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PubMed2005

Development of a refined database of mammalian relative potency estimates for dioxin-like compounds.

The toxic equivalency factor (TEF) approach has been widely accepted as the most feasible method available at present for evaluating potential health risks associated with exposure to mixtures of dioxin-like compounds (DLCs). The current mammalian TEFs for the DLCs were established by the World Health Organization (WHO) following the meeting of an international expert panel in June of 1997. The TEFs recommended by WHO were determined based on a consensus of scientific judgment and were presented as point estimates. However, the relative potency estimates (REPs) underlying the TEFs were derived from a heterogeneous data set and often span several orders of magnitude. In this article, we present a refined database of mammalian REPs that we believe will facilitate better characterization of the variability and uncertainty inherent in the data. The initial step involved reviewing the REP database used by the WHO panel during its review in 1997. A set of criteria was developed to identify REPs that were determined to be the most representative measure of a biological response and of adequate quality for use in quantitative analyses. REPs were determined to be inappropriate for use in quantitative analyses if any of the established exclusion criteria were met. Comparison of data records to the established exclusion criteria resulted in the identification of a substantial number of REPs believed to be inappropriate for use in quantitative analyses. Next, studies published after 1997 were added to the database. The availability of such a refined database will improve risk assessment for this class of compounds by including additional information from new studies and facilitating the use of quantitative approaches in the further development of TEFs.

Animals↗
PubMed1992

Influence of a computer database and problem exercises on students' knowledge of bacteriology.

This study compared the performances of students at the University of North Carolina at Chapel Hill School of Medicine who had access to sets of problem exercises and a computer database to support their learning of bacteriology with the performances of students at the University of Iowa College of Medicine who did not have such access. The study also examined the extent of a student's database use as a predictor of posttest performance. The students studied were randomly selected groups of 32-44 first-year students per year at each school; the study was conducted in three academic years (1988-1990) with some modifications in the intervention as the host environment evolved. The criterion measure was a posttest created from the same pool of problems used to generate the problem sets. The students at the intervention school scored significantly higher on the posttest in two of the three years, and overall. Also in two of the three years and overall, there was a significant relationship between the extent of a student's database use and his or her posttest score. Although the observed effects may have been due to other factors in this quasi-experimental design, the authors conclude that the use of problem sets and a computer database had a positive influence on the students' learning.

Bacteriology↗
PubMed2001

Introduction of a genitourinary trauma database for use as a multi-institutional urologic trauma registry.

BACKGROUND: Injury and/or work up of patients involved in genitourinary (GU) trauma often has a urologic component. By implementing a simple, versatile database to categorizing such injuries, we hoped to elucidate issues involved in the treatment of GU trauma. METHODS: The Genitourinary Trauma Database was created using commercially available software (Microsoft Access). It occupies 848 KB (kilobytes) of hard drive memory and is organized into five categories: Patient Demographics, History/Physical Examination/Etiology, Radiologic Evaluation, Operative Intervention, and Disposition and Complications. RESULTS: All GU trauma patients seen since 1995 have been entered. Thus far, the database has helped assess indications for bladder evaluation of blunt trauma and pelvic fracture and has allowed us to develop a protocol for performing retrograde computed tomographic cystogram in conjunction with abdominal/pelvic computed tomographic scan. CONCLUSION: Ease of creating and using this database demonstrate that it could serve as a multi-institutional GU trauma registry and prove invaluable in developing and refining future trauma protocols.

Abdominal Injuries↗
PubMed2002

Searching literature databases for health care economic evaluations: how systematic can we afford to be?

BACKGROUND: As the health care economic-evaluation literature continues to grow, a need for sound methods to conduct systematic reviews of the existing evidence is emerging. So far, reviews of economic evaluations have relied upon noncomprehensive sources and have adopted simplistic search methods, both likely to lead to biased results. OBJECTIVE: To provide evidence of the performance of alternative approaches for identifying published health care economic evaluations and to illustrate what forms of bias may affect systematic reviews of such studies. METHODS: The sensitivity and specificity of alternative search strategies were tested for the period January to March 1997, using seven major medical and social science literature databases, one economic evaluation database and a published bibliography. Studies were selected blindly by pairs of reviewers (agreement 94.1%-96.5%), using a two-stage procedure. RESULTS: By limiting the scope of a review to Medline and by using appropriate search strategies, researchers may significantly reduce the number of nonrelevant references retrieved by their electronic searches (sensitivity 72%, specificity 75%, compared with more extensive strategies), which require exclusion by manual screening. The yield of searches based on specialized bibliographies and databases may be different because of variations in selection criteria, coverage and time lag for inclusion of references. CONCLUSIONS: Medline is the key source for reviews of economic evaluations. Researchers may select from the search strategies proposed in this paper the one that offers an optimal balance between sensitivity and specificity in relation to the aims of their review. Manual searches and searches of databases other than Medline have a limited incremental yield. The sensitivity of all search strategies increases when tighter methodological standards are set, but more research is needed on methods for identifying methodologically sound studies.

Bias↗
PubMedDate not supplied

A strategy for converting clinical data into research databases.

The process of converting clinical information into a research database is complex. Following assemblage of a team including clinicians and researchers (supplemented by statisticians and informatics personnel as needed) a three-phase, eight-step process may be followed for clinical information conversion and database generation. The amount, type, and variety of data stored will greatly increase in the future. This increased availability of databases is useful in research and can expand the opportunities to conduct clinical nursing research. The case study presentation illustrates how individuals from various organizations collaborate to develop accountability systems that best serve the public interest. The purpose of this joint venture was the development and conversion of measures into a database to determine the quality of care for people with diabetes. In addition, opportunities exist for extracting data to examine outcome criteria for patient care.

Databases, Factual↗
PubMed1997

Spine update. Administrative databases in spine research.

The use of administrative health care databases for the storage and retrieval of information is increasing. The data collection, entry, and collation follows a predictable process for hospital admissions. Many conclusions have been drawn from research performed using administrative databases. These conclusions can have significant and important implications for patients, providers, and society at large, to the extent that such data inform participants in the current health care policy debate. In an effort to better understand the significance of conclusions drawn from studies that rely on electronic administrative databases as their source of information, the present report addresses the process, strengths, weaknesses, and future plans for the use of administrative databases in spine research.

Databases, Factual↗
PubMed1995

Public health issues in the development of centralized health care databases.

The establishment of centralized databases, in conjunction with health care reform, offers us an opportunity to enhance the collection of data supportive of public health functions. However, this opportunity may be lost without the informed, persuasive, and persistent participation of the public health community in the database development process. Maryland's effort to construct a statewide database illustrates the political forces and technical complexity involved in the task. It also demonstrates how public health officials, by making their views known, can influence database design and health care reform.

Cost Control↗
PubMed2004

Database production and maintenance.

The advent of computers and electronic databases have revolutionized the way that clinical research is done. If study inclusion criteria are saved in the database, creating a study population can be accomplished by constructing an electronic query. Prospectively-entered outcome data related to a particular patient population then can be accessed and exported to a statistical software application for analysis. The senior author has more than 2 decades of experience with computer-based clinical outcome databases. In the context of his personal experience, this review offers some insights related to database design and maintenance.

Arthroplasty, Replacement, Hip↗
PubMed2005

Coagulation factor XI: a database of mutations and polymorphisms associated with factor XI deficiency.

Hereditary factor XI deficiency is a rare bleeding disorder that is found worldwide. Rapidly increasing numbers of mutations and polymorphisms in various populations have been reported. However, the number of identified mutations given in recent literature and available databases is named to be not more than 35. We assumed that this is clearly too low and that to date no comprehensive survey of mutations associated with factor XI deficiency is available. To provide a complete database of mutations and polymorphisms associated with factor XI deficiency we collected all available data on hereditary factor XI deficiency from main biological and medical databases [http://ncbi.nlm.nih.gov/pubmed and http://ncbi.nlm.nih.gov/omim (OMIM reference 264900) and the Human Gene Mutation Database for F11 mutations http://uwcmml1s.uwcm.ac.uk/uwcm/mg/search/119891.html] as well as from contributions to international congresses. As of 8 June 2004 the number of reported causative mutations is 81, of which 12 have been described in unrelated individuals by more than one study group. For three frequently observed mutations [type II and type III mutations (Gln116Stop and Phe283Leu) and Cys38Arg] common founders have been described. Furthermore, 20 polymorphisms have been described in association with factor XI deficiency, three of which have been reported by two independent study groups. For the majority, allele frequencies have been published for in the Caucasian and/or Black population.

Data Collection↗
PubMed2005

Underestimating injury mortality using statewide databases.

BACKGROUND: This study examines the potential for misclassifying injury-related deaths reported in Vital Statistics and assesses the rate of postdischarge death among injured patients released from hospital, emergency department (ED), and emergency medical services (EMS) care. METHODS: Statewide death certificate, inpatient, ED, and EMS databases for 1996 through 1997 were probabilistically linked and information in each database compared. RESULTS: One thousand two hundred ninety-four injured inpatients or ED patients were matched with a death certificate record that listed an injury (56.3%) or illness (43.7%) as the primary cause of death. Injured decedents with an illness-coded cause of death were older (p < 0.001), with causes of death indicative of chronic medical conditions. Few deaths occurred within 30 days of inpatient discharge (6%); however, 38% and 9% of deaths in ED and EMS databases occurred after discharge from health care, respectively. Many deaths among EMS and ED patients occur in subsequent phases of care. CONCLUSION: Estimates of injury mortality substantially increase when using multiple independent databases.

Adult↗
PubMed2000

An interactive web-based Pseudomonas aeruginosa genome database: discovery of new genes, pathways and structures.

Using the complete genome sequence of Pseudomonas: aeruginosa PAO1, sequenced by the Pseudomonas: Genome Project (ftp://ftp.pseudomonas. com/data/pacontigs.121599), a genome database (http://pseudomonas. bit.uq.edu.au/) has been developed containing information on more than 95% of all ORFs in Pseudomonas: aeruginosa. The database is searchable by a variety of means, including gene name, position, keyword, sequence similarity and Pfam domain. Automated and manual annotation, nucleotide and peptide sequences, Pfam and SMART domains (where available), Medline and GenBank links and a scrollable, graphical representation of the surrounding genomic landscape are available for each ORF. Using the database has revealed, among other things, that P. aeruginosa contains four chemotaxis systems, two novel general secretion pathways, at least three loci encoding F17-like thin fimbriae, six novel filamentous haemagglutinin-like genes, a number of unusual composite genetic loci related to vgr/RHS: elements in Escherichia coli, a number of fix-like genes encoding a micro-oxic respiration system, novel biosynthetic pathways and 38 genes containing domains of unknown function (DUF1/DUF2). It is anticipated that this database will be a useful bioinformatic tool for the Pseudomonas: community that will continue to evolve.

Adhesins, Bacterial↗
PubMed2001

A cSNP map and database for human chromosome 21.

Single nucleotide polymorphisms (SNPs) are likely to contribute to the study of complex genetic diseases. The genomic sequence of human chromosome 21q was recently completed with 225 annotated genes, thus permitting efficient identification and precise mapping of potential cSNPs by bioinformatics approaches. Here we present a human chromosome 21 (HC21) cSNP database and the first chromosome-specific cSNP map. Potential cSNPs were generated using three approaches: (1) Alignment of the complete HC21 genomic sequence to cognate ESTs and mRNAs. Candidate cSNPs were automatically extracted using a novel program for context-dependent SNP identification that efficiently discriminates between true variation, poor quality sequencing, and paralogous gene alignments. (2) Multiple alignment of all known HC21 genes to all other human database entries. (3) Gene-targeted cSNP discovery. To date we have identified 377 cSNPs averaging ~1 SNP per 1.5 kb of transcribed sequence, covering 65% of known genes in the chromosome. Validation of our bioinformatics approach was demonstrated by a confirmation rate of 78% for the predicted cSNPs, and in total 32% of the cSNPs in our database have been confirmed. The database is publicly available at http://csnp.unige.ch or http://csnp.isb-sib.ch. These SNPs provide a tool to study the contribution of HC21 loci to complex diseases such as bipolar affective disorder and allele-specific contributions to Down syndrome phenotypes.

Base Composition↗
PubMed2001

Argus--a new database system for Web-based analysis of multiple microarray data sets.

The ongoing revolution in microarray technology allows biologists studying gene expression to routinely collect >10(5) data points in a given experiment. Widely accessible and versatile database software is required to process this large amount of raw data into a format that facilitates the development of new biological insights. Here, we present a novel microarray database software system, named Argus, designed to process, analyze, manage, and publish microarray data. Argus imports the intensities and images of externally quantified microarray spots, performs normalization, and calculates ratios of gene expression between conditions. The database can be queried locally or over the Web, providing a convenient format for Web-publishing entire microarray data sets. Searches for regulated genes can be conducted across multiple experiments, and the integrated results incorporate images of the actual hybridization spots for artifact screening. Query results are presented in a clone- or gene-oriented fashion to rapidly identify highly regulated genes, and scatterplots of expression ratios allow an individual ratio to be interpreted in the context of all data points in the experiment. Algorithms were developed to optimize response times for queries of regulated genes. Supporting databases are updated easily to maintain current gene identity information, and hyperlinks to the Web provide access to descriptions of gene function. Query results also can be exported for higher-order analyses of expression patterns. This combination of features currently is not available in similar software. Argus is available at http://vessels.bwh.harvard.edu/software/Argus.

Databases, Factual↗
PubMed1997

Incognito rRNA and rDNA in databases and libraries.

Both ribosomal DNA (rDNA) and ribosomal RNA (rRNA) are over-represented in the starting material for genomic and cDNA libraries; thus, their sequences have the potential of repeatedly entering the various databases. When DNA (both transcribed and intergenic spacer regions) is used as query sequence, a great number of matches are found in the databases, particularly in the EST database, and to a lesser extent among genomic sequences and STSs, which are not identified as rDNA. We discuss the following explanations for the widespread occurrence of rDNA in cDNA and genomic DNA libraries: pseudogenes of rRNA in other genomic locations, mRNA-derived pseudogenes that reside in rDNA, cDNAs derived from rRNA [either by self-priming or by internal oligo(dT) priming], cDNAs derived from actual transcripts of the rDNA intergenic spacer, and genomic DNA contamination of RNA preparations. Because so many database entries contain unidentified rDNA, we recommend that all sequence submissions be checked (by the submitters) for the presence of structural RNAs in addition to repetitive sequences.

DNA, Ribosomal↗
PubMed2003

Kinase pathway database: an integrated protein-kinase and NLP-based protein-interaction resource.

Protein kinases play a crucial role in the regulation of cellular functions. Various kinds of information about these molecules are important for understanding signaling pathways and organism characteristics. We have developed the Kinase Pathway Database, an integrated database involving major completely sequenced eukaryotes. It contains the classification of protein kinases and their functional conservation, ortholog tables among species, protein-protein, protein-gene, and protein-compound interaction data, domain information, and structural information. It also provides an automatic pathway graphic image interface. The protein, gene, and compound interactions are automatically extracted from abstracts for all genes and proteins by natural-language processing (NLP). The method of automatic extraction uses phrase patterns and the GENA protein, gene, and compound name dictionary, which was developed by our group. With this database, pathways are easily compared among species using data with more than 47,000 protein interactions and protein kinase ortholog tables. The database is available for querying and browsing at http://kinasedb.ontology.ims.u-tokyo.ac.jp/.

Animals↗
PubMed2004

GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.

High-throughput gene expression analysis has become a frequent and powerful research tool in biology. At present, however, few software applications have been developed for biologists to query large microarray gene expression databases using a Web-browser interface. We present GENEVESTIGATOR, a database and Web-browser data mining interface for Affymetrix GeneChip data. Users can query the database to retrieve the expression patterns of individual genes throughout chosen environmental conditions, growth stages, or organs. Reversely, mining tools allow users to identify genes specifically expressed during selected stresses, growth stages, or in particular organs. Using GENEVESTIGATOR, the gene expression profiles of more than 22,000 Arabidopsis genes can be obtained, including those of 10,600 currently uncharacterized genes. The objective of this software application is to direct gene functional discovery and design of new experiments by providing plant biologists with contextual information on the expression of genes. The database and analysis toolbox is available as a community resource at https://www.genevestigator.ethz.ch.

Arabidopsis↗
PubMed2006

A liquid chromatography-mass spectrometry-based metabolome database for tomato.

For the description of the metabolome of an organism, the development of common metabolite databases is of utmost importance. Here we present the Metabolome Tomato Database (MoTo DB), a metabolite database dedicated to liquid chromatography-mass spectrometry (LC-MS)- based metabolomics of tomato fruit (Solanum lycopersicum). A reproducible analytical approach consisting of reversed-phase LC coupled to quadrupole time-of-flight MS and photodiode array detection (PDA) was developed for large-scale detection and identification of mainly semipolar metabolites in plants and for the incorporation of the tomato fruit metabolite data into the MoTo DB. Chromatograms were processed using software tools for mass signal extraction and alignment, and intensity-dependent accurate mass calculation. The detected masses were assigned by matching their accurate mass signals with tomato compounds reported in literature and complemented, as much as possible, by PDA and MS/MS information, as well as by using reference compounds. Several novel compounds not previously reported for tomato fruit were identified in this manner and added to the database. The MoTo DB is available at http://appliedbioinformatics.wur.nl and contains all information so far assembled using this LC-PDA-quadrupole time-of-flight MS platform, including retention times, calculated accurate masses, PDA spectra, MS/MS fragments, and literature references. Unbiased metabolic profiling and comparison of peel and flesh tissues from tomato fruits validated the applicability of the MoTo DB, revealing that all flavonoids and alpha-tomatine were specifically present in the peel, while several other alkaloids and some particular phenylpropanoids were mainly present in the flesh tissue.

Chromatography, Liquid↗
PubMed2005

Representing structural databases in a self-organizing map.

This paper presents a way to accomodate large numbers of crystal structures, as present in e.g. the Cambridge Structural Database (CSD), in a self-organizing map. The structures are represented by their calculated powder diffraction patterns. The use of a recently introduced similarity criterion is essential: the weighted cross-correlation. This accurately reflects the similarities of the powder patterns and therefore, indirectly measures the resemblance of crystal packings. It will be shown that good results are obtained, even if the network is trained with a small subset of a complete database. This makes it possible to construct the map on common hardware in a few hours. Such a map provides several possibilities for two-dimensional visualization, but additionally has a number of important applications. Two such applications are fast and easy screening of a database, and providing an overview of the contents of a database in terms of structural diversity of specific chemical classes of compounds, e.g. steroids or peptides. A third is the selection of archetypical structures, covering the complete structural space.

Algorithms↗