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Relational Database (relational + database)

Distribution by Scientific Domains

Information Science and Computing	38%
Chemistry	30%
Medical Sciences	15%

Selected Abstracts

Relational Database Driven Two-Dimensional Chemical Graph Analysis

CHEMICAL BIOLOGY & DRUG DESIGN, Issue 3 2006
Steven J. Wilkens
This manuscript presents a method for pre-computing and storing molecular features or ,,scaffolds'' that can be used for rapid clustering of diverse compound sets within the context of a relational database based on hierarchies of scaffold structures. In addition, a method for rapid structure-based profiling of a large compound collection is demonstrated. Pre-organizing compounds by shared structural features in this way facilitates the merger of chemical features and biological data within a relational database. [source]

Automatic capture and efficient storage of e-Science experiment provenance

CONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 5 2008
Roger S. Barga
Abstract For the first provenance challenge, we introduce a layered model to represent workflow provenance that allows navigation from an abstract model of the experiment to instance data collected during a specific experiment run. We outline modest extensions to a commercial workflow engine so it will automatically capture provenance at workflow runtime. We also present an approach to store this provenance data in a relational database. Finally, we demonstrate how core provenance queries in the challenge can be expressed in SQL and discuss the merits of our layered representation. Copyright © 2007 John Wiley & Sons, Ltd. [source]

Effective database processing for classification and regression with continuous variables

INTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS, Issue 12 2007
E. Di Tomaso
This article proposes a method for manipulating a database of instances relative to discrete and continuous variables. A fuzzy partition is used to discretize continuous domains. A reorganized form of representing a relational database is proposed. The new form of representation is called an effective database. The effective database is tested on classification and regression problems using general Bayesian networks and Näive Bayes classifiers. The structures and the parameters of the classifiers are estimated from the effective database. An algorithm for updating with soft evidence is used to test the induced models, when continuous variables are present. The experiments show that the effective database procedure produces a selection of relevant information from data, which improves in some cases the prediction accuracy of the classifiers. © 2007 Wiley Periodicals, Inc. Int J Int Syst 22: 1271,1285, 2007. [source]

Answers to queries concerning uncertain and imprecise information in fuzzy relational databases

INTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS, Issue 6 2005
Nan-Chen Hsieh
A model of an extended fuzzy relational database was proposed to accommodate uncertain and imprecise information. We use two supplementary measurements, satisfactory degree and extra degree, for determining the quality of answers to Select-Project-Join (SPJ) queries. The method of measurement determines how much satisfactory information is provided and how much truth information is required for a query. The answers to the query thus contain sure answers and maybe answers. The core of this study is the detailed discussion on the quality of answers in an extended fuzzy relation to query processing. © 2005 Wiley Periodicals, Inc. Int J Int Syst 20: 647,668, 2005. [source]

Handling indefinite and maybe information in logical fuzzy relational databases

INTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS, Issue 3 2004
Nan-Chen Hsieh
In this article, fuzzy set theory uses an extension of the classical logical relational database model. A logical fuzzy relational database model was developed with the aim of manipulating imprecise information and adding deduction capabilities to the database system. The essence of this work is the detailed discussion on fuzzy definite, fuzzy indefinite, and fuzzy maybe information and the development of an information theoretical approach of query evaluation on the logical fuzzy relational database. We define redundancies among fuzzy tuples and the operator of their removal. A complete set of fuzzy relational operations in relational algebra and the calculus of linguistically quantified propositions are included also. © 2004 Wiley Periodicals, Inc. [source]

Uncertain fuzzy values still in the framework of first-order logic

INTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS, Issue 9 2002
O. Pons
In this article, we first summarize the more important aspects of a fuzzy logic relational database and show how a fuzzy relational database can be represented and handled using first-order logic. Given that the results obtained for fuzzy databases are satisfactory, we then tackle the problem of uncertain fuzzy databases, considering that the fuzzy values stored in the database have a certainty value attached. Because it is still possible we are still in the framework of first-order logic, a transformation function on uncertain fuzzy values is introduced. The idea is to transform uncertainty into imprecision in such a way that an uncertain fuzzy value is transformed into a more imprecise but certain fuzzy value. With this transformation, all the original uncertain fuzzy values become true, and truth levels are not needed. © 2002 Wiley Periodicals, Inc. [source]

Management of metadata and automation for mail-in measurements with the APS 11-BM high-throughput, high-resolution synchrotron powder diffractometer

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2009
Brian H. Toby
A high-resolution and high-throughput synchrotron powder diffractometer has been automated for use with samples that are mailed in by Advanced Photon Source users. Implementation of a relational database with web interfaces for both outside users and beamline staff, which is integrated into the facility-wide proposal and safety system, allows all aspects of beamline management to be integrated. This system permits users to request kits for mounting samples, to provide sample safety information, to obtain their collected data and to provide usage information upon project completion in a quick and simple manner. Beamline staff use a separate interface to note receipt of samples, schedule and collect diffraction data, post-process and quality-check data, and dispose of samples. The design of the software and database are discussed in detail. [source]

MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments

JOURNAL OF SYNCHROTRON RADIATION, Issue 5 2010
José Gabadinho
The design and features of a beamline control software system for macromolecular crystallography (MX) experiments developed at the European Synchrotron Radiation Facility (ESRF) are described. This system, MxCuBE, allows users to easily and simply interact with beamline hardware components and provides automated routines for common tasks in the operation of a synchrotron beamline dedicated to experiments in MX. Additional functionality is provided through intuitive interfaces that enable the assessment of the diffraction characteristics of samples, experiment planning, automatic data collection and the on-line collection and analysis of X-ray emission spectra. The software can be run in a tandem client-server mode that allows for remote control and relevant experimental parameters and results are automatically logged in a relational database, ISPyB. MxCuBE is modular, flexible and extensible and is currently deployed on eight macromolecular crystallography beamlines at the ESRF. Additionally, the software is installed at MAX-lab beamline I911-3 and at BESSY beamline BL14.1. [source]

IgA nephropathy and mesangial cell proliferation: shared global gene expression profiles

NEPHROLOGY, Issue 2002
Hideto SAKAI
SUMMARY: It is well established that mesangial cell proliferation plays a major role in glomerular injury and progressive renal injury. the expression of a number of different genes has been reported in proliferative mesangial cells in culture. However, the relevance of these genes to renal injury in general and IgA nephropathy (IgAN) remains to be established. Assessment of gene activity on a global genome-wide scale is a fundamental and newly developed molecular strategy to expand the scope of clinical investigation from a single gene to studying all genes at once in a systematic pattern. Capitalizing on the recently developed methodology of high cDNA array hybridization, the simultaneous expression of thousands of genes in primary human proliferating mesangial cells was monitored and compared with renal tissue of IgAN. Complex [,- 33P]-labelled cDNA targets were prepared from cultured mesangial cells, remnant tissue from five IgAN renal biopsies and four nephrectomies (controls). Each target was hybridized to a high-density array of 18 326 paired target genes. the radioactive hybridization signals were analysed by phosphorimager. Approximately 8212±530 different gene transcripts were detected per target. Close to 5% (386±90 genes) were full-length mRNA human transcripts (HT) and the remainder were expressed sequence tags (EST). Using a relational database, electronic subtraction was performed and matching was carried out to allow identification of 203 HT with shared expression in proliferative mesangial cells and IgAN renal biopsies. In addition hierarchical clustering analysis was performed on the HT of IgAN and controls to establish differential expression profiles of mesangial HT in IgAN and controls. Collectively the presented data constitutes a preliminary renal bioinformatics database of the transcriptional profiles in IgAN. More importantly, the information may help to speed up the discovery of genes underlying human IgAN. [source]

New Powder Diffraction File (PDF-4) in relational database format: advantages and data-mining capabilities

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3-1 2002
Soorya N. Kabekkodu
The International Centre for Diffraction Data (ICDD) is responding to the changing needs in powder diffraction and materials analysis by developing the Powder Diffraction File (PDF) in a very flexible relational database (RDB) format. The PDF now contains 136,895 powder diffraction patterns. In this paper, an attempt is made to give an overview of the PDF-4, search/match methods and the advantages of having the PDF-4 in RDB format. Some case studies have been carried out to search for crystallization trends, properties, frequencies of space groups and prototype structures. These studies give a good understanding of the basic structural aspects of classes of compounds present in the database. The present paper also reports data-mining techniques and demonstrates the power of a relational database over the traditional (flat-file) database structures. [source]

Relational Database Driven Two-Dimensional Chemical Graph Analysis

4 A Multimedia Web-based Interactive Quiz Module for the Education of Emergency Medical Personnel

ACADEMIC EMERGENCY MEDICINE, Issue 2008
James D'Agostino
A dynamic database-driven website was introduced in 2002. This site has served successfully as a learning tool with its annual update and addition of interactive case and quiz modules. To extend web-based learning as an educational tool, we developed a multimedia web-based module for emergency medicine, with video and audio enhancements to simulate patient encounters in the emergency ward setting. Central to the web-module development is the creation of a relational database. We use FileMaker Pro with search, storage, retrieval, image, video and audio incorporation functions, and a built-in interface that allows display of database contents in web templates. Initially the patient's history and presentation are presented with a 30,60 second video followed by key physical findings. The diagnostic studies and management of the patient are then available through sequential interactive quizzes and feedback replies, presented in audio-, video- and image-oriented formats. The format of the quizzes themselves simulates medical board questions. Initial feedback has been favorable. The majority of emergency medicine personnel feel that this module complements and enhances regular lecture sessions. In addition, it enables preservation of interesting and/or infrequently encountered cases for viewing by all residents in Emergency Medicine. [source]