Data Retrieval System Research Articles

LUNARINFO: A Data Archiving and Retrieving System for the Circumlunar Explorer Based on XML/Web Services

Abstract It is essential to build a modern information management system to store and manage data of our circumlunar explorer in order to realize the scientific objectives. It is difficult for an information system based on traditional distributed technology to communicate information and work together among heterogeneous systems in order to meet the new requirement of Internet development. XML and Web Services, because of their open standards and self‐containing properties, have changed the mode of information organization and data management. Now they can provide a good solution for building an open, extendable, and compatible information management system, and facilitate interchanging and transferring of data among heterogeneous systems. On the basis of the three‐tiered browse/server architectures and the Oracle 9i Database as an information storage platform, we have designed and implemented a data archiving and retrieval system for the circumlunar explorer—LUNARINFO. We have also successfully realized the integration between LUNARINFO and the cosmic dust database system. LUNARINFO consists of five function modules for data management, information publishing, system management, data retrieval, and interface integration. Based on XML and Web Services, it not only is an information database system for archiving, long‐term storing, retrieving and publication of lunar reference data related to the circumlunar explorer, but also provides data web Services which can be easily developed by various expert groups and connected to the common information system to realize data resource integration.

인체측정자료의 사용성 제고를 위한 인체측정변수 분류 방법

Anthropometric data is a fundamental resource in developing ergonomic products and workplaces. However, designers often experience difficulty in searching anthropometric data relevant to the design due to the technicality of anthropometric terminologies, ambiguity in the description of measurement method for some anthropometric variables, and inefficiency of existing search methods for anthropometric data. The present study suggests a method to develop a classification system of anthropometric variables for systematic, efficient search of anthropometric data. The proposed method first classifies anthropometric variables according to body segment and type of variable, and then arranges anthropometric variables of the same body segment and variable type by comparing the heights of their reference points. The proposed classification method was applied to establish a classification system of 66 anthropometric variables that were selected for an automotive interior design. Then the established anthropometric classification system was utilized to design a search interface of a web-based anthropometric data retrieval system.

Status of the Tore Supra continuous data acquisition and retrieval system

The long pulse operation of the Tore Supra tokamak, with 4 min pulses obtained in 2002, has required improvements of the data acquisition and retrieval systems. Physicists need to have pressure trends between pulses, accurate calorimetric accounting, and continuous diagnostic monitoring. So, new functionalities have been added to our DAS to acquire, store, and access continuous values 24 h a day, 365 days a year. This paper reports the current status of the system and presents an overview of the solutions we used to implement these upgrades.

Long-Term Outcome of Pancreatic Duct Stone Removal in Patients with Chronic Pancreatitis

AIM: Determine the long-term outcome and clinical course after PD stone removal in pts with pain induced by chronic pancreatitis (CP) and PD obstruction. Improvement in pain has been previously reported after endoscopic stone removal and restoration of pancreatic drainage. METHODS: A retrospective review of all pts who had attempted stone removal from the PD (1991-2003) was done using a computer assisted data retrieval system. Pancreatic sphincterotomy was performed in all pts prior to stone removal. Attempts were made to remove MPD stones by balloon &/or basket/mechanical lithotripsy. If unsuccessful, PD stents were placed and the ERCP was repeated within 6-12 wks. If repeatedly unsuccessful, ESWL or EHL was used. Pain relief was assessed using an analog pain scale (0-10). Fisher's exact test was used to compare data. RESULTS: 78 pts (33 M, 45 F) with attempted PD stone removal were identified. The mean age was 54 yr (range 19-90). Etiology was determined to be: ETOH (24/78, 31%) idiopathic (38/78, 49%), divisum (9/78, 11%), hereditary (7/78, 9%). Stones were removed by: balloon &/or basket (54/78, 69%) and ESWL/EHL in addition to balloon &/or basket (24/78, 31%). Other characteristics of stones were: mean diameter 5.6 mm (range 2-18mm), single in 28 pts (36%) and multiple in 50 (64%). Complications were seen in 6% (5/78): bleeding (1), exacerbation of CP (4). Stricture of the MPD was seen in 69% (54/78) of pts. PD stents were placed in 92% (72/78) of pts to manage strictures and to facilitate stone removal. Mean number of stents used were 3.4 and they were exchanged on a regular basis. After multiple Rx interventions 30/78 (38%) had complete clearance of stones. Stone clearance was incomplete in 48/78 (62%). Average ERCPs needed in pts who had complete clearance of stones was 4.8. Four pts had pancreatic surgery during follow-up. Seven pts died during F/U. Among pts with complete ductal clearance, 27% (n=8) had no/partial relief of pain and 73% (n=22) had substantial relief. In pts with partial clearance 62% (n=30) had no/partial relief and 38% (n=18) had substantial relief. Analysis showed that substantial relief of pain was associated (p<0.01) with complete ductal clearance of stones. CONCLUSION: Substantial relief of pain in CP was significantly associated with complete stone clearance. Endoscopic attempts at removal of PD stones are worthwhile, although several ERCP sessions are required for complete stone clearance.

The PIR integrated protein databases and data retrieval system

The CODATA&nbsp;Data Science Journal&nbsp;is a peer-reviewed, open access, electronic journal, publishing papers on the management, dissemination, use and reuse of research data and databases across all research domains, including science, technology, the humanities and the arts. The scope of the journal includes descriptions of data systems, their implementations and their publication, applications, infrastructures, software, legal, reproducibility and transparency issues, the availability and usability of complex datasets, and with a particular focus on the principles, policies and practices for open data.All data is in scope, whether born digital or converted from other sources.

Construction of an Enormous Science Database and Development of an Efficient Data Retrieval and Distribution System

Construction of an Enormous Science Database and Development of an Efficient Data Retrieval and Distribution System

Evidence that intrauterine and postnatal androgens affect the development of pyloric stenosis.

It is rather well established that the causal antecedents of pyloric stenosis (PS) contain both genetic and environmental factors. However, in spite of substantial quantities of epidemiological data, no widespread environmental causal agent has yet been established. There have been recent extensions of our knowledge of the endocrine consequences of fetal growth restriction and of the endocrine determinants of sex ratio. It seemed worth reviewing the epidemiological data on PS in the light of these new developments to see whether this would provide a basis for a plausible hypothesis on these suspected environmental causes of PS. The search terms "pyloric stenosis" and ("epidemiology" or "risk factors") were combined on the Ovid Medline data base for the years 1966 onwards. The data from the resulting papers were augmented by notes occasioned by almost daily reading at the Library of the Royal Society of Medicine (London) for the past 25 years. (Electronic data retrieval systems do not access incidentally recorded data such as sib sex ratios). It is hypothesized that high intrauterine and early postnatal androgen levels constitute an environmental cause of PS.

Indexing genomic sequence libraries

This paper describes an extensible, open-source (GPL) data repository and retrieval system that supports fast, efficient, keyword based retrieval of genomic sequences from multiple libraries with retrieved sequences post-processed by FASTA, Smith–Waterman and other analysis software. This application is implemented for Linux and is written in Mumps, C, and C++ with supporting components that include the Berkeley Data Base, the Perl Compatible Regular Expression Library, GLADE, and tools such as FASTA, Smith–Waterman, and modules from EMBOSS. The package described here can quickly index data sets of up to 256 terabytes using a B-tree based multi-dimensional data model. An example is presented that indexes the text of the full NCBI Genbank library.

CIBEX: Center for Information Biology gene EXpression database

We describe the current status of the gene expression database CIBEX (Center for Information Biology gene EXpression database, http://cibex.nig.ac.jp), with a data retrieval system in compliance with MIAME, a standard that the MGED Society has developed for comparing and data produced in microarray experiments at different laboratories worldwide. CIBEX serves as a public repository for a wide range of high-throughput experimental data in gene expression research, including microarray-based experiments measuring mRNA, serial analysis of gene expression (SAGE tags), and mass spectrometry proteomic data. To cite this article: K. Ikeo et al., C. R. Biologies 326 (2003).

The pyramid of injury: Using ecodes to accurately describe the burden of injury

Study objective Although much is known about injury-related deaths from the use of external cause of injury codes (ecodes) on death certificates, the contribution of nonfatal injury is unknown, with most information based on estimates from national surveys. Some states mandate ecoding of charts for hospitalized patients, but few require ecode assignment for emergency department (ED) records. Missouri and Nebraska mandated ecoding of ED records in 1993 and 1994, respectively, allowing for a more complete description of injuries in those states. We describe fatal and nonfatal injury frequencies in Missouri and Nebraska by using ecodes, with graphic representation in the form of injury pyramids. Methods Ecode frequencies for 1996 to 1998 for all injury causes in Missouri and Nebraska were reported directly from their respective health departments. The ecode frequencies were grouped according to the Centers for Disease Control and Prevention's ecode matrix for presenting injury and mortality data. Results During the study period, 13,052 deaths, 131,210 hospitalizations, and 1,914,140 ED visits occurred as the result of injury. The most frequent lethal injuries were unintentional motor vehicle crashes (32.3% of total deaths), self-inflicted gunshot wound (13.2%), unintentional falls (11.3%), gunshot wound from an assault (7.7%), and unintentional poisoning (4.3%). The leading causes of injury-related hospitalization were unintentional falls (47.8% of total hospitalizations), unintentional motor vehicle crashes (15.5%), self-inflicted poisoning (6.5%), and overexertion or strenuous movements (2.4%). Of 1.9 million ED injury visits, unintentional falls accounted for 24.3%, unintentionally being struck by an object or person for 14.6%, unintentional motor vehicle crashes for 11.4%, unintentionally being cut or pierced for 10.7%, and overexertion or strenuous movements for 8.5%. Conclusion Ecoding in Missouri and Nebraska provides a comprehensive data retrieval system that allows for a graphic depiction of the burden of injury derived from real patient encounters within specific geographic regions.

EURISWEB--Web-based epidemiological surveillance of antibiotic-resistant pneumococci in day care centers.

BackgroundEURIS (European Resistance Intervention Study) was launched as a multinational study in September of 2000 to identify the multitude of complex risk factors that contribute to the high carriage rate of drug resistant Streptococcus pneumoniae strains in children attending Day Care Centers in several European countries. Access to the very large number of data required the development of a web-based infrastructure – EURISWEB – that includes a relational online database, coupled with a query system for data retrieval, and allows integrative storage of demographic, clinical and molecular biology data generated in EURIS.MethodsAll components of the system were developed using open source programming tools: data storage management was supported by PostgreSQL, and the hypertext preprocessor to generate the web pages was implemented using PHP. The query system is based on a software agent running in the background specifically developed for EURIS.ResultsThe website currently contains data related to 13,500 nasopharyngeal samples and over one million measures taken from 5,250 individual children, as well as over one thousand pre-made and user-made queries aggregated into several reports, approximately. It is presently in use by participating researchers from three countries (Iceland, Portugal and Sweden).ConclusionAn operational model centered on a PHP engine builds the interface between the user and the database automatically, allowing an easy maintenance of the system. The query system is also sufficiently adaptable to allow the integration of several advanced data analysis procedures far more demanding than simple queries, eventually including artificial intelligence predictive models.

Airway Foreign Bodies in Adults

The objective of this study was to evaluate the efficacy of flexible bronchoscopy in the management of tracheobronchial foreign bodies (TFB) in adults (≥16 y) from 1990 through 2002. TFB was defined as the presence of any foreign object below the vocal cords. Patients with gastric aspiration or regurgitation were excluded. We reviewed Mayo Clinic Rochester's medical data retrieval system to obtain information on patients with TFBs. Data abstracted included demographics, clinical symptoms, physical examination findings, bronchoscopic techniques used for extraction, success rates, and complications. A total of 65 adults with TFB aspiration were identified. There were 44 males (68%) and 21 females (32%) with a mean age of 60.8 years. A recognized predisposition to aspiration was evident in 35 patients (54%). The right lower lobe was the most common site for lodgment of aspirated TFB (24 of 65 patients; 37%), followed by the bronchus intermedius in 14 patients (22%), trachea in 7 (11%), left main stem bronchus in 7 (11%), and other locations in the rest. The most common symptom was cough (58 of 65 patients; 89%). The most common finding on physical examination was wheezing, seen in 20 patients (31%). Chest radiographs were obtained in 59 patients (91%) and were abnormal in 54 (92%). TFB was seen or its presence was suggested on the chest radiograph in 19 patients (32%). TFBs extracted included dental pieces in 14 patients (22%), nuts in 12 (18%), corn kernels in 7 (11%), vegetable matter in 7 (11%), bones in 6 (9%), plastic pieces in 4 (6%), pills in 2 (3%), and one each of the following: meat, nail, laryngeal polyp, folded drinking straw, broken piece of an endotracheal tube, broken piece of a voice prosthesis, tracheostomy cleaning brush, foil, surgical staple, surgical pledget, balloon fragment, sunflower seed, and a sewing needle. The flexible bronchoscope was used in 61 of the 65 patients (94%) and was successful in 54 of these patients (89%). Flexible bronchoscopy was unsuccessful in 7 patients, 6 of whom underwent successful TFB extraction by rigid bronchoscopy. One patient required a thoracotomy for the removal of a TFB in the right lower lobe. Complications from bronchoscopy were minimal and consisted of minor bleeding in 3 patients. Flexible bronchoscopic procedures were successful in the extraction of 89% of tracheobronchial foreign bodies in adults. Our experience also indicates that flexible bronchoscopic removal of TFBs in adults can be safely performed with minimal complications.

Water chlorination and birth defects: a systematic review and meta-analysis.

The authors used the Medline data retrieval system for 1966-2001 to identify and synthesize the epidemiological evidence for adverse effects of prenatal exposure to chlorination byproducts on birth defects. For 5 studies that provided estimates of the effect of exposure on 1 or several birth defects, the authors calculated summary odds ratios and 95% confidence intervals using the Mantel-Haenszel method for a fixed-effects model, and the DerSimonian-Laird method for a random-effects model. The results of this meta-analysis provide evidence for an effect of exposure to chlorination byproducts on the risk of any birth defect, and of neural tube and urinary system defects. The results for respiratory system, major cardiac, and oral cleft defects were heterogeneous and inconclusive. Differences in the susceptibility of populations, and different approaches in exposure assessment, may explain the heterogeneity of the results.

The PEDANT genome database.

The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based user interface. One hundred and seventy seven completely sequenced and unfinished genomes have been processed so far, including large eukaryotic genomes (mouse, human) published recently. In this contribution, we describe the current status of the PEDANT database and novel analytical features added to the PEDANT server in 2002. Those include: (i) integration with the BioRS data retrieval system which allows fast text queries, (ii) pre-computed sequence clusters in each complete genome, (iii) a comprehensive set of tools for genome comparison, including genome comparison tables and protein function prediction based on genomic context, and (iv) computation and visualization of protein-protein interaction (PPI) networks based on experimental data. The availability of functional and structural predictions for 650 000 genomic proteins in well organized form makes PEDANT a useful resource for both functional and structural genomics.

Assessment of TID activity from GPS phase data collected in a dense network of GPS receivers

GPS data from a dense network of receivers can be an important source of information on Travelling Ionospheric Disturbances (TIDs), especially for smaller scale fluctuations (small and medium scale TIDs). Since absolute TEC ``calibration'' is not necessary it is sufficient to work with GPS differential phase data. We are using data from a dense network of GPS receivers distributed over Austria to assess TID activities on a bi-hourly basis. The raw data are stored in the well-known RINEX format. The phase differences are extracted and after correction of ``cycle slips'' the data are subjected to band-pass filtering. Cycle slip correction is a tricky but necessary process. The use of ``cycle slip free'' time intervals would leave only a fraction of available data for TID activity assessment. We describe the data retrieval and preparation system and show first results (case studies and preliminary results).

New data storage and retrieval systems for JET data

Since the start of the Joint European Torus (JET), an IBM mainframe has been the main platform for data analysis and storage (J. Comput. Phys. 73 (1987) 85). The mainframe was removed in June 2001 and Solaris and Linux are now the main data storage and analysis platforms. New data storage and retrieval systems have therefore been developed: the Data Warehouse, the JET pulse file server, and the processed pulse file system. In this paper, the new systems will be described, and the design decisions that led to the final systems will be outlined.

Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags.

MAGEST is a database for maternal gene expression information for an ascidian, Halocynthia roretzi. The ascidian has become an animal model in developmental biological research because it shows a simple developmental process, and belongs to one of the chordate groups. Various data are deposited into the MAGEST database, e.g. the 3'- and 5'-tag sequences from the fertilized egg cDNA library, the results of similarity searches against GenBank and the expression data from whole mount in situ hybridization. Over the last 2 years, the data retrieval systems have been improved in several aspects, and the tag sequence entries have increased to over 20 000 clones. Additionally, we constructed a database, translated MAGEST, for the amino acid fragment sequences predicted from the EST data sets. Using this information comprehensively, we should obtain new information on gene functions. The MAGEST database is accessible via the Internet at http://www.genome.ad.jp/magest/.

Transcriptome analysis and related databases of Lactococcus lactis.

Several complete genome sequences of Lactococcus lactis and their annotations will become available in the near future, next to the already published genome sequence of L. lactis ssp. lactis IL 1403. This will allow intraspecies comparative genomics studies as well as functional genomics studies aimed at a better understanding of physiological processes and regulatory networks operating in lactococci. This paper describes the initial set-up of a DNA-microarray facility in our group, to enable transcriptome analysis of various Gram-positive bacteria, including a ssp. lactis and a ssp. cremoris strain of Lactococcus lactis. Moreover a global description will be given of the hardware and software requirements for such a set-up, highlighting the crucial integration of relevant bioinformatics tools and methods. This includes the development of MolGenIS, an information system for transcriptome data storage and retrieval, and LactococCye, a metabolic pathway/genome database of Lactococcus lactis.

Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more.

Genome Information Broker (GIB) is a powerful tool for the study of comparative genomics. GIB allows users to retrieve and display partial and/or whole genome sequences together with the relevant biological annotation. GIB has accumulated all the completed microbial genome and has recently been expanded to include Arabidopsis thaliana genome data from DDBJ/EMBL/GenBank. In the near future, hundreds of genome sequences will be determined. In order to handle such huge data, we have enhanced the GIB architecture by using XML, CORBA and distributed RDBs. We introduce the new GIB here. GIB is freely accessible at http://gib.genes.nig.ac.jp/.

ASCOT: a comprehensive clinical database for gastro-oesophageal cancer surgery

We report the development of a multicentre prospective database for gastro-oesophageal cancer surgery. The ASCOT project aims to collect detailed prospective data on co-morbidity, surgery, stage and outcome in a large cohort of patients from a wide variety of hospitals in the UK. We describe the rationale for the initiative, the process of defining the dataset, the database software and structure, the system for data recording and retrieval and the operating rules of the ASCOT co-operative group. Thirty Trusts are currently submitting data, and the first 1000 cases have now been entered. A first annual report has been produced, showing anonymized comparative figures for patient characteristics and outcomes of interest, and a second is due shortly. The collection of detailed comparable data, including co-morbidity evaluation, on a large scale is likely to prove valuable for unit specialist accreditation, surgeon re-validation, audit and research.