Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Data Storage And Retrieval”

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 415 records · Page 23Linked to original sources
PubMed1996

A cholinesterase genes server (ESTHER): a database of cholinesterase-related sequences for multiple alignments, phylogenetic relationships, mutations and structural data retrieval.

We have built a database of sequences phylogenetically related to cholinesterases (ESTHER) for esterases, alpha/beta hydrolase enzymes and relatives). These sequences define a homogeneous group of enzymes (carboxylesterases, lipases and hormone-sensitive lipases) with some related proteins devoid of enzymatic activity. The purpose of ESTHER is to help comparison and alignment of any new sequence appearing in the field, to favour mutation analysis of structure-function relationships and to allow structural data recovery. ESTHER is a World Wide Web server with the URL http://www.montpellier.inra.fr:70/cholinesterase.

Amino Acid Sequence↗
PubMed2005

AKA-Glucose: a program for kinetic and epidemiological analysis of frequently sampled intravenous glucose tolerance test data using database technology.

BACKGROUND: The Bergman Minimal Model enables estimation of two key indices of glucose/ insulin dynamics: glucose effectiveness and insulin sensitivity. METHODS AND RESULTS: In this paper we describe AKA-Glucose, a program that combines MINMOD Millennium (minimal model analysis software) with relational database technologies. AKA-Glucose enables the fitting of individual frequently sampled intravenous glucose tolerance test (FSIGT) data sets to the Minimal Model and the secure storage in a dedicated database (and retrieval from) of thousands of individual subjects' demographic data, their individual FSIGT data, and each subject's parameters and indices derived from minimal model analysis. AKA-Glucose also enables the population analysis of various strata or subpopulations within the database. AKA-Glucose has all of the capabilities of MINMOD Millennium, provides Minimal Model parameter estimates that are concordant with estimates from previous MINMOD software, and allows importation of data files from earlier versions of the MINMOD software. CONCLUSIONS: By combining FSIGT data fitting, population analysis, and relational database technologies, AKA-Glucose is the first minimal model software designed specifically for researchers confronted with minimal model and epidemiological analysis of large numbers of either human or animal FSIGT data sets.

Adult↗
PubMed2006

Experimental challenges to theories of classical conditioning: application of an attentional model of storage and retrieval.

Several studies have recently challenged the accuracy of traditional models of classical conditioning that account for some experimental data in terms of a storage deficit. Among other results, it has been reported that extinction of the blocking or overshadowing stimulus results in the recovery of the response to the blocked or overshadowed stimulus, backward blocking shows spontaneous recovery, extinction of the training context results in the recovery from latent inhibition, interposing a delay between conditioning and testing in latent inhibition increases latent inhibition, and latent inhibition antagonizes overshadowing. An existing neural network model of classical conditioning (N. A. Schmajuk, Y. Lam, & J. A. Gray, 1996), which includes an attentional mechanism controlling both storage and retrieval of associations, is able to quantitatively describe these results.

Animals↗
PubMed2005

Retrieving rules for behavior from long-term memory.

Human behavior is often dictated by rules or prescribed guides for action. Little is currently known regarding how these rules are stored in long-term memory or retrieved and implemented. Here, we examined the roles of ventrolateral prefrontal cortex (VLPFC) and posterior middle temporal gyrus (postMTG) in rule use. We tested two hypotheses: first, that knowledge about actions associated with abstract visual symbols is stored in postMTG, and second, that VLPFC is involved in the controlled retrieval of rule meanings. Subjects viewed a series of road signs during event-related fMRI data collection. Three types of signs were intermixed: highly familiar signs, novel signs whose meaning was explained to subjects prior to scanning, and novel signs whose meaning was not explained. Subjects were asked to think about the meaning of each sign as it was presented during scanning and then to give its meaning in a post-scan test. Left postMTG was more active when subjects viewed signs whose meaning they knew than signs whose meaning they did not know, consistent with a role in storing rule meanings. This region was not modulated by experience, in that it was equally engaged by newly trained and well-learned signs. In contrast, right VLPFC was more active for newly trained signs than for either well-learned or incorrect ones, consistent with a role in controlled retrieval. Left VLPFC was reliably engaged while subjects attempted to interpret the signs but did not differ according to knowledge or experience. These data implicate postMTG in rule storage and VLPFC in rule retrieval.

Adult↗
PubMed2006

De novo peptide sequencing using exhaustive enumeration of peptide composition.

We introduce the use of a peptide composition lookup table indexed by residual mass and number of amino acids for de novo sequencing of polypeptides. Polypeptides of 1600 Daltons (Da) or more can be sequenced effectively through exhaustive compositional analysis of MS/MS spectra obtained by unimolecular decomposition (without CID) in a MALDI TOF/TOF despite a fragment mass accuracy of 50 mDa. Peaks are referenced against the lookup table to obtain a complete profile of amino acid combinations, and combinations are assembled into series of increasing length. Concatenating the differences between successive entries in compositional series yields peptide sequences that can be scored and ranked according to signal intensity. While the current work involves measurements acquired on MALDI TOF-TOF, such general treatment of the data anticipates extension to other types of mass analyzers.

Algorithms↗
PubMed2004

Fast and accurate database homology search using upper bounds of local alignment scores.

MOTIVATION: It is widely recognized that homology search and ortholog clustering are very useful for analyzing biological sequences. However, recent growth of sequence database size makes homolog detection difficult, and rapid and accurate methods are required. RESULTS: We present a novel method for fast and accurate homology detection, assuming that the Smith-Waterman (SW) scores between all similar sequence pairs in a target database are computed and stored. In this method, SW alignment is computed only if the upper bound, which is derived from our novel inequality, is higher than the given threshold. In contrast to other methods such as FASTA and BLAST, this method is guaranteed to find all sequences whose scores against the query are higher than the specified threshold. Results of computational experiments suggest that the method is dozens of times faster than SSEARCH if genome sequence data of closely related species are available.

Algorithms↗
PubMed2000

Annotating sequence data using Genotator.

In this postgenomic era, it is no longer necessary to argue the need for automated methods for sequence annotation. Many researchers have designed tools for analyzing DNA sequences, but running multiple tools and interpreting the results can be tedious and confusing. In the last few years, many analysis workbenches have been developed to help streamline the process of sequence annotation. Genotator, developed in 1996, is still a popular choice owing to its ease of use and its configurability. This article will review annotating sequence data using the Genotator.

Amino Acid Sequence↗
PubMedDate not supplied

[Certain methodological problems concerning the study of occupational morbidity and morbidity related to work].

Research on occupational and occupationally-related morbidity is essential for setting up a system of measures designed to promote health and well-being in industrial workers. The right conclusions can only be drawn and the adequate decisions made after data on occupational and occupationally-related diseases have been accurately stored, processed, interpreted and evaluated. Starting from the vast amount of information collected in some branches of national economy and yielded by routine statistic procedures, the author attempts to assess systems of storage and retrieval currently used for decision-oriented data. It is suggested that essential changes could be effected in today's system for analysing data on occupational and occupationally-related diseases on the basis of decentralized evidence.

Bulgaria↗
PubMed2001

Indexing medical WWW documents by morphemes.

Assisting users to search medical information on the WWW is here considered from two perspectives--the linguistic complexity of medical terms, nominal compounds in particular, and cross-lingual relationships between monolingual medical terminologies. In order to solve the first problem, we present an approach to automatic indexing in which medically plausible morphological units are used. Semantic value is added to these index terms by a compact domain-specific thesaurus. We further discuss tools for morphological segmentation and morphosemantic normalization of HTML documents, as well as an adaptation of a standard WWW search engine for morpheme-based retrieval. The second problem, cross-lingual medical document retrieval, is dealt with by defining cross-lingual equivalence relations on the emerging morpheme sets.

Abstracting and Indexing↗
PubMed1976

Storage and retrieval of SNOP-coded pathologic diagnoses using offsite computing and optical character recognizing systems.

A computerized cross-reference system for retrieving autopsy and surgical pathology cases on the basis of case number or diagnosis has been implemented. The system achieves economy and flexibility by using offsite computer service bureaus for job production, eliminating the need for expensive onsite equipment. Coded diagnoses may be typed using the OCR (Optical Character Recognition) font simultaneously with or separately from the clinical documentation. The flexibility of new OCR equipment permits production of machine-readable code sheets with an ordinary pencil and completely eliminates the need for typing. The system produces year-to-date books that list all diagnoses, on an accumulating basis, in alphabetic order by SNOP* topology, morphology, etiology and function, and will be compatible with SNOMed. Because all data are stored on magnetic tape, they may be manipulated and retrieved as desired through user programming. The initial setup cost was dollar 1,000 for programming and testing, and production runs and all report printing cost about dollar 1,000 per year (autopsies and surgical pathology cases), which is about 1.1 cents per diagnosis.

Computer Systems↗
PubMed2005

DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus.

MOTIVATION: Polymorphism studies are one of the main research areas of this genomic era. To date, however, no comprehensive secondary databases have been designed to provide searchable collections of polymorphic sequences with their associated diversity measures. RESULTS: We define a data model for the storage, representation and analysis of genotypic and haplotypic data. Under this model we have created DPDB, 'Drosophila Polymorphism Database', a web site that provides a daily updated repository of all well-annotated polymorphic sequences in the Drosophila genus. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity, linkage disequilibrium and codon bias. For data collection, analysis and updating we use PDA, a pipeline that automates the process of sequence retrieval, grouping, alignment and estimation of nucleotide diversity from Genbank sequences in different functional regions. The web site also includes analysis tools for sequence comparison and the estimation of genetic diversity, a page with real-time statistics of the database contents, a help section and a collection of selected links. AVAILABILITY: DPDB is freely available at http://dpdb.uab.es and can be downloaded via FTP.

Animals↗
PubMed2002

ENDscript: a workflow to display sequence and structure information.

UNLABELLED: ENDscript is a web server grouping popular programs such as BLAST, Multalin and DSSP. It uses as query the co-ordinates file of a protein in Protein Data Bank format and generates PostScript and png figures showing: residues conserved after a multiple alignment against homologous sequences, secondary structure elements, accessibility, hydropathy and intermolecular contacts. Thus, the user can relate quickly 1D, 2D and 3D information of a protein of known structure. AVAILABILITY: http://genopole.toulouse.inra.fr/ENDscript

Amino Acid Sequence↗
PubMed1998

Database on the structure of large ribosomal subunit RNA.

The rRNA WWW Server at URL http://rrna.uia.ac.be/ now provides a database of 496 large subunit ribosomal RNA sequences. All these sequences are aligned, incorporate secondary structure information, and can be obtained in a number of formats. Other information about the sequences, such as literature references, accession numbers and taxonomic information is also available and searchable. If necessary, the data on the server can also be obtained by anonymous ftp.

Animals↗
PubMed2005

Recent Hits Acquired by BLAST (ReHAB): a tool to identify new hits in sequence similarity searches.

BACKGROUND: Sequence similarity searching is a powerful tool to help develop hypotheses in the quest to assign functional, structural and evolutionary information to DNA and protein sequences. As sequence databases continue to grow exponentially, it becomes increasingly important to repeat searches at frequent intervals, and similarity searches retrieve larger and larger sets of results. New and potentially significant results may be buried in a long list of previously obtained sequence hits from past searches. RESULTS: ReHAB (Recent Hits Acquired from BLAST) is a tool for finding new protein hits in repeated PSI-BLAST searches. ReHAB compares results from PSI-BLAST searches performed with two versions of a protein sequence database and highlights hits that are present only in the updated database. Results are presented in an easily comprehended table, or in a BLAST-like report, using colors to highlight the new hits. ReHAB is designed to handle large numbers of query sequences, such as whole genomes or sets of genomes. Advanced computer skills are not needed to use ReHAB; the graphics interface is simple to use and was designed with the bench biologist in mind. CONCLUSIONS: This software greatly simplifies the problem of evaluating the output of large numbers of protein database searches.

Algorithms↗