author's name was poor in all three databases. Each database uses accurate indexing methods, but these methods fail to result in consistency or coherence for specific entries. The likely causes of inconsistency are: (1) use by authors of variants of their names during their publication careers, (2) lack of authority control in all three databases, (3) the use of an inappropriate indexing method for Spanish names in SCI, (4) authors' inconsistent behaviors, and (5) possible editorial interventions by some journals. We offer some suggestions as to how to avert the proliferation of author name variants in the databases.

Databases, Bibliographic↗
PubMed2002

Draft secure medical database standard.

Medical database security is a particularly important issue for all Healthcare establishments. Medical information systems are intended to support a wide range of pertinent health issues today, for example: assure the quality of care, support effective management of the health services institutions, monitor and contain the cost of care, implement technology into care without violating social values, ensure the equity and availability of care, preserve humanity despite the proliferation of technology etc.. In this context, medical database security aims primarily to support: high availability, accuracy and consistency of the stored data, the medical professional secrecy and confidentiality, and the protection of the privacy of the patient. These properties, though of technical nature, basically require that the system is actually helpful for medical care and not harmful to patients. These later properties require in turn not only that fundamental ethical principles are not violated by employing database systems, but instead, are effectively enforced by technical means. This document reviews the existing and emerging work on the security of medical database systems. It presents in detail the related problems and requirements related to medical database security. It addresses the problems of medical database security policies, secure design methodologies and implementation techniques. It also describes the current legal framework and regulatory requirements for medical database security. The issue of medical database security guidelines is also examined in detailed. The current national and international efforts in the area are studied. It also gives an overview of the research work in the area. The document also presents in detail the most complete to our knowledge set of security guidelines for the development and operation of medical database systems.

Computer Security↗
PubMed2005

[The Danish Hysterectomy Database seen from a public health-economic perspective].

INTRODUCTION: National clinical databases are a tool for quality improvement in clinical divisions. Furthermore, they can be used to make the quality of health care contributions visible to the population, as part of the free choice of hospital. Using data from one of the Danish nationwide databases, this article is the first to illustrate the potential economic resource gains from the use of these databases. MATERIALS AND METHODS: The calculations performed are based on the Danish Hysterectomy Database. This database has selected quality indicators and measures for quality improvements for a three years period and include reduction of complications to one in three (from 18% to 6%), reduction of admission to one in two (from 4 to 2 days) and reduction of rehospitalisation and reoperation to one in two (from 6% to 3%). RESULTS: Provided the proposed improvements are achieved, the expected resource gain will be approximately Dkr. 22 million (depending on the method of calculation). In-bed per day charges and "hotel charges" may vary considerably among hospitals. DISCUSSION: Every year, Dkr. 15 million are allocated to the national clinical databases, and in 2003, 34 different databases received financial support. The maximum amount that each database can receive is Dkr. 500,000. The amount currently allocated to quality monitoring is small compared to the potential resource gains from these databases and the annual expenditures by the Danish health care sector, which amount to a total of Dkr. 48 billion.

Clinical Competence↗
PubMed1994

Performance of online biomedical databases in rheumatology.

OBJECTIVE: To compare the performance of MEDLINE, EMBASE, and BIOSIS in selected rheumatology topics. METHODS: Online literature searches were conducted with regard to the epidemiology of rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and ankylosing spondylitis (AS), as well as for 3 specific questions representing clinical, clinical/laboratory, and therapeutic topics in rheumatology. Total number of citations retrieved, type and language of publication, percentage of contribution from rheumatology journals, and degree of overlap among the databases were recorded. Publications retrieved for the 3 specific questions were also graded for relevance. RESULTS: For 1991, each online biomedical database (OBD) retrieved more than 1,100 citations for RA, over 600 for SLE, and over 110 for AS. For the epidemiology subtopic, fewer than 25% of the citations were retrieved by more than one of the databases. About 3/4 of the citations obtained for the specific search questions were retrieved by a single database. No major differences were observed among databases in relation to number of relevance of citations retrieved. Over 60% of the papers assessed had low relevance in relation to the topic of the search. Efficiency was estimated as the percentage of all relevant citations retrieved by each OBD. Results varied according to the topic, but in most cases each database retrieved at least 50% of the relevant citations. About 45% of the citations retrieved for the 3 search questions were published in nonrheumatology journals. CONCLUSION: No database was superior in all respects. The majority of the citations were retrieved by a single database. A high percentage of the articles retrieved were not relevant, implying low specificity. If a comprehensive online search in rheumatology is required, 2 or more databases should be utilized.

Arthritis, Rheumatoid↗
PubMed1996

Maintaining patient confidentiality in the public domain Internet Autopsy Database (IAD).

The Internet provides the opportunity of permitting public access to large databases containing patient information that can be shared and utilized by epidemiologists, health planners, and medical researchers. Until now, large databases containing patient information have been held in strict confidence, with database access available only to approved researchers or to researchers with access limited to only specific portions of the database. The Internet Autopsy Database (IAD) consists of demographic and pathologic data from over 49,000 autopsies contributed by over a dozen academic medical institutions. Each autopsy record in the public database consists of a uniform set of demographics and SNOMED-compatible terms. To make the database publicly available, a strategy had to be devised that assured the privacy of every person included in the database. A key step involved translating the autopsy facesheets into a listing of SNOMED-compatible terms that effectively eliminated identifying terminology, replacing free text with a generic nomenclature that preserves diagnostic information. The entire database is available on the Internet at: http:@www.med.jhu.edu/pathology/iad.html

Autopsy↗
PubMed1996

Use of large databases for resolving critical care problems.

Large databases allow for rapid access to large volumes of data. To convert raw data to information, large numbers of data points must be correlated into a descriptive pattern that can be interpreted by the user. Databases must be constructed so as to allow reliable extraction of the raw data into a format that supports analysis of events in a meaningful, objective, and reproducible manner. Databases must be responsive to a variety of users. They must not demand unrealistic amounts of effort on those responsible for data entry. Standard protocols in various stages of development will make databases easier to use and more reliable. Database management tools such as the Internet and the National Library of Medicine will become more integrated into the practice of critical care medicine at all levels, including administration, clinical care, and research. This article provides an overview of the capabilities and difficulties associated with large databases. The major areas of use of large databases in the hospital setting are administration, bibliographic, patient care, research, and education. Each of these areas has different requirements and is supported by different types of databases. The advantages and disadvantages of linear, relational, and object-oriented databases are discussed. Issues relating to methods of data entry and the accuracy and reliability of data are discussed. The challenges involving integration of various sources of data and the interfacing of devices are reviewed.

Critical Care↗
PubMed2003

AraCyc: a biochemical pathway database for Arabidopsis.

AraCyc is a database containing biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource (http://www.arabidopsis.org). The aim of AraCyc is to represent Arabidopsis metabolism as completely as possible with a user-friendly Web-based interface. It presently features more than 170 pathways that include information on compounds, intermediates, cofactors, reactions, genes, proteins, and protein subcellular locations. The database uses Pathway Tools software, which allows the users to visualize a bird's eye view of all pathways in the database down to the individual chemical structures of the compounds. The database was built using Pathway Tools' Pathologic module with MetaCyc, a collection of pathways from more than 150 species, as a reference database. This initial build was manually refined and annotated. More than 20 plant-specific pathways, including carotenoid, brassinosteroid, and gibberellin biosyntheses have been added from the literature. A list of more than 40 plant pathways will be added in the coming months. The quality of the initial, automatic build of the database was compared with the manually improved version, and with EcoCyc, an Escherichia coli database using the same software system that has been manually annotated for many years. In addition, a Perl interface, PerlCyc, was developed that allows programmers to access Pathway Tools databases from the popular Perl language. AraCyc is available at the tools section of The Arabidopsis Information Resource Web site (http://www.arabidopsis.org/tools/aracyc).

Arabidopsis↗
PubMedDate not supplied

Exploring performance issues for a clinical database organized using an entity-attribute-value representation.

BACKGROUND: The entity-attribute-value representation with classes and relationships (EAV/CR) provides a flexible and simple database schema to store heterogeneous biomedical data. In certain circumstances, however, the EAV/CR model is known to retrieve data less efficiently than conventionally based database schemas. OBJECTIVE: To perform a pilot study that systematically quantifies performance differences for database queries directed at real-world microbiology data modeled with EAV/CR and conventional representations, and to explore the relative merits of different EAV/CR query implementation strategies. METHODS: Clinical microbiology data obtained over a ten-year period were stored using both database models. Query execution times were compared for four clinically oriented attribute-centered and entity-centered queries operating under varying conditions of database size and system memory. The performance characteristics of three different EAV/CR query strategies were also examined. RESULTS: Performance was similar for entity-centered queries in the two database models. Performance in the EAV/CR model was approximately three to five times less efficient than its conventional counterpart for attribute-centered queries. The differences in query efficiency became slightly greater as database size increased, although they were reduced with the addition of system memory. The authors found that EAV/CR queries formulated using multiple, simple SQL statements executed in batch were more efficient than single, large SQL statements. CONCLUSION: This paper describes a pilot project to explore issues in and compare query performance for EAV/CR and conventional database representations. Although attribute-centered queries were less efficient in the EAV/CR model, these inefficiencies may be addressable, at least in part, by the use of more powerful hardware or more memory, or both.

Database Management Systems↗
PubMed2004

[The application of human mutation databases].

Researches on genome mutation are becoming more and more important with the finish of human genome DNA draft. This review is to classify the existing human mutation databases, including mutation database, SNP(single nucleotide polymorphisms) databases, mutation databases about disease, mutation databases about proteins, mutation databases about map and mutation information about specific gene. We also give advice on how to utilize these mutation databases, and discuss problems of existing databases.

Databases, Factual↗
PubMed1989

Maintenance of a nutrient database for clinical trials.

Maintenance of a nutrient database for use in dietary analysis for clinical trials and other medical research studies is described. The database, maintained at the University of Minnesota's Nutrition Coordinating Center (NCC), has been used to calculate dietary intake data for a wide range of diet-disease related investigations including studies on cardiovascular disease, hypertension, cancer, gastroenterology, and osteoporosis. Potential sources of error associated with nutrient databases are identified. Criteria are provided for the selection of a nutrient database to meet study objectives and to minimize the potential for errors and inconsistencies. NCC database maintenance procedures, designed to provide updated and verified nutrient calculations for clinical research, involve adherence to standardized procedures for all aspects of database maintenance including data selection, imputations, quality control, recipe calculations, and documentation. By maintaining multiple versions of the database, the NCC is able to update and expand a working version of the database while providing database stability for individual research studies.

Clinical Trials as Topic↗