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PubMed1998

Use of the UK General Practice Research Database for pharmacoepidemiology.

The last decade has seen a surge in the use of computerized health care data for pharmacoepidemiology. Of all European databases, the General Practice Research Database (GPRD) in the UK, has been the most widely used for pharmacoepidemiological research. Since 1994, this database has belonged to the UK Department of Health, and is maintained by the Office of National Statistics (ONS). Currently, around 1500 general practitioners with a population coverage in excess of 3 million, systematically provide their computerized medical data anonymously to ONS. Validation studies of the GPRD have documented the recording of medical data into general practitioners' computers to be near to complete. The GPRD collects truly population-based data, has a size that makes it possible to follow-up large cohorts of users of specific drugs, and includes both outpatient and inpatient clinical information. The access to original medical records is excellent. Desirable improvements to the GPRD would be additional computerized information on certain variables and linkage to other health care databases. Most published studies to date have been in the area of drug safety. The General Practice Research Database has proved that valuable data can be collected in a general practice setting. The full potential of this rich computerized database has yet to come. This experience should serve to encourage others to develop similar population-based data in other countries.

Databases, Factual↗

PubMed1997

Post-processing of BLAST results using databases of clustered sequences.

MOTIVATION: When evaluating the results of a sequence similarity search, there are many situations where it can be useful to determine whether sequences appearing in the results share some distinguishing characteristic. Such dependencies between database entries are often not readily identifiable, but can yield important new insights into the biological function of a gene or protein. RESULTS: We have developed a program called CBLAST that sorts the results of a BLAST sequence similarity search according to sequence membership in user-defined 'clusters' of sequences. To demonstrate the utility of this application, we have constructed two cluster databases. The first describes clusters of nucleotide sequences representing the same gene, as documented in the UNIGENE database, and the second describes clusters of protein sequences which are members of the protein families documented in the PROSITE database. Cluster databases and the CBLAST post-processor provide an efficient mechanism for identifying and exploring relationships and dependencies between new sequences and database entries.

Algorithms↗

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↗

PubMed1997

Histone and histone fold sequences and structures: a database.

A database of aligned histone protein sequences has been constructed based on the results of homology searches of the major public sequence databases. In addition, sequences of proteins identified as containing the histone fold motif and structures of all known histone and histone fold proteins have been included in the current release. Database resources include information on conflicts between similar sequence entries in different source databases, multiple sequence alignments, and links to the Entrez integrated information retrieval system at the National Center for Biotechnology Information (NCBI). The database currently contains over 1000 protein sequences. All sequences and alignments in this database are available through the World Wide Web at: http: //www.ncbi.nlm.nih.gov/Baxevani/HISTONES/ .

Amino Acid Sequence↗

PubMed1997

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI) and constitutes Europe's primary nucleotide sequence resource. Database releases are produced quarterly and are distributed on CD-ROM. EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases.

Academies and Institutes↗

PubMed1998

Histone Sequence Database: new histone fold family members.

Searches of the major public protein databases with core and linker chicken and human histone sequences have resulted in the compilation of an annotated set of histone protein sequences. In addition, new database searches with two distinct motif search algorithms have identified several members of the histone fold family, including human DRAP1 and yeast CSE4. Database resources include information on conflicts between similar sequence entries in different source databases, multiple sequence alignments, links to the Entrez integrated information retrieval system, structures for histone and histone fold proteins, and the ability to visualize structural data through Cn3D. The database currently contains >1000 protein sequences, which are searchable by protein type, accession number, organism name, or any other free text appearing in the definition line of the entry. All sequences and alignments in this database are available through the World Wide Web at http://www.nhgri.nih. gov/DIR/GTB/HISTONES or http://www.ncbi.nlm.nih. gov/Baxevani/HISTONES

Amino Acid Sequence↗

PubMed1994

An acute care physical therapy clinical practice database for outcomes research.

Clinical practice databases are frequently used to assess outcomes in various medical specialties. Formulating a computerized physical therapy medical record requires standardization of clinical assessments among the users. The purpose of this article is to describe an acute care physical therapy database system that emphasizes high-quality measures of function. The logic underlying the development of a physical therapy computerized medical record is described. Selected uses of the database are demonstrated by projects that assess data quality, generate clinical hypotheses, manage clinical data, develop clinical measures, and generate pilot data on patient variability. Patients seen in physical therapy for total joint replacement, pain, and decreased ambulation were studied to demonstrate some of the present capabilities of the database. Clinical practice databases contribute to the overall research mission, provided the data are of high quality. The use of databases in conjunction with randomized clinical trials may serve an important role in determining effective physical therapy interventions to reduce disability.

Database Management Systems↗

PubMed1996

Adopting a corporate perspective on databases. Improving support for research and decision making.

The Veterans Health Administration (VHA) is at the forefront of designing and managing health care information systems that accommodate the needs of clinicians, researchers, and administrators at all levels. Rather than using one single-site, centralized corporate database VHA has constructed several large databases with different configurations to meet the needs of users with different perspectives. The largest VHA database is the Decentralized Hospital Computer Program (DHCP), a multisite, distributed data system that uses decoupled hospital databases. The centralization of DHCP policy has promoted data coherence, whereas the decentralization of DHCP management has permitted system development to be done with maximum relevance to the users'local practices. A more recently developed VHA data system, the Event Driven Reporting system (EDR), uses multiple, highly coupled databases to provide workload data at facility, regional, and national levels. The EDR automatically posts a subset of DHCP data to local and national VHA management. The development of the EDR illustrates how adoption of a corporate perspective can offer significant database improvements at reasonable cost and with modest impact on the legacy system.

Database Management Systems↗

PubMed1995

A database of cardiac arrhythmias.

OBJECTIVE: To describe a database of cardiac arrhythmia recordings, useful for the development and testing of ECG rhythm processing or monitoring algorithms and devices. METHODS: The raw data were acquired within the Wisconsin-Dane County emergency medical technician-defibrillation program and contained emergency rhythm recordings of an average length of 30 minutes. The raw data were integrated into a software platform designed for the annotation and visualization of the recordings. RESULTS: Currently the database contains the following arrhythmia episodes: ventricular fibrillation (56), asystole (65), electromechanical dissociation (31), and other arrhythmias (42). The software, resident on personal computers, also can transmit any of the database recordings, through a digital-to-analog converter board, to a device under test. CONCLUSIONS: The database technique described will provide a useful means of objectively assessing electronic devices for their ability to detect arrhythmias. The database is unique in that it contains lengthy episodes of arrhythmias. The database will be extended to include additional cases.

Arrhythmias, Cardiac↗

PubMed1997

Linking large administrative databases: a method for conducting emergency medical services cohort studies using existing data.

OBJECTIVE: To evaluate probabilistic matching for linking a cohort of cardiac arrest (CA) patients identified in the Metro Toronto Ambulance (MTA) database in Toronto, Ontario, Canada, to their appropriate record in either the Vital Statistics Information System (VSIS) or the Canadian Institute of Health Information (CIHI) databases and thus establish their clinical outcomes. METHODS: A linkage of a large administrative database was performed. A cohort of patients who suffered an out-of-hospital CA during the calendar years 1988-1993 was identified. To determine the patients' outcomes, the cohort was probabilistically linked to patient records in the VSIS and CIHI databases. Identifying variables used during the process of linking records included: names (first and last); New York State Identification and Intelligence System (NYSIIS) code; date of event; date of death; city; admitting hospital number; mode of admission to hospital; age; and sex. RESULTS: A cohort of 7,079 CA patients was identified from the MTA database; 6,448 (91%) patients were accurately linked to records in 1 of the 2 outcome databases (CIHI, VSIS). Missing data for > or = 1 of the linking variables were responsible for unlinked records. Using these longitudinal data, it was possible to determine the number of patients surviving their out-of-hospital CAs to be admitted to hospital (n = 833) (16%). No differences in survival rates (p = 0.06) or median lengths of hospital stay among the survivors (p = 0.15) were observed between admitting hospitals. CONCLUSIONS: Probabilistic matching is an effective method by which researchers can use existing administrative data to determine outcomes of population cohorts. This is especially valuable in situations where controlled intervention studies are not feasible or may be inappropriate. In this analysis, in-hospital management of admitted CA patients, as determined by hospital-specific survival rates and length of stay, suggests no measurable differences in the care provided to these patients by hospitals in Toronto.

Algorithms↗

PubMed1997

Multicenter evaluation of the updated and extended API (RAPID) Coryne database 2.0.

In a multicenter study, 407 strains of coryneform bacteria were tested with the updated and extended API (RAPID) Coryne system with database 2.0 (bioMérieux, La-Balme-les-Grottes, France) in order to evaluate the system's capability of identifying these bacteria. The design of the system was exactly the same as for the previous API (RAPID) Coryne strip with database 1.0, i.e., the 20 biochemical reactions covered were identical, but database 2.0 included both more taxa and additional differential tests. Three hundred ninety strains tested belonged to the 49 taxa covered by database 2.0, and 17 strains belonged to taxa not covered. Overall, the system correctly identified 90.5% of the strains belonging to taxa included, with additional tests needed for correct identification for 55.1% of all strains tested. Only 5.6% of all strains were not identified, and 3.8% were misidentified. Identification problems were observed in particular for Corynebacterium coyleae, Propionibacterium acnes, and Aureobacterium spp. The numerical profiles and corresponding identification results for the taxa not covered by the new database 2.0 were also given. In comparison to the results from published previous evaluations of the API (RAPID) Coryne database 1.0, more additional tests had to be performed with version 2.0 in order to completely identify the strains. This was the result of current changes in taxonomy and to provide for organisms described since the appearance of version 1.0. We conclude that the new API (RAPID) Coryne system 2.0 is a useful tool for identifying the diverse group of coryneform bacteria encountered in the routine clinical laboratory.

Actinomycetales↗

PubMedDate not supplied

Information retrieved from a database and the augmentation of personal knowledge.

OBJECTIVE: To assess the degree to which information retrieved from a biomedical database can augment personal knowledge in addressing novel problems, and how the ability to retrieve information evolves over time. DESIGN: This longitudinal study comprised three assessments of two cohorts of medical students. The first assessment occurred just before student course experience in bacteriology, the second occurred just after the course, and the third occurred five months later. At each assessment, the students were initially given a set of bacteriology problems to solve using their personal knowledge only. Each student was then reassigned a sample of problems he or she had answered incorrectly, to work again with assistance from a database containing information about bacteria and bacteriologic concepts. The initial pass through the problems generated a "personal knowledge" score; the second pass generated a "database-assisted" score for each student at each assessment. RESULTS: Over two cohorts, students' personal knowledge scores were very low (approximately 12%) at the first assessment. They rose substantially at the second assessment (approximately 48%) but decreased six months later (approximately 25%). By contrast, database-assisted scores rose linearly: from approximately 44% at the first assessment to approximately 57% at the second assessment, to approximately 75% at the third assessment. CONCLUSION: The persistent increase in database-assisted scores, even when personal knowledge had attenuated, was the most remarkable finding of this study. While some of the increase may be attributed to artifacts of the design, the pattern seems to result from the retained ability to recognize problem-relevant information in a database even when it cannot be recalled.

Bacteriology↗

PubMedDate not supplied

Development of a replicated database of DHCP data for evaluation of drug use.

This case report describes development and testing of a method to extract clinical information stored in the Veterans Affairs (VA) Decentralized Hospital Computer System (DHCP) for the purpose of analyzing data about groups of patients. The authors used a microcomputer-based, structured query language (SQL)-compatible, relational database system to replicate a subset of the Nashville VA Hospital's DHCP patient database. This replicated database contained the complete current Nashville DHCP prescription, provider, patient, and drug data sets, and a subset of the laboratory data. A pilot project employed this replicated database to answer questions that might arise in drug-use evaluation, such as identification of cases of polypharmacy, suboptimal drug regimens, and inadequate laboratory monitoring of drug therapy. These database queries included as candidates for review all prescriptions for all outpatients. The queries demonstrated that specific drug-use events could be identified for any time interval represented in the replicated database.

Databases, Factual↗

PubMedDate not supplied

UMLS-based conceptual queries to biomedical information databases: an overview of the project ARIANE. Unified Medical Language System.

OBJECTIVE: The aim of the project ARIANE is to model and implement seamless, natural, and easy-to-use interfaces with various kinds of heterogeneous biomedical information databases. DESIGN: A conceptual model of some of the Unified Medical Language System (UMLS) knowledge sources has been developed to help end users to query information databases. A query is represented by a conceptual graph that translates the deep structure of an end-user's interest in a topic. A computational model exploits this conceptual model to build a query interactively represented as query graph. A query graph is then matched to the data graph built with data issued from each record of a database by means of a pattern-matching (projection) rule that applies to conceptual graphs. RESULTS: Prototypes have been implemented to test the feasibility of the model with different kinds of information databases. Three cases are studied: 1) information in records is structured according to the UMLS knowledge sources; 2) information is able to be structured without error in the frame of the UMLS knowledge; 3) information cannot be structured. In each case the pattern-matching is processed by the projection rule according to the structure of information that has been implemented in the databases. CONCLUSION: The conceptual graphs theory provides with a homogeneous and powerful formalism able to represent both concepts, instances of concepts in medical contexts, and associations by means of relationships, and to represent data at different levels of details. The conceptual-graphs formalism allows powerful capabilities to operate a semantic integration of information databases using the UMLS knowledge sources.

Databases as Topic↗

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↗

PubMed1993

Crossover comparison of drug information online database vendors: Dialog and MEDLARS.

OBJECTIVE: To compare Dialog EMBASE with the National Library of Medicine's (NLM's) MEDLARS MEDLINE, TOXLINE, and TOXLIT to evaluate differences among the databases and vendors in a method consistent with routine drug information practice. DESIGN: Crossover comparison. METHODS: NLM MEDLARS databases MEDLINE, TOXLINE, and TOXLIT were searched directly. EMBASE was searched via Dialog Information Services. MEDLINE was searched back to 1980; TOXLINE and TOXLIT were searched back to 1981, reflecting the different database structures. EMBASE was searched back to 1980. To control bias, searches were randomized; identical strategies were used during the same session and were performed by the same trained searcher. RESULTS: Twenty-six drug information requests were compared. The MEDLARS and Dialog databases were generally similar, with no significant differences in the number of potentially relevant references, English references, clinically relevant references, available abstracts, unique citations, time online, and number of questions answered. EMBASE searches were more costly (p = 0.0005). TOXLIT was costlier than TOXLINE and MEDLINE (p = 0.0018). CONCLUSIONS: NLM MEDLARS databases were comparable to Dialog EMBASE. Although MEDLARS provided more total and English-language citations, the differences were small and did not influence the proportion of questions answered. The greatest difference between the vendors was the significantly lower cost of searching on MEDLARS. Although this difference may be partially offset by the significantly shorter search times on EMBASE, the mean 1.9 minutes saved would not recoup the mean $7.89 difference in cost. MEDLARS databases are less expensive for routine drug information requests.

Costs and Cost Analysis↗

PubMed1997

Evaluation of drug interaction document citation in nine on-line bibliographic databases.

OBJECTIVE: To compare nine on-line bibliographic databases to obtain bibliographic references on specific drug interactions. DESIGN: Seven bibliographic databases were selected for their ability to provide information concerning drug interactions: EMBASE, MEDLINE, TOXLINE, BIOSIS, Chemical Abstracts (CAS), PHARMLINE, and International Pharmaceutical Abstracts (IPA). Two French on-line bibliographic databases (i.e., PASCAL, BIBLIOGRAPHIF) were also tested to compare them with the other international databases. Twenty drug interactions were selected randomly using the journal Reactions Weekly 1993. MAIN OUTCOMES MEASURES: The total number of references, the number of potentially relevant references, the number of case report references, the number of unique references in the total number of references, and the number of unique references between potentially relevant references were analyzed by using the Friedman two-way ANOVA by ranks. For each database, relevance and relative recall were calculated. RESULTS: For the total number of references, EMBASE was significantly more comprehensive then all other databases (p < 0.05). EMBASE had a significantly greater number of potentially relevant references than IPA, PHARMLINE, CAS, and BIBLIOGRAPHIF (p < 0.05). For the total number of case report references, only one significant difference, between EMBASE and BIBLIOGRAPHIF (p < 0.05), was observed. MEDLINE and TOXLINE had the lowest cost per potentially relevant reference. CONCLUSIONS: To obtain bibliographic references on drug interactions, the first step should be to search MEDLINE or TOXLINE; the second step, for completeness, should be to search EMBASE.

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↗