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.

SourceResearch connectionFrom yearThrough year

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

At least 721 records · Page 40Linked to original sources

PubMed1995

Development of distributed image database combined with clinical information in hospital information system.

We have developed a distributed image database system composed of the data in our medium-scale PACS that provides diagnostic-quality images and the data in our HIS. INFORMIX software was used to construct the distributed relational database. The data in HIS were retrieved using several programs written in COBOL. Image data in PACS were retrieved using ACR-NEMA protocols. The data retrieved from the HIS database involved medication, disease entities, laboratory test results, etc. Therefore, the image data on a given patient can be retrieved by specifying the name of the disease in our database system. Our method offers a practical one to make a global database system to maintain the integrity of the data in the HIS and the PACS. The combination of image data and disease made it quite easy to make a sample database for developing a computer-aided diagnostic system.

Computer Communication Networks↗

PubMed1996

Applying the object paradigm to a centralized database for a cardiology division.

In order to master the overwhelming quantity of data produced by the different laboratories of our Cardiology Division, we are presently developing a centralized database. Our aim is to improve the quality of diagnoses and therapies by constituting patient centered medical files integrating logically the results of the results of the different examinations and allowing for a rapid access to the patient data. The database has to be accessible from an heterogeneous set of PC, MacIntoshes and UNIX workstations. It must have an ergonomic graphic user interface and generate reports which can be sent to the patient physician. It is well known that the requirements for a medical database make its conceptual analysis very difficult. As medical knowledge continually evolves, the examination protocols change and, therefore, the data sets have to be updated. The maintenance of classical databases is usually expensive because it requires specialized staff to alter the database structure and to adapt the user interface. To allow for flexibility, modularity, code reusability and reliability, the object paradigm was applied to a classical relational database. Thanks to the combination of both data structure and behavior in single entities, it is possible to build generic user interfaces which can be easily tailored to the needs of every laboratory of our Cardiology Division.

Cardiology↗

PubMed1999

Mammography status using patient self-reports and computerized radiology database.

OBJECTIVES: This study sought to compare self-reported mammography use of low-income women utilizing an inner-city public hospital with a computerized hospital database for tracking mammography use. METHODS: A survey of all age-eligible women using the hospital's internal medicine clinic was done; responses were matched with the radiology database. We examined concordance among the two data sources. RESULTS: Concordance between self-report and the database was high (82%) when using "ever had a mammogram at the hospital," but low (58%) when comparing self-reported last mammogram with the information contained in the database. CONCLUSIONS: Disagreements existed between self-reports and the database. Because we sought to ensure that women would know exactly what a mammogram entailed by including a picture of a woman having a mammogram, it is possible that women's responses were accurate, leading to concerns that discrepancies might be present in the database. Physicians and staff must ensure that they understand the full history of a woman's experience with mammography before recommending for or against the procedure.

Aged↗

PubMed2003

Performance change of mammographic CAD schemes optimized with most-recent and prior image databases.

RATIONALE AND OBJECTIVES: The authors evaluated performance changes in the detection of masses on "current" (latest) and "prior" images by computer-aided diagnosis (CAD) schemes that had been optimized with databases of current and prior mammograms. MATERIALS AND METHODS: The authors selected 260 pairs of matched consecutive mammograms. Each current image depicted one or two verified masses. All prior images had been interpreted originally as negative or probably benign. A CAD scheme initially detected 261 mass regions and 465 false-positive regions on the current images, and 252 corresponding mass regions (early signs) and 471 false-positive regions on prior images. These regions were divided into two training and two testing databases. The current and prior training databases were used to optimize two CAD schemes with a genetic algorithm. These schemes were evaluated with two independent testing databases. RESULTS: The scheme optimized with current images produced areas under the receiver operating characteristic curve of (0.89 +/- 0.01 and 0.65 +/- 0.02 when tested with current images and prior images, respectively. The scheme optimized with prior images produced areas under the receiver operating characteristic curve of 0.81 +/- 0.02 and 0.71 +/- 0.02 when tested with current images and prior images, respectively. Performance changes for both current and prior testing databases were significant (P < .01) for the two schemes. CONCLUSION: CAD schemes trained with current images do not perform optimally in detecting masses depicted on prior images. To optimize CAD schemes for early detection, it may be important to include in the training database a large fraction of prior images originally reported as negative and later proven to be positive.

Algorithms↗

PubMedDate not supplied

A framework for the evaluation of chemical structure databases.

Access to desk-top structure and reaction databases through applications such as Chemical Abstracts' SciFinder, MDL's Beilstein CrossFire, and ISIS Reaction Browser has led to changes in information seeking habits of research chemists, the impact of which has implications when database purchasing decisions are made. A semiquantitative assessment is proposed which takes into account key aspects of structure and reaction databases. Assessment criteria are identified which can be weighted according to an organization's information needs. Values are then assigned to criteria for each data source, after which a formula is applied which leads to an indication of the relative value of systems under consideration. The formula takes into account the cost of database products and also the incremental benefit of adding a new system to an existing collection. This work is presented as a generic approach to the evaluation of databases and is not limited in scope to only structure and reactions databases.

Journal Article↗

PubMed2000

Fullerene data mining using bibliometrics and database tomography

Database tomography (DT) is a textual database analysis system consisting of two major components: (1) algorithms for extracting multiword phrase frequencies and phrase proximities (physical closeness of the multiword technical phrases) from any type of large textual database, to augment (2) interpretative capabilities of the expert human analyst. DT was used to derive technical intelligence from a fullerenes database derived from the Science Citation Index and the Engineering Compendex. Phrase frequency analysis by the technical domain experts provided the pervasive technical themes of the fullerenes database, and phrase proximity analysis provided the relationships among the pervasive technical themes. Bibliometric analysis of the fullerenes literature supplemented the DT results with author/journal/institution publication and citation data. Comparisons of fullerenes results with past analyses of similarly structured near-earth space, chemistry, hypersonic/supersonic flow, aircraft, and ship hydrodynamics databases are made. One important finding is that many of the normalized bibliometric distribution functions are extremely consistent across these diverse technical domains and could reasonably be expected to apply to broader chemical topics than fullerenes that span multiple structural classes. Finally, lessons learned about integrating the technical domain experts with the data mining tools are presented.

Journal Article↗

PubMed1989

Overview of the LiMB database.

The rapidly increasing number of databases relevant to molecular biology has given rise to a need for a coordinated effort to identify, characterize, and link them. The LiMB database, which contains information about molecular biology and related databases, is a step in that direction. It serves molecular biologists seeking data sets containing information relevant to their research, and is also intended to anticipate the needs of database designers and managers building software links for related data sets. We present an abbreviated version of the database here; the full database is available free of charge as described below.

Information Systems↗

PubMed1989

A relational database of protein structures designed for flexible enquiries about conformation.

A relational database of protein structure has been developed to enable rapid and flexible enquiries about the occurrence of many aspects of protein architecture. The coordinates of 294 proteins from the Brookhaven Data Bank have been processed by standard computer programs to generate many additional terms that quantify aspects of protein structure. These terms include solvent accessibility, main-chain and side-chain dihedral angles, and secondary structure. In a relational database, the information is stored in tables with columns holding the different terms and rows holding the different entries for the terms. The different relational base tables store the information about the protein coordinate set, the different chains in the protein, the amino acid residues and ligands, the atomic coordinates, the salt bridges, the hydrogen bonds, the disulphide bridges and the close tertiary contacts. The database was established under ORACLE management system. Enquiries are constructed in ORACLE using SQL (structured query language) which is simple to use and alleviates the need for extensive computer programs. A single table can be searched for entries that meet various criteria, e.g. all protein solved to better than a given resolution. The power of the database occurs when several tables, or the entries in a single table, are cross-correlated. For example the dihedral angles of proline in the fourth position in an alpha-helix in high resolution structures can be rapidly obtained. The structural database provides a powerful tool to obtain empirical rules about protein conformation. This database of protein structures is part of a joint project between Birkbeck College and Leeds University to establish an integrated data resource of protein sequences and structures (ISIS) that encodes the complex patterns of residues and coordinates that define protein conformation. The entire data resource (ISIS) will provide a system to guide all areas of protein modelling including structure prediction, site-directed mutagenesis and de novo protein design. The availability of ISIS is described in the paper.

Computer Simulation↗

PubMed1990

An object-oriented database for protein structure analysis.

An object-oriented database system has been developed which is being used to store protein structure data. The database can be queried using the logic programming language Prolog or the query language Daplex. Queries retrieve information by navigating through a network of objects which represent the primary, secondary and tertiary structures of proteins. Routines written in both Prolog and Daplex can integrate complex calculations with the retrieval of data from the database, and can also be stored in the database for sharing among users. Thus object-oriented databases are better suited to prototyping applications and answering complex queries about protein structure than relational databases. This system has been used to find loops of varying length and anchor positions when modelling homologous protein structures.

Amino Acid Sequence↗

PubMed2002

CRYSTMET: a database of the structures and powder patterns of metals and intermetallics.

CRYSTMET is a database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) and associated bibliographic, chemical and physical information. Also included are simulated powder diffraction patterns for all of the entries. The database currently contains almost 70,000 entries and covers the literature exhaustively from 1922 to the present. The database is available on CD-ROM with search/analysis software for use on personal computers. This software can be used with any database in the appropriate format; currently CRYSTMET and the ICSD databases are available. This paper describes the database content, the procedures used in its construction, the software made available to the user and a number of potential uses for the data.

Journal Article↗

PubMedDate not supplied

Canadian health databases relevant to Great Lakes Basin research.

Several population-based health databases exist in Canada which provide valuable systematic information for facilitating epidemiological evaluation of human health in the Great Lakes Basin. They include the long-established Canadian Mortality Database, a national birth defects registry, a provincial hospitalization database, and provincial and national cancer registry systems. The most recent addition is the National Enhanced Cancer Surveillance System which currently is being implemented to allow for detailed evaluation of air and water quality concerns in relation to a range of cancer types. The system includes statistical evaluation of geographical cancer incidence patterns; development of a national environmental quality database; and systematic collection of individual risk factor information for a large number of newly diagnosed cancer cases and a population control group. A brief description of each database and examples of relevant research using each of these databases is presented.

Abnormalities, Drug-Induced↗

PubMed2005

The uses of provincial administrative health databases for research on palliative care: Insights from British Columbia, Canada.

BACKGROUND: Research indicating that people increasingly prefer to die at home suggests that palliative care is likely to play a more prominent role in the future of Canada's health care system. Unfortunately, at a time when research evidence should be informing policy and service delivery, little is known about health service utilization by Canadians at the end of life. One existing mechanism that can help address this gap is provincial administrative health data. The purpose of this study was to explore the potential of administrative health data to identify characteristics of palliative care users, patterns of formal service utilization and predictors of palliative care use. METHODS: Bivariate and multivariate analyses were used to examine data from the Capital Health Region, British Columbia Linked Health Databases for the period 1992/93 to 1998/99. The databases examined include continuing care, physician claims, hospital separations, and vital statistics. As the name implies, these databases can be linked at the individual level using unique identifiers so that health services utilization can be tracked across sectors. RESULTS: General patterns of service use among palliative care patients suggest that general practitioner and medical specialist visits have decreased over time and the utilization of hospital beds has increased. Utilization of community-based services (i.e. home support and home nursing care) shows an overall pattern of decline. However, when compared to non-palliative care patients, palliative care patients spent fewer nights in hospital, used fewer hours of home support, and had a greater number of home nursing care visits. CONCLUSIONS: Administrative health databases can provide valuable information for examining service utilization patterns over time. However, given that decisions surrounding the designation of palliative care include factors beyond the scope of administrative databases (such as quality of life, personal preferences, social support), these databases should only be seen as one source of information to inform service delivery and policy decision making.

Journal Article↗

PubMed2005

A national, geographic database of CDC-funded HIV prevention services: development challenges and potential applications.

BACKGROUND: From 2000-2002, the Centers for Disease Control and Prevention (CDC) funded a study that was designed to improve the information available to program planners about the geographic distribution of CDC-funded HIV prevention services provided by community-based organizations (CBOs). Program managers at CDC recognized the potential of a geographic information system (GIS) to organize and analyze information about HIV prevention services and they made GIS a critical component of the study design. The primary objective of this study was to construct a national, geographically-referenced database of HIV prevention services provided by CDC-funded CBOs. We designed a survey instrument to collect information about the geographic service areas where CBOs provided HIV prevention services, then collected data from CBOs that received CDC funding for these services during fiscal year 2000. We developed a GIS database to link questionnaire responses with GIS map layers in a manner that would incorporate overlapping geographies, risk populations and prevention services. We collected geographic service area data in two formats: 1) geopolitical boundaries and 2) geographic distance. RESULTS: The survey response rate was 70.3%, i.e. 1,020 of 1,450 community-based organizations responded. The number of HIV prevention programs administered by each CBO ranged from 1 to 23. The survey provided information about 3,028 prevention programs, including descriptions of intervention types, risk populations, race and ethnicity, CBO location and geographic service area. We incorporated this information into a large GIS database, the HIV Prevention Services Database. The use of geopolitical boundaries provided more accurate results than geographic distance. The use of a reference map with the questionnaire improved completeness, accuracy and precision of service area data. CONCLUSION: The survey instrument design and database development procedures that we used for this study successfully met our objective. The development of the HIV Prevention Services Database for CDC is an important step toward the implementation of a spatial decision support system. Due to the costs involved in a nationwide survey such as this, we recommend that future data collection efforts use Web-based survey methodologies that incorporate interactive maps.

Journal Article↗

PubMed2006

Estimating probabilities of peptide database identifications to LC-FTICR-MS observations.

BACKGROUND: The field of proteomics involves the characterization of the peptides and proteins expressed in a cell under specific conditions. Proteomics has made rapid advances in recent years following the sequencing of the genomes of an increasing number of organisms. A prominent technology for high throughput proteomics analysis is the use of liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS). Meaningful biological conclusions can best be made when the peptide identities returned by this technique are accompanied by measures of accuracy and confidence. METHODS: After a tryptically digested protein mixture is analyzed by LC-FTICR-MS, the observed masses and normalized elution times of the detected features are statistically matched to the theoretical masses and elution times of known peptides listed in a large database. The probability of matching is estimated for each peptide in the reference database using statistical classification methods assuming bivariate Gaussian probability distributions on the uncertainties in the masses and the normalized elution times. RESULTS: A database of 69,220 features from 32 LC-FTICR-MS analyses of a tryptically digested bovine serum albumin (BSA) sample was matched to a database populated with 97% false positive peptides. The percentage of high confidence identifications was found to be consistent with other database search procedures. BSA database peptides were identified with high confidence on average in 14.1 of the 32 analyses. False positives were identified on average in just 2.7 analyses. CONCLUSION: Using a priori probabilities that contrast peptides from expected and unexpected proteins was shown to perform better in identifying target peptides than using equally likely a priori probabilities. This is because a large percentage of the target peptides were similar to unexpected peptides which were included to be false positives. The use of triplicate analyses with a "2 out of 3" reporting rule was shown to have excellent rejection of false positives.

Journal Article↗

PubMedDate not supplied

Design and implementation of secure medical database systems.

Medical database security plays an important role in the overall security of medical information systems and networks. This is both because of the nature of this technology and its widespread use today. Database security not only involves fundamental ethical principles, but also essential prerequisites for effective medical care. The development of appropriate secure medical database design and implementation methodologies is an important research problem in the area and a necessary prerequisite for the successful development of such systems. The general framework and requirements for medical database security are given and a number of parameters of the secure medical database design and implementation problem are presented and discussed in this paper. A secure medical database development methodology is also presented which could help overcome some of the problems currently encountered.

Computer Security↗

PubMed1998

A multimedia database for dermatology.

The World Health Organisation (WHO) Radiation Emergency Medical Preparedness (REMPAN) centres have built up the International Computer Database for Radiation Accident Case Histories (ICDREC) to document the treatment of acute radiation syndrome (ARS) patients. Radiation induced skin lesions may cause severe late effects in radiation accident patients. Dermatological multimedia documentation is included into the ICDREC. In particular, retrieval and display of digitised skin photographs and medical reports serves to improve patient care, medical education, and scientific analysis concerning the cutaneous radiation syndrome (CRS). The database has been built up as a client/server system. A particular focus has been set on using commercial off-the-shelf software components. The medical data including the multimedia data are stored in a relational database system. The database can be accessed by inexpensive personal computers in the dermatologist's workplace. Authorised institutions can access the database via the Internet. Retrieval of one skin photograph via local area network (LAN) requires approximately 3 seconds. The current state of the application is illustrated with the skin lesion treatment of a Chernobyl patient. An example is given on how to access the ICDREC from a dermatologist's desktop personal computer. The discussion focuses on the advantages of storing the textual and pictorial data in one central database to be accessed from different care centres and how the results can be generalised for medical multimedia information systems.

Dermatology↗

PubMed2003

Coding accuracy of administrative drug claims in the Ontario Drug Benefit database.

BACKGROUND: Every year in Ontario, the records of over 42 million prescriptions dispensed to persons eligible for Ontario Drug Benefit (ODB) benefits are transmitted to a central database. The ODB database is the second largest database of medications in Canada, containing records on almost half of all medications dispensed in Ontario. There is no information about the reliability of the coding on the ODB drug claims database and, therefore, the objective of this study was to estimate the reliability of coding of the Drug Identification Number, and the date, quantity and duration of the dispensation on claims sent to the ODB. METHODS: To meet this objective, approximately 100 randomly selected prescriptions dispensed from each of 50 pharmacies in southern Ontario between July 1, 1998 and December 31, 1999 were audited. For each claim, the written information on the prescription was compared with the electronic information submitted to the ODB database. Logistic regression was used to test the association between coding errors and the location, owner affiliation, and productivity of each pharmacy (defined as the annual volume of dispensations divided by the annual number of hours worked by all pharmacists and pharmacy assistants). RESULTS: Of the 183 pharmacies owners invited to participate, consent to abstract information was obtained in 50, yielding a participation rate of 27%. Of the 5155 dispensed prescriptions, 37 errors were found, yielding an overall error rate of 0.7% (95% CI 0.5% to 0.9%). None of the characteristics of pharmacies that were examined (location, owner affiliation, productivity) was associated with coding errors. CONCLUSIONS: Pharmacists almost always dispense the medication that is prescribed and this information is reliably transmitted to the ODB drug claims database. This means that any conclusions drawn by researchers using these data are not likely to be compromised by low coding reliability.

Clinical Pharmacy Information Systems↗

PubMed2001

[Personal identifiability in the Health Sector Database.].

INTRODUCTION: Personal identifiability is a fundamental question in the debate about the Bill and Act on the Health Sector Database (HSD). If the data are personally identifiable, Iceland's international committments dictate that a priori consent be obtained from patients for the use of their health records data. The HSD Act presumes that one way encryption renders the data non-personally identifiable and that therefore an a priori consent is not required. RESULTS: The history of the concept of personal identifiability during the debate on the HSD reveals changes made to the concept. In the first instance a reference was made to Recommendation R(97)5 of the Council of Europe Committee of Ministers which was changed by adopting a direct translation of the definition of personal data from the Directive 95/46/EC of the European Parliament and of the Council. These changes were made in response to the Data Protection Commission's opinion on the HSD Bill submitted to the Minister of Health that overturned the ideology previously used regarding indentifiability of persons. Information is identifiable if there exists a key and it makes no difference who holds the key. One way encryption was then adopted as a method that was supposed to mean that a key does not exist. Nevertheless, the database proponents now admit that a key exists. The making of keys for opening up the database is discussed. The database is a longitudinal collection and linkage of records on each individual and therefore the method of encryption must remain stable. Therefore, anyone with access to the method can easily make a lookup-table containing side by side the names and the personal numbers produced by the encryption. Although it may be hard to go from a personal number directly back to a name, given the table it always is possible to look up what personal number belongs to a certain person or what person stands behind a certain personal number. This is a key. If the method of encryption was lost or access to it was not available it would nevertheless be possible to make a key. The intention is to encrypt the genealogy of the entire nation using the same encryption method used for the HSD. The genealogy of the nation with names is also generally available. The patterns of family trees become unique when one family is connected to another through marriage and childbirth. A comparison of the encrypted genealogy containing personal numbers with the same genealogy containing names is therefore a method for making a key. Finally a key can be made from the context of general information. Even if the names were irreversibly removed there will be enough available bits of general information connected to a personal number to allow re-identification of the person in a large number of instances. This amounts to making a key. CONCLUSIONS: The information in the Health Sector Database is personal information. Therefore it is both right and reasonable to obtain an a priori consent of patients for the transfer of their health data to the database as Iceland's international obligations stipulate. Anything less is unreasonable.

English Abstract↗