Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Database”

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

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

At least 1,261 records · Page 70Linked to original sources
PubMed2002

An analytical and structural database provides a strategy for sequencing O-glycans from microgram quantities of glycoproteins.

A sensitive, rapid, quantitative strategy has been developed for O-glycan analysis. A structural database has been constructed that currently contains analytical parameters for more than 50 glycans, enabling identification of O-glycans at the subpicomole level. The database contains the structure, molecular weight, and both normal and reversed-phase HPLC elution positions for each glycan. These observed parameters reflect the mass, three-dimensional shape, and hydrophobicity of the glycans and, therefore, provide information relating to linkage and arm specificity as well as monosaccharide composition. Initially the database was constructed by analyzing glycans released by mild hydrazinolysis from bovine serum fetuin, synthetic glycopeptides, human glycophorin A, and serum IgA1. The structures of the fluorescently labeled sugars were determined from a combination of HPLC data, mass spectrometric composition and mass fragmentation data, and exoglycosidase digestions. This approach was then applied to human neutrophil gelatinase B and secretory IgA, where 18 and 25 O-glycans were identified, respectively, and the parameters of these glycans were added to the database. This approach provides a basis for the analysis of subpicomole quantities of O-glycans from normal levels of natural glycoproteins.

Animals↗
PubMed1998

A database of experimental results on globin gene expression.

Information on gene expression and regulation is expanding rapidly, and the complexity of the experimental design and data makes unique demands on databases to store the results. We describe a prototype database containing experimental results on the expression of mammalian beta-like globin genes, along with several query methods for accessing the information. The database has tables for DNA transfer experiments, protein-DNA binding results, and positions of DNase hypersensitive sites, which make extensive use of nested data structures. Comparison of data from various mammals is accomplished by providing a common coordinate system via a simultaneous alignment of matching DNA sequences. Interactive access to the database is available at a site called the Globin Gene Server on the World Wide Web (http://globin.cse. psu.edu). This software should be useful for any genetic system in which DNA sequence data are available.

Animals↗
PubMed1995

SCOP: a structural classification of proteins database for the investigation of sequences and structures.

To facilitate understanding of, and access to, the information available for protein structures, we have constructed the Structural Classification of Proteins (scop) database. This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure. It also provides for each entry links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references. Two search facilities are available. The homology search permits users to enter a sequence and obtain a list of any structures to which it has significant levels of sequence similarity. The key word search finds, for a word entered by the user, matches from both the text of the scop database and the headers of Brookhaven Protein Databank structure files. The database is freely accessible on World Wide Web (WWW) with an entry point to URL http: parallel scop.mrc-lmb.cam.ac.uk magnitude of scop.

Amino Acid Sequence↗
PubMed1995

A sequence property approach to searching protein databases.

Currently available sequence alignment programs are generally not capable of detecting functional and structural homologs in the twilight zone of sequence similarity, i.e. when the sequence identity falls below about 25%. Here we attempt to detect such weak similarities using an approach based on a notion of protein sequence similarity radically different from that used in sequential alignment. The approach defines protein sequence dissimilarity (or distance) as a weighted sum of differences of compositional properties such as singlet and doublet amino acid composition, molecular weight, isoelectric point (protein property search or PropSearch). With PropSearch, either single sequences can be used for a database query, or multiple sequences can be merged into an "average" sequence reflecting the average composition of a protein family. First, we show that members of structural protein families have a low mutual PropSearch distance when the weights are optimized to discriminate maximally between structural families. Second, we demonstrate the results of database searches using the PropSearch method. Such searches are very rapid when scanning a preprocessed database and do not require alignments. In cases in which conventional alignment tools fail to detect similarities, PropSearch can be used to generate hypotheses about possible structural or functional relationships between a new sequence and sequences in the database.

Algorithms↗
PubMed2005

Effects of healthy aging measured by intracranial compartment volumes using a designed MR brain database.

A publicly available database of high-quality, multi-modal MR brain images of carefully screened healthy subjects, equally divided by sex, and with an equal number of subjects per age decade, would be of high value to investigators interested in the statistical study of disease. This report describes initial use of an accumulating healthy database currently comprising 50 subjects aged 20-72. We examine changes by age and sex to the volumes of gray matter, white matter and cerebrospinal fluid for subjects within the database. We conclude that traditional views of healthy aging should be revised. Significant atrophy does not appear in healthy subjects 60 or 70 years old. Gray matter loss is not restricted to senility, but begins in early adulthood and is progressive. The percentage of white matter increases with age. A carefully-designed healthy database should be useful in the statistical analysis of many age- and non-age-related diseases.

Adult↗
PubMed1994

DNA typing of grapevines: a universal methodology and database for describing cultivars and evaluating genetic relatedness.

With established ampelographic techniques for grapevine identification it is often difficult to achieve a satisfactory, objective result. We have developed a DNA typing system using sequence-tagged microsatellite site markers as a means of differentiating cultivars of grapevine. A semi-automated analysis procedure was linked to an electronic database and found to be an objective and reliable system for cultivar identification using this simple marker type. The accumulated DNA typing data from over eighty cultivars demonstrated that cultivars that are difficult to differentiate phenotypically using ampelographic techniques can be distinguished by DNA typing. Parentage analysis uncovered errors in parent assignment or cultivar identification in specific cases. The electronic database has a conservative format to take into account the occurrence of null alleles and the possibility of missed alleles. Computer-assisted comparisons of cultivars in the database can be performed and various approaches for estimating the match probability that two unrelated cultivars have the same genotype simply due to chance are discussed. We suggest that further development of the database through international co-operation using standardised sequence-tagged site markers offers the possibility of achieving a universal grapevine identification system.

DNA, Plant↗
PubMed1993

Database for serial magnetic resonance imaging in multiple sclerosis.

The unique sensitivity of magnetic resonance imaging (MRI) in detecting disease activity in multiple sclerosis (MS) and the objective nature of the information obtained suggest that MRI will be a useful and reliable way of monitoring treatment trials. There is a need to develop an appropriate database which would provide a standardised means of assessment, not only of MRI, but also of essential clinical information. As part of the program of Concerted Action in Multiple Sclerosis, funded by the Commission of the European Community (CEC), we have developed a database for recording serial brain MRI results. The database consists of core, entry and follow-up sections. Both entry and follow-up parts are subdivided into clinical, MR system and MRI data. We expect that the use of this database will maximise efficiency of MRI monitoring in MS treatment trials, particularly in multicentre studies.

Brain↗
PubMed1991

A relational database for sequence-specific protein NMR data.

A protein NMR database has been designed and is being implemented. The database is intended to contain solution NMR results from proteins and peptides (larger than 12 residues). A relational database format has been chosen that indexes data by: primary journal citation, molecular species, sequence-related and atom-specific assignments, and experimental conditions. At present, all data are entered from the primary refereed literature. Examples are given of sample queries to the database. Possible distribution formats are discussed.

Animals↗
PubMed1998

Digital cloning: identification of human cDNAs homologous to novel kinases through expressed sequence tag database searching.

Identification of novel kinases based on their sequence conservation within kinase catalytic domain has relied so far on two major approaches, low-stringency hybridization of cDNA libraries, and PCR method using degenerate primers. Both of these approaches at times are technically difficult and time-consuming. We have developed a procedure that can significantly reduce the time and effort involved in searching for novel kinases and increase the sensitivity of the analysis. This procedure exploits the computer analysis of a vast resource of human cDNA sequences represented in the expressed sequence tag (EST) database. Seventeen novel human cDNA clones showing significant homology to serine/threonine kinases, including STE-20, CDK- and YAK-related family kinases, were identified by searching EST database. Further sequence analysis of these novel kinases obtained either directly from EST clones or from PCR-RACE products confirmed their identity as protein kinases. Given the rapid accumulation of the EST database and the advent of powerful computer analysis software, this approach provides a fast, sensitive, and economical way to identify novel kinases as well as other genes from EST database.

Amino Acid Sequence↗
PubMed1995

Computer assisted data analysis in intensive care: the ICDEV project--development of a scientific database system for intensive care (Intensive Care Data Evaluation Project).

INTRODUCTION: Patient Data Management Systems (PDMS) for ICUs collect, present and store clinical data. Various intentions make analysis of those digitally stored data desirable, such as quality control or scientific purposes. The aim of the Intensive Care Data Evaluation project (ICDEV), was to provide a database tool for the analysis of data recorded at various ICUs at the University Clinics of Vienna. SETTINGS: General Hospital of Vienna, with two different PDMSs used: CareVue 9000 (Hewlett Packard, Andover, USA) at two ICUs (one medical ICU and one neonatal ICU) and PICIS Chart+ (PICIS, Paris, France) at one Cardiothoracic ICU. CONCEPT AND METHODS: Clinically oriented analysis of the data collected in a PDMS at an ICU was the beginning of the development. After defining the database structure we established a client-server based database system under Microsoft Windows NI and developed a user friendly data quering application using Microsoft Visual C++ and Visual Basic; RESULTS: ICDEV was successfully installed at three different ICUs, adjustment to the different PDMS configurations were done within a few days. The database structure developed by us enables a powerful query concept representing an 'EXPERT QUESTION COMPILER' which may help to answer almost any clinical questions. Several program modules facilitate queries at the patient, group and unit level. Results from ICDEV-queries are automatically transferred to Microsoft Excel for display (in form of configurable tables and graphs) and further processing. CONCLUSIONS: The ICDEV concept is configurable for adjustment to different intensive care information systems and can be used to support computerized quality control. However, as long as there exists no sufficient artifact recognition or data validation software for automatically recorded patient data, the reliability of these data and their usage for computer assisted quality control remain unclear and should be further studied.

Austria↗
PubMed2002

Congenital heart surgery nomenclature and database project. Update and proposed data harvest.

In 1998, the first report of the Society of Thoracic Surgery (STS) National Congenital Heart Surgery Database defined clinical features for 18 congenital heart disease categories, providing a significant amount of important information and pinpointing database strengths and weaknesses. Following this report, the STS Congenital Heart Surgery Committee, working with the European Association of Cardio-Thoracic Surgery and the European Congenital Heart Surgeons Foundation, initiated the International Congenital Heart Surgery and Nomenclature Database Project. To standardize nomenclature and reporting strategies and establish a foundation for an international congenital heart surgery database. The project's first report was published in the Annals of Thoracic Surgery in April 2000. The current report outlines modifications to the minimal dataset and diagnosis and procedure short lists.

Databases, Factual↗
PubMed1999

Transparent image access in a distributed picture archiving and communications system: the Master Database broker.

A distributed design is the most cost-effective system for small-to medium-scale picture archiving and communications systems (PACS) implementations. However, the design presents an interesting challenge to developers and implementers: to make stored image data, distributed throughout the PACS network, appear to be centralized with a single access point for users. A key component for the distributed system is a central or master database, containing all the studies that have been scanned into the PACS. Each study includes a list of one or more locations for that particular dataset so that applications can easily find it. Non-Digital Imaging and Communications in Medicine (DICOM) clients, such as our worldwide web (WWW)-based PACS browser, query the master database directly to find the images, then jump to the most appropriate location via a distributed web-based viewing system. The Master Database Broker provides DICOM clients with the same functionality by translating DICOM queries to master database searches and distributing retrieval requests transparently to the appropriate source. The Broker also acts as a storage service class provider, allowing users to store selected image subsets and reformatted images with the original study, without having to know on which server the original data are stored.

CD-ROM↗
PubMed2005

Candidate gene database and transcript map for peach, a model species for fruit trees.

Peach (Prunus persica) is a model species for the Rosaceae, which includes a number of economically important fruit tree species. To develop an extensive Prunus expressed sequence tag (EST) database for identifying and cloning the genes important to fruit and tree development, we generated 9,984 high-quality ESTs from a peach cDNA library of developing fruit mesocarp. After assembly and annotation, a putative peach unigene set consisting of 3,842 ESTs was defined. Gene ontology (GO) classification was assigned based on the annotation of the single "best hit" match against the Swiss-Prot database. No significant homology could be found in the GenBank nr databases for 24.3% of the sequences. Using core markers from the general Prunus genetic map, we anchored bacterial artificial chromosome (BAC) clones on the genetic map, thereby providing a framework for the construction of a physical and transcript map. A transcript map was developed by hybridizing 1,236 ESTs from the putative peach unigene set and an additional 68 peach cDNA clones against the peach BAC library. Hybridizing ESTs to genetically anchored BACs immediately localized 11.2% of the ESTs on the genetic map. ESTs showed a clustering of expressed genes in defined regions of the linkage groups. [The data were built into a regularly updated Genome Database for Rosaceae (GDR), available at (http://www.genome.clemson.edu/gdr/).].

Breeding↗
PubMed2003

Intensive care admission decisions for a patient with limited survival prospects: a questionnaire and database analysis.

OBJECTIVE: To explore the concept of futility by asking clinicians for estimates of survival and admission decisions for an intensive care unit patient with little chance of survival, and to compare these estimates with results from an intensive care database. DESIGN: Questionnaire based on the presenting features of a genuine patient. It asked for estimated hospital survival, decision on intensive care admission, resuscitation status and importance of family views. Analysis of a regional intensive care database. SETTING: Physicians working in British intensive care units. PARTICIPANTS: We received 169 replies, 146 from consultants. MEASUREMENTS AND RESULTS: Median estimated hospital survival was 5%; 60% of consultants and 76% of trainees would have admitted the patient, with 9% and 14%, respectively, prepared to perform further cardiopulmonary resuscitation. Among those estimating survival probability as less than 1%, 17.2% would have admitted the patient. Family opinions were vital to 4.3% of respondents and unimportant to 9.8%. There were 251 patients in the database with similar physiological derangements. Their observed hospital mortality was 91%. At intensive care admission an admitting physician assessed 111 of these patients as 'expected to die'. Mortality in this group was 99.1% (one survivor). CONCLUSIONS: Experienced intensivists did not agree on estimated survival. Even when estimates agreed, admission decisions varied. Database analysis suggested that clinical judgement is relevant when assessing the risk of dying. Lack of consensus on survival estimates and admission decisions suggests that it would be difficult to achieve agreement on appropriate use of intensive care resources and on what constitutes futile treatment.

Critical Illness↗
PubMed2000

The need for a shared database infrastructure: combining X-ray crystallography and electron microscopy.

Advances in structural biology are opening greater opportunities for understanding biological structures from the cellular to the atomic level. Particularly promising are the links that can be established between the information provided by electron microscopy and the atomic structures derived from X-ray crystallography and nuclear magnetic resonance spectroscopy. Combining such different kinds of structural data can result in novel biological information on the interaction of biomolecules in large supramolecular assemblies. As a consequence, the need to develop new databases in the field of structural biology that allow for an integrated access to data from all the experimental techniques is becoming critical. Pilot studies performed in recent years have already established a solid background as far as the basic information that an integrated macromolecular structure database should contain, as well as the basic principles for integration. These efforts started in the context of the BioImage project, and resulted in a first complete database prototype that provided a versatile platform for the linking of atomic models or X-ray diffraction data with electron microscopy information. Analysis of the requirements needed to combine data at different levels of resolution have resulted in sets of specifications that make possible the integration of all these different types in the context of a web environment. The case of a structural study linking electron microscopy and X-ray data, which is already contained within the BioImage data base and in the Protein Data Bank, is used here to illustrate the current approach, while a general discussion highlights the urgent need for integrated databases.

Crystallography, X-Ray↗
PubMed2005

A publicly accessible Monte Carlo database for validation purposes in emission tomography.

Monte Carlo (MC) methods provide ideal data sets to assess reconstruction and correction techniques in emission tomography (ET). Although several ET-dedicated MC codes are available, their use is hindered by the heavy computation burden required for high statistics simulations as well as by the need to adapt the code to the purpose of the individual user. In this work a publicly accessible database of MC-simulated ET data sets (the MC-ET database) was created and published on an Internet web site (http://www.ibfm.cnr.it/mcet/index.html), in order to provide MC-simulated data ready to be downloaded and used by researchers at different sites with similar evaluation purposes. At present, the MC-ET database provides direct access to MC-simulated raw data of unscattered, scattered and total events: (a) obtained by different MC codes, (b) relative to different radioactive sources, from simple geometrical phantoms to studies of normal and pathological subjects and (c) derived from different SPECT and PET scanners. The main features of the MC-ET data sets are: (a) validation by comparison with measured data, (b) classification according to pre-defined database characteristics, (c) common-use file format and (d) easy and free access and download.

Algorithms↗
PubMed2001

Transfer of normal 99mTc-ECD brain SPET databases between different gamma cameras.

A stereotactic, normal perfusion database is imperative for optimal clinical brain single-photon emission tomography (SPET). However, interdepartmental use of normal data necessitates accurate transferability of these data sets. The aim of this study was to investigate transfer of three normal perfusion databases obtained in the same large population of healthy volunteers who underwent sequential scanning using multihead gamma cameras with different resolution. Eighty-nine healthy adults (46 females, 43 males; aged 20-81 years) were thoroughly screened by history, biochemistry, physical and full neurological examination, neuropsychological testing and magnetic resonance imaging. After injection of 925 MBq technetium-99m labelled ethyl cysteinate dimer (ECD) under standard conditions, 101 scans were acquired from all subjects (12 repeat studies) on a triple-head Toshiba GCA-9300A (measured average FWHM 8.1 mm). Ninety-one sequential scans were performed on a dual-head Elscint Helix camera (FWHM 9.6 mm) and 22 subjects also underwent imaging on a triple-head Prism 3000 (FWHM 9.6 mm). Images were transferred to the same processing platform and reconstructed by filtered back-projection with the same Butterworth filter (order 8, cut-off 0.9 cycles/cm) and uniform Sorensen attenuation correction (mu = 0.09). After automated rigid intrasubject registration, all subjects were automatically reoriented to a stereotactic template by a nine-parameter affine transformation. The databases were analysed using 35 predefined volumes of interest (VOIs) with normalisation on total VOI counts. For comparison, the high-resolution data were smoothed with a 3D Gaussian kernel to achieve more similar spatial resolution. Hoffman phantom measurements were conducted on all cameras. Partial volume effects after smoothing varied between -6.5% and 10%, depending on VOI size. Between-camera reproducibility was 2.5% and 2.7% for the Toshiba camera versus the Helix and the Prism database, respectively. The highest reduction in between-camera variability was achieved by resolution adjustment in combination with linear washout correction and a Hoffman phantom-based correction. In conclusion, transfer of normal perfusion data between multihead gamma cameras can be accurately achieved, thereby enabling widespread interdepartmental use, which is likely to have a positive impact on the diagnostic capabilities of clinical brain perfusion SPET.

Adult↗
PubMed2004

An interactive bovine in silico SNP database (IBISS).

An interactive bovine in silico SNP (IBISS) database has been created through the clustering and aligning of bovine EST and mRNA sequences. Approximately 324,000 EST and mRNA sequences were clustered to produce 29,965 clusters (producing 48,679 consensus sequences) and 48,565 singletons. A SNP screening regime was placed on variations detected in the multiple sequence alignment files to determine which SNPs are more likely to be real rather than sequencing errors. A small subset of predicted SNPs was validated on a diverse set of bovine DNA samples using PCR amplification and sequencing. Fifty percent of the predicted SNPs in the "putative >1" category were polymorphic in the population sampled. The IBISS database represents more than just a SNP database; it is also a genomic database containing uniformly annotated predicted gene mRNA and protein sequences, gene structure, and genomic organization information.

Animals↗