SEARCH · PubMed Health

Results for “Database”

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 55 records · Page 3Linked to original sources

PubMed1988

Microcomputer-assisted filing system of cardiac catheterization records using a relational database management system.

To efficiently store and retrieve cardiac catheterization records, we have developed a computer-assisted database, which comprises a 16-bit microcomputer with dual floppy disk drives, a 20 MB random-access memory, hard disk drive, and a line printer. All programmings were accomplished using a relational database management system (R:base 5000, Microrim, Inc.). Data inquiry procedures could be performed with direct operational commands of the system as well as with preprogrammed command files, and final results of searches were printed out with a line printer. The major advantages of the present system described in this report include: (1) the relatively easy and rapid creation of the database, (2) ease of modification of the database structures even after the system design is finished, (3) operational commands in combination with conditional operator(s) are flexible and powerful enough to allow the end user to retrieve data based on various kinds of criteria, (4) a high-level programming language provided by the R:base automates a series of database procedures with relative ease, (5) relational capabilities of the database management system can enhance the possibility of reconstruction of a new data file from a single or several preexisting data files, and (6) the system can be realized at reasonable cost.

Cardiac Catheterization↗

PubMed1991

The gene-protein database of Escherichia coli: edition 4.

The gene-protein database of Escherichia coli has as its core an index that links each of the protein spots from a two-dimensional polyacrylamide gel to the gene that encodes the protein. Additional information about each protein and its gene is generated from two-dimensional gel analysis or collated from the literature to form the database. Earlier editions of the database have provided periodic updates of information. The current edition does this, but also introduces a new reference gel image produced by an electrophoresis system recently adopted in this laboratory. The new gel system was chosen because it offers an improved opportunity for other investigations to produce close replicas of the reference gel pattern, thereby allowing easier access to the information of the database and encouraging independent contribution to the database. The new gel format also is larger and hence more compatible with computer assisted image analysis, which has become essential for a project of this magnitude. This edition continues the use of the former reference gel images, but adds a reference image of an equilibrium gel of E. coli strain W3110 produced by the new standardized gel system. At this time, 55% of the protein spots annotated on the previous equilibrium reference gel for this organism have been located on the new reference image, and these identifications are included in the tables of the database.

Bacterial Proteins↗

PubMed1992

Mouse liver protein database: a catalog of proteins detected by two-dimensional gel electrophoresis.

Alterations in the abundance or structure of mouse liver proteins are being studied using two-dimensional gel electrophoresis (2-DE) to build a database of protein changes correlating with exposure to ionizing radiation or toxic chemicals. Thus far, studies have included the analysis of proteins from the offspring of exposed parents or from the exposed individuals themselves. In order to characterize and identify proteins found altered by such exposures, sex- and strain-related differences in protein patterns have been analyzed, and the subcellular locations of a large portion of the mapped proteins have been determined. As part of these studies, data are collected and stored using a variety of computer hardware and software tools that allow the accumulation of information on the origin of samples, gel identification, experiment description, and protein similarities and differences. This accumulation of information constitutes the mouse liver protein database. Relational database software is used to tie the different facets of the database together so that the results of a variety of experiments can be compared and interrelated. The database optimizes the information obtained from 2-DE gel sets by allowing use of the data for many purposes, including monitoring of gel resolution to ensure the collection of high quality data and correlation of protein effects induced by different agents. This first edition of the Argonne National Laboratory mouse liver protein database lays the foundation for future work and communication that should elucidate the significance of observed protein effects as possible markers of exposure to toxic agents.

Animals↗

PubMed1991

Practice databases and their uses in clinical research.

A few large clinical information databases have been established within larger medical information systems. Although they are smaller than claims databases, these clinical databases offer several advantages: accurate and timely data, rich clinical detail, and continuous parameters (for example, vital signs and laboratory results). However, the nature of the data vary considerably, which affects the kinds of secondary analyses that can be performed. These databases have been used to investigate clinical epidemiology, risk assessment, post-marketing surveillance of drugs, practice variation, resource use, quality assurance, and decision analysis. In addition, practice databases can be used to identify subjects for prospective studies. Further methodologic developments are necessary to deal with the prevalent problems of missing data and various forms of bias if such databases are to grow and contribute valuable clinical information.

Clinical Medicine↗

PubMed1992

Genome-related datasets within the E. coli Genetic Stock Center database.

The contents of the E. coli Genetic Stock Center database and the availability in electronic form of the subset of information most relevant to sequence databases are described. The database uses the long-standing Stock Center records (developed and curated by Dr B.J.Bachmann) in describing genotypes of mutant derivatives of E.coli K-12 in terms of alleles, structural mutations, mating type, and plasmids as well as the derivation, names and originators of the strain, and references. The database includes descriptions of mutations, mutation properties, genes, gene properties, and gene products, with EC number identifiers for enzymes. Sequence information is not included, but entries refer to sequence database accession numbers for sequenced regions. A gene is described as a subtype of a more general category of chromosome interval called Site. Since sites are used to describe any chromosomal interval, mapping information is associated with sites. Alleles are described as mutations of those sites and they are not primary map objects, but inherit map position information from the corresponding site description. The database design is intended to preserve richness of detail where it is known and uncertainty of measurements or information as it occurs in order to represent the stock center records as accurately as possible.

Bacterial Proteins↗

PubMed1991

Comparison and evaluation of nine bibliographic databases concerning adverse drug reactions.

Few evaluations and statistical comparisons of bibliographic databases have been published. As a drug information center, we were particularly interested in databases providing references on adverse drug reactions (ADRs). Ten drugs were randomly chosen from the 2000 files at our center. Nine databases were selected according to the high frequency of references concerning ADRs: eight online systems (MEDLINE, BIOSIS, TOXLINE, Iowa Drug Information System, PASCAL, EMBASE, PHARMLINE, and International Pharmaceutical Abstracts [IPA]), and one Compact Disk Read Only Memory (CD-ROM) system (Core MEDLINE). The total number of references, the number of references from 1987 to 1989, and the number of relevant references from 1987 to 1989 were analyzed using the Friedman two-way ANOVA by ranks. The overlap between databases for only one drug, carboplatin, and the quality:cost ratio were also studied. Considering the total number of references, TOXLINE and EMBASE were significantly superior to IPA, PHARMLINE, PASCAL, and Core MEDLINE. For the period 1987-1989, EMBASE was significantly superior to PASCAL, IPA, PHARMLINE, and Core MEDLINE with regard to total number of references, and significantly superior to PASCAL, Core MEDLINE, and IPA with regard to relevance. MEDLINE, TOXLINE, and EMBASE had the best quality:cost ratio. EMBASE had the slightest overlap of references, with 53 percent of the unique references on carboplatin. This comparative evaluation showed that the ability of bibliographic databases to provide information on ADRs is dependent on both the size and the quality of each database.

Databases, Bibliographic↗

PubMed1991

Examples of uses of databases for quantitative and qualitative correlation studies between genotoxicity and carcinogenicity.

In this paper we give some examples of using databases of genotoxicity and carcinogenicity for quantitative and qualitative correlation studies between short-term tests and carcinogenicity. The quality of the databases is obviously important, but one of the major deficiencies of present databases is that they are too small. Using relatively small, different databases, different results can be obtained. With small databases it is difficult to disaggregate data for homogeneous chemical classes or other types of subsets. Using the databases of Gold (carcinogenicity) and Würgler (genotoxicity), we have investigated the carcinogenic potency of genotoxic and nongenotoxic carcinogens for different chemical classes.

Animals↗

PubMed1991

Aspects of database construction and interrogation of relevance to the accurate prediction of rodent carcinogenicity and mutagenicity.

Attempts to reconcile qualitative carcinogenicity databases with qualitative mutagenicity database continue to indicate that there is no useful relationship between mutagenicity/genotoxicity and rodent carcinogenicity. It is suggested that recognition of two classes of carcinogen, genotoxic and nongenotoxic, is the first step in finding meaningful correlations between the above parameters. This then leads to purposeful intervention into the databases, including rejecting low quality data, abandoning some assays from the database, and clustering certain end points as repetitive rather that independent of each other. Seeking specific correlations within a focused database may yield knowledge from the current wealth of information. The effort required to build databases, particularly quantitative ones, has so far prevented the equally arduous task of their correct interrogation. Preliminary indications are the mutagenicity is closely correlated with genotoxic carcinogenesis and completely independent of nongenotoxic carcinogenesis.

Animals↗

PubMedDate not supplied

Design of hospital database systems in a non-relational environment.

The lack of an appropriate, widely accepted, design procedure for use with non-relational database management systems has been a major, common problem in many efforts to develop an integrated hospital database. The availability of such a design procedure is particularly important today since the majority of the database management systems currently in use are non-relational. A database design procedure is proposed which should assist with the design of optimal non-relational hospital database systems. The proposed design procedure is separated into two distinct steps: the development of an appropriate intermediate relational database structure and the subsequent development of an equivalent non-relational one. A set of rules is given for the move from the proposed intermediate relational to the equivalent non-relational structure. An example application from the hospital environment is also included in order to better demonstrate the process.

Computer Communication Networks↗

PubMedDate not supplied

Creating a resource database for nursing service administration.

In response to the current information explosion in nursing service administration (NSA), the authors felt a need to collect and organize available resources for use by their faculty and graduate students. An electronic database was developed to facilitate the use of the collected print and software resources. This article describes the creation of the NSA Resource Database from the time the need for it was realized to its completion. There is discussion regarding the criteria used for writing the database, what the database screens look like and why and what the database contains. The article also discusses the use and users of the NSA Resource Database to date.

Databases, Bibliographic↗

PubMed1987

Developing drug-use indicators with a computerized drug database and a personal computer software package.

The use of a multihospital drug- and patient-database system, a personal computer (PC), and a standard PC software package to monitor drug-use indicators is described, and a five-step method for analyzing a set of data is presented. An integrated spread-sheet, database, and graphics program (Lotus 1-2-3), which is compatible with an IBM PC, can manipulate data obtained from a multihospital database system. To demonstrate the utility of this system, a previously published procedure for analyzing drug-use indicators (e.g., length of stay, drug cost per patient, number of drugs received) for patients in two diagnosis-related groups was repeated using the database and PC software. The records of patients in each DRG were randomly selected from the database. The following steps were applied to the data: (1) data (as a whole) were characterized statistically, (2) data were examined to identify subgroups of interest, (3) groups of data were characterized statistically and compared with each other, (4) the effect of changing the characteristics of one or more subgroups was predicted, and (5) the results of the data manipulations were presented in tables and graphs. A multihospital database can serve as a source for obtaining large quantities of hospital-specific data. These data can be manipulated and presented in tabular or graphic form on a personal computer and used by hospitals to monitor various drug-use indicators.

Data Display↗

PubMed1989

Computerized, comprehensive databases of cellular and secreted proteins from normal human embryonic lung MRC-5 fibroblasts: identification of transformation and/or proliferation sensitive proteins.

Databases of protein information from human embryonal lung fibroblasts (MRC-5) have been established using computer analyzed two-dimensional gel electrophoresis. One thousand four hundred and eighty-two cellular proteins (1060 with isoelectric focusing and 422 with nonequilibrium pH gradient electrophoresis, in the first dimension) ranging in molecular mass between 8 and 234 kDa were separated and numbered. Information entered in the database (in most cases for major proteins) includes: protein name, HeLa protein catalog number, mouse protein catalog number, proteins matched in transformed human epithelial amnion cells (AMA) and peripheral blood mononuclear cells (PBMC), transformation and/or proliferation sensitive proteins, synthesis in quiescent cells, cell cycle regulated proteins, mitochondrial and heat shock proteins, cytoskeletal proteins and proteins whose synthesis is affected by interferons. Additional information entered for a few transformation-sensitive proteins that have been selected for future studies includes levels of synthesis and amounts in fetal human tissues. A total of four hundred and seventy-six [35S]methionine labeled polypeptides (258 isoelectric focusing; 218, nonequilibrium pH gradient electrophoresis) secreted by MRC-5 fibroblasts were separated and recorded (J. E. Celis et al., Leukemia 1987, 1, 707-717). Information entered in this database includes molecular weight and transformation sensitive proteins. These databases, as well as those of epithelial and lymphoid cell proteins (J. E. Celis et al., Leukemia 1988, 9, 561-601), represent the initial stages of a systematic effort to establish comprehensive databases of human protein information. In the long run, these databases are expected to offer a useful framework in which to focus the human genome sequencing effort.

Cell Line, Transformed↗

PubMed1989

Database and search techniques for two-dimensional gel protein data: a comparison of paradigms for exploratory data analysis and prospects for biological modeling.

Two-dimensional (2-D) polyacrylamide gel electrophoresis can detect thousands of polypeptides, separating them by apparent molecular weight (Mr) and isoelectric point (pI). Thus it provides a more realistic and global view of cellular genetic expression than any other technique. This technique has been useful for finding sets of key proteins of biological significance. However, a typical experiment with more than a few gels often results in an unwiedly data management problem. In this paper, the GELLAB-II system is discussed with respect to how data reduction and exploratory data analysis can be aided by computer data management and statistical search techniques. By encoding the gel patterns in a "three-dimensional" (3-D) database, an exploratory data analysis can be carried out in an environment that might be called a "spread sheet for 2-D gel protein data". From such databases, complex parametric network models of protein expression during events such as differentiation might be constructed. For this, 2-D gel databases must be able to include data from other domains external to the gel itself. Because of the increasing complexity of such databases, new tools are required to help manage this complexity. Two such tools, object-oriented databases and expert-system rule-based analysis, are discussed in this context. Comparisons are made between GELLAB and other 2-D gel database analysis systems to illustrate some of the analysis paradigms common to these systems and where this technology may be heading.

Algorithms↗

PubMed1991

Methods for the analysis and assessment of clinical databases: the clinician's perspective.

Innovative approaches to analysing clinical databases can be considered from a perspective of innovations that improve the analytical approach or from a more global perspective in which clinical databases themselves are evaluated as a technology. The analytic approach for using a database to estimate risk can be considered as a matrix of three methodologic concerns: the predictive method; the assessment of the quality of the predictions; and the assessment of the validity or generalizability of the predictions. Considering databases as a technology places in perspective the merit of clinical databases and defines their potential value to the health care system. An awareness of both the clinical and analytic problem encourages innovation and can lead to creative solutions to the many problems present in the analysis of clinical databases.

Clinical Medicine↗

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↗

PubMed1991

Extensions to the time-oriented database model to support temporal reasoning in medical expert systems.

Physicians faced with diagnostic and therapeutic decisions must reason about clinical features that change over time. Database-management systems (DBMS) can increase access to patient data, but most systems are limited in their ability to store and retrieve complex temporal information. The Time-Oriented Databank (TOD) model, the most widely used data model for medical database systems, associates a single time stamp with each observation. The proper analysis of most clinical data requires accounting for multiple concurrent clinical events that may alter the interpretation of the raw data. Most medical DBMSs cannot retrieve patient data indexed by multiple clinical events. We describe two logical extensions to TOD-based databases that solve a set of temporal reasoning problems we encountered in constructing medical expert systems. A key feature of both extensions is that stored data are partitioned into groupings, such as sequential clinical visits, clinical exacerbations, or other abstract events that have clinical decision-making relevance. The temporal network (TNET) is an object-oriented database that extends the temporal reasoning capabilities of ONCOCIN, a medical expert system that provides chemotherapy advice. TNET uses persistent objects to associate observations with intervals of time during which "an event of clinical interest" occurred. A second object-oriented system called the extended temporal network (ETNET), is both an extension and a simplification of TNET. Like TNET, ETNET uses persistent objects to represent relevant intervals; unlike the first system, however, ETNET contains reasoning methods (rules) that can be executed when an event "begins", and that are withdrawn when that event "concludes". TNET and ETNET capture temporal relationships among recorded information that are not represented in TOD-based databases. Although they do not solve all temporal reasoning problems found in medical decision making, these new structures enable patient database systems to encode complex temporal relationships, to store and retrieve patient data based on multiple clinical contexts and, in ETNET, to modify the reasoning methods available to an expert system based on the onset or conclusion of specific clinical events.

Diagnosis, Computer-Assisted↗