Science.gov

Sample records for access relational database

  1. Mandatory and Location-Aware Access Control for Relational Databases

    NASA Astrophysics Data System (ADS)

    Decker, Michael

    Access control is concerned with determining which operations a particular user is allowed to perform on a particular electronic resource. For example, an access control decision could say that user Alice is allowed to perform the operation read (but not write) on the resource research report. With conventional access control this decision is based on the user's identity whereas the basic idea of Location-Aware Access Control (LAAC) is to evaluate also a user's current location when making the decision if a particular request should be granted or denied. LAAC is an interesting approach for mobile information systems because these systems are exposed to specific security threads like the loss of a device. Some data models for LAAC can be found in literature, but almost all of them are based on RBAC and none of them is designed especially for Database Management Systems (DBMS). In this paper we therefore propose a LAAC-approach for DMBS and describe a prototypical implementation of that approach that is based on database triggers.

  2. Reflective Database Access Control

    ERIC Educational Resources Information Center

    Olson, Lars E.

    2009-01-01

    "Reflective Database Access Control" (RDBAC) is a model in which a database privilege is expressed as a database query itself, rather than as a static privilege contained in an access control list. RDBAC aids the management of database access controls by improving the expressiveness of policies. However, such policies introduce new interactions…

  3. CORAL Server and CORAL Server Proxy: Scalable Access to Relational Databases from CORAL Applications

    NASA Astrophysics Data System (ADS)

    Valassi, A.; Bartoldus, R.; Kalkhof, A.; Salnikov, A.; Wache, M.

    2011-12-01

    The CORAL software is widely used at CERN by the LHC experiments to access the data they store on relational databases, such as Oracle. Two new components have recently been added to implement a model involving a middle tier "CORAL server" deployed close to the database and a tree of "CORAL server proxies", providing data caching and multiplexing, deployed close to the client. A first implementation of the two new components, released in the summer 2009, is now deployed in the ATLAS online system to read the data needed by the High Level Trigger, allowing the configuration of a farm of several thousand processes. This paper reviews the architecture of the software, its development status and its usage in ATLAS.

  4. CORAL Server and CORAL Server Proxy: Scalable Access to Relational Databases from CORAL Applications

    SciTech Connect

    Valassi, A.; Bartoldus, R.; Kalkhof, A.; Salnikov, A.; Wache, M.; /Mainz U., Inst. Phys.

    2012-04-19

    The CORAL software is widely used at CERN by the LHC experiments to access the data they store on relational databases, such as Oracle. Two new components have recently been added to implement a model involving a middle tier 'CORAL server' deployed close to the database and a tree of 'CORAL server proxies', providing data caching and multiplexing, deployed close to the client. A first implementation of the two new components, released in the summer 2009, is now deployed in the ATLAS online system to read the data needed by the High Level Trigger, allowing the configuration of a farm of several thousand processes. This paper reviews the architecture of the software, its development status and its usage in ATLAS.

  5. Database Access Integration Services (DAIS)

    SciTech Connect

    Mitchell, P. . Sensor and System Development Center); Nordell, D. )

    1992-12-01

    The Database Access Integration Services (DAIS) is a collection of services that facilitate access to data among diverse data systems in an electric utility communications network. DAIS provides access to data in distributed, heterogeneous data systems that include relational database management systems, other database management systems, control systems, file systems, and application systems. It also provides a common method for describing data, common data access operations and essential support services including a data dictionary, a data directory and distributed data access management capabilities. The DAIS project has developed specifications intended for vendor and third-party implementation. The software developed is only to implement a data access integration demonstration. These specifications can serve as a basis for influencing industry standards development. One important consequence of this strategy is that most actual software development will be performed by vendors, not utilities. DAIS is a tool to support data access. It is policy neutral regarding issues such as local or central administration of data or standardization of information model contents (e.g., EPRI Plant Information Network). As a tool, it can be used to help realize such policies. The DAIS does not provide data storage facilities, schema integration, distributed query processing, distributed applications or cooperative processing. Rather, DAIS is complementary to these functions and can be used with other software that does provide these functions. This project documented the requirements for the DAIS. These requirements are the basis for design of the DAIS specifications. The key requirements for a DAIS are: Uniform access to heterogeneous utility data systems, remote update; coexistence with local data systems; local autonomy ; Security and access restriction enforcement; OSI compatibility; open architecture and extensibility; and operating platform independence.

  6. New tools and methods for direct programmatic access to the dbSNP relational database

    PubMed Central

    Saccone, Scott F.; Quan, Jiaxi; Mehta, Gaurang; Bolze, Raphael; Thomas, Prasanth; Deelman, Ewa; Tischfield, Jay A.; Rice, John P.

    2011-01-01

    Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale. PMID:21037260

  7. Correlates of Access to Business Research Databases

    ERIC Educational Resources Information Center

    Gottfried, John C.

    2010-01-01

    This study examines potential correlates of business research database access through academic libraries serving top business programs in the United States. Results indicate that greater access to research databases is related to enrollment in graduate business programs, but not to overall enrollment or status as a public or private institution.…

  8. Access to Emissions Distributions and Related Ancillary Data through the ECCAD database

    NASA Astrophysics Data System (ADS)

    Darras, Sabine; Enriquez, Edgar; Granier, Claire; Liousse, Catherine; Boulanger, Damien; Fontaine, Alain

    2016-04-01

    The ECCAD database (Emissions of atmospheric Compounds and Compilation of Ancillary Data) provides a user-friendly access to global and regional surface emissions for a large set of chemical compounds and ancillary data (land use, active fires, burned areas, population,etc). The emissions inventories are time series gridded data at spatial resolution from 1x1 to 0.1x0.1 degrees. ECCAD is the emissions database of the GEIA (Global Emissions InitiAtive) project and a sub-project of the French Atmospheric Data Center AERIS (http://www.aeris-data.fr). ECCAD has currently more than 2200 users originating from more than 80 countries. The project benefits from this large international community of users to expand the number of emission datasets made available. ECCAD provides detailed metadata for each of the datasets and various tools for data visualization, for computing global and regional totals and for interactive spatial and temporal analysis. The data can be downloaded as interoperable NetCDF CF-compliant files, i.e. the data are compatible with many other client interfaces. The presentation will provide information on the datasets available within ECCAD, as well as examples of the analysis work that can be done online through the website: http://eccad.aeris-data.fr.

  9. VIEWCACHE: An incremental database access method for autonomous interoperable databases

    NASA Technical Reports Server (NTRS)

    Roussopoulos, Nick; Sellis, Timoleon

    1991-01-01

    The objective is to illustrate the concept of incremental access to distributed databases. An experimental database management system, ADMS, which has been developed at the University of Maryland, in College Park, uses VIEWCACHE, a database access method based on incremental search. VIEWCACHE is a pointer-based access method that provides a uniform interface for accessing distributed databases and catalogues. The compactness of the pointer structures formed during database browsing and the incremental access method allow the user to search and do inter-database cross-referencing with no actual data movement between database sites. Once the search is complete, the set of collected pointers pointing to the desired data are dereferenced.

  10. PMAG: Relational Database Definition

    NASA Astrophysics Data System (ADS)

    Keizer, P.; Koppers, A.; Tauxe, L.; Constable, C.; Genevey, A.; Staudigel, H.; Helly, J.

    2002-12-01

    The Scripps center for Physical and Chemical Earth References (PACER) was established to help create databases for reference data and make them available to the Earth science community. As part of these efforts PACER supports GERM, REM and PMAG and maintains multiple online databases under the http://earthref.org umbrella website. This website has been built on top of a relational database that allows for the archiving and electronic access to a great variety of data types and formats, permitting data queries using a wide range of metadata. These online databases are designed in Oracle 8.1.5 and they are maintained at the San Diego Supercomputer Center. They are directly available via http://earthref.org/databases/. A prototype of the PMAG relational database is now operational within the existing EarthRef.org framework under http://earthref.org/databases/PMAG/. As will be shown in our presentation, the PMAG design focuses around the general workflow that results in the determination of typical paleo-magnetic analyses. This ensures that individual data points can be traced between the actual analysis and the specimen, sample, site, locality and expedition it belongs to. These relations guarantee traceability of the data by distinguishing between original and derived data, where the actual (raw) measurements are performed on the specimen level, and data on the sample level and higher are then derived products in the database. These relations may also serve to recalculate site means when new data becomes available for that locality. The PMAG data records are extensively described in terms of metadata. These metadata are used when scientists search through this online database in order to view and download their needed data. They minimally include method descriptions for field sampling, laboratory techniques and statistical analyses. They also include selection criteria used during the interpretation of the data and, most importantly, critical information about the

  11. Access to Japanese aerospace-related scientific and technical information: The NASA Aerospace Database

    NASA Technical Reports Server (NTRS)

    Hoetker, Glenn P.; Lahr, Thomas F.

    1993-01-01

    With Japan's growing R&D strength in aerospace-related fields, it is increasingly important for U.S. researchers to be aware of Japanese advances. However, several factors make it difficult to do so. After reviewing the diffusion of aerospace STI in Japan, four factors which make it difficult for U.S. researchers to gather this information are discussed: language, the human network, information scatter, and document acquisition. NASA activities to alleviate these difficulties are described, beginning with a general overview of the NASA STI Program. The effects of the new National Level Agreement between NASA and NASDA are discussed.

  12. Selective access and editing in a database

    NASA Technical Reports Server (NTRS)

    Maluf, David A. (Inventor); Gawdiak, Yuri O. (Inventor)

    2010-01-01

    Method and system for providing selective access to different portions of a database by different subgroups of database users. Where N users are involved, up to 2.sup.N-1 distinguishable access subgroups in a group space can be formed, where no two access subgroups have the same members. Two or more members of a given access subgroup can edit, substantially simultaneously, a document accessible to each member.

  13. Challenges in Database Design with Microsoft Access

    ERIC Educational Resources Information Center

    Letkowski, Jerzy

    2014-01-01

    Design, development and explorations of databases are popular topics covered in introductory courses taught at business schools. Microsoft Access is the most popular software used in those courses. Despite quite high complexity of Access, it is considered to be one of the most friendly database programs for beginners. A typical Access textbook…

  14. Distributed Access View Integrated Database (DAVID) system

    NASA Technical Reports Server (NTRS)

    Jacobs, Barry E.

    1991-01-01

    The Distributed Access View Integrated Database (DAVID) System, which was adopted by the Astrophysics Division for their Astrophysics Data System, is a solution to the system heterogeneity problem. The heterogeneous components of the Astrophysics problem is outlined. The Library and Library Consortium levels of the DAVID approach are described. The 'books' and 'kits' level is discussed. The Universal Object Typer Management System level is described. The relation of the DAVID project with the Small Business Innovative Research (SBIR) program is explained.

  15. Optimal access to large databases via networks

    SciTech Connect

    Munro, J.K.; Fellows, R.L.; Phifer, D. Carrick, M.R.; Tarlton, N.

    1997-10-01

    A CRADA with Stephens Engineering was undertaken in order to transfer knowledge and experience about access to information in large text databases, with results of queries and searches provided using the multimedia capabilities of the World Wide Web. Data access is optimized by the use of intelligent agents. Technology Logic Diagram documents published for the DOE facilities in Oak Ridge (K-25, X-10, Y-12) were chosen for this effort because of the large number of technologies identified, described, evaluated, and ranked for possible use in the environmental remediation of these facilities. Fast, convenient access to this information is difficult because of the volume and complexity of the data. WAIS software used to provide full-text, field-based search capability can also be used, through the development of an appropriate hierarchy of menus, to provide tabular summaries of technologies satisfying a wide range of criteria. The menu hierarchy can also be used to regenerate dynamically many of the tables that appeared in the original hardcopy publications, all from a single text database of the technology descriptions. Use of the Web environment permits linking many of the Technology Logic Diagram references to on-line versions of these publications, particularly the DOE Orders and related directives providing the legal requirements that were the basis for undertaking the Technology Logic Diagram studies in the first place.

  16. Access Techniques for Document Image Databases.

    ERIC Educational Resources Information Center

    Walker, Frank L.; Thoma, George R.

    1990-01-01

    Describes access and retrieval techniques implemented as part of a research and development program in electronic imaging applied to document storage and retrieval at the National Library of Medicine. Design considerations for large image databases are discussed. (six references) (EAM)

  17. Village Green Project: Web-accessible Database

    EPA Science Inventory

    The purpose of this web-accessible database is for the public to be able to view instantaneous readings from a solar-powered air monitoring station located in a public location (prototype pilot test is outside of a library in Durham County, NC). The data are wirelessly transmitte...

  18. NATIONAL URBAN DATABASE AND ACCESS PROTAL TOOL

    EPA Science Inventory

    Current mesoscale weather prediction and microscale dispersion models are limited in their ability to perform accurate assessments in urban areas. A project called the National Urban Database with Access Portal Tool (NUDAPT) is beginning to provide urban data and improve the para...

  19. An incremental database access method for autonomous interoperable databases

    NASA Technical Reports Server (NTRS)

    Roussopoulos, Nicholas; Sellis, Timos

    1994-01-01

    We investigated a number of design and performance issues of interoperable database management systems (DBMS's). The major results of our investigation were obtained in the areas of client-server database architectures for heterogeneous DBMS's, incremental computation models, buffer management techniques, and query optimization. We finished a prototype of an advanced client-server workstation-based DBMS which allows access to multiple heterogeneous commercial DBMS's. Experiments and simulations were then run to compare its performance with the standard client-server architectures. The focus of this research was on adaptive optimization methods of heterogeneous database systems. Adaptive buffer management accounts for the random and object-oriented access methods for which no known characterization of the access patterns exists. Adaptive query optimization means that value distributions and selectives, which play the most significant role in query plan evaluation, are continuously refined to reflect the actual values as opposed to static ones that are computed off-line. Query feedback is a concept that was first introduced to the literature by our group. We employed query feedback for both adaptive buffer management and for computing value distributions and selectivities. For adaptive buffer management, we use the page faults of prior executions to achieve more 'informed' management decisions. For the estimation of the distributions of the selectivities, we use curve-fitting techniques, such as least squares and splines, for regressing on these values.

  20. An open access thyroid ultrasound image database

    NASA Astrophysics Data System (ADS)

    Pedraza, Lina; Vargas, Carlos; Narváez, Fabián.; Durán, Oscar; Muñoz, Emma; Romero, Eduardo

    2015-01-01

    Computer aided diagnosis systems (CAD) have been developed to assist radiologists in the detection and diagnosis of abnormalities and a large number of pattern recognition techniques have been proposed to obtain a second opinion. Most of these strategies have been evaluated using different datasets making their performance incomparable. In this work, an open access database of thyroid ultrasound images is presented. The dataset consists of a set of B-mode Ultrasound images, including a complete annotation and diagnostic description of suspicious thyroid lesions by expert radiologists. Several types of lesions as thyroiditis, cystic nodules, adenomas and thyroid cancers were included while an accurate lesion delineation is provided in XML format. The diagnostic description of malignant lesions was confirmed by biopsy. The proposed new database is expected to be a resource for the community to assess different CAD systems.

  1. SUPERSITES INTEGRATED RELATIONAL DATABASE (SIRD)

    EPA Science Inventory

    As part of EPA's Particulate Matter (PM) Supersites Program (Program), the University of Maryland designed and developed the Supersites Integrated Relational Database (SIRD). Measurement data in SIRD include comprehensive air quality data from the 7 Supersite program locations f...

  2. High-Performance Secure Database Access Technologies for HEP Grids

    SciTech Connect

    Matthew Vranicar; John Weicher

    2006-04-17

    The Large Hadron Collider (LHC) at the CERN Laboratory will become the largest scientific instrument in the world when it starts operations in 2007. Large Scale Analysis Computer Systems (computational grids) are required to extract rare signals of new physics from petabytes of LHC detector data. In addition to file-based event data, LHC data processing applications require access to large amounts of data in relational databases: detector conditions, calibrations, etc. U.S. high energy physicists demand efficient performance of grid computing applications in LHC physics research where world-wide remote participation is vital to their success. To empower physicists with data-intensive analysis capabilities a whole hyperinfrastructure of distributed databases cross-cuts a multi-tier hierarchy of computational grids. The crosscutting allows separation of concerns across both the global environment of a federation of computational grids and the local environment of a physicist’s computer used for analysis. Very few efforts are on-going in the area of database and grid integration research. Most of these are outside of the U.S. and rely on traditional approaches to secure database access via an extraneous security layer separate from the database system core, preventing efficient data transfers. Our findings are shared by the Database Access and Integration Services Working Group of the Global Grid Forum, who states that "Research and development activities relating to the Grid have generally focused on applications where data is stored in files. However, in many scientific and commercial domains, database management systems have a central role in data storage, access, organization, authorization, etc, for numerous applications.” There is a clear opportunity for a technological breakthrough, requiring innovative steps to provide high-performance secure database access technologies for grid computing. We believe that an innovative database architecture where the

  3. Database Access Integration Services (DAIS). Volume 2, Specification: Final report

    SciTech Connect

    Mitchell, P.; Nordell, D.

    1992-12-01

    The Database Access Integration Services (DAIS) is a collection of services that facilitate access to data among diverse data systems in an electric utility communications network. DAIS provides access to data in distributed, heterogeneous data systems that include relational database management systems, other database management systems, control systems, file systems, and application systems. It also provides a common method for describing data, common data access operations and essential support services including a data dictionary, a data directory and distributed data access management capabilities. The DAIS project has developed specifications intended for vendor and third-party implementation. The software developed is only to implement a data access integration demonstration. These specifications can serve as a basis for influencing industry standards development. One important consequence of this strategy is that most actual software development will be performed by vendors, not utilities. DAIS is a tool to support data access. It is policy neutral regarding issues such as local or central administration of data or standardization of information model contents (e.g., EPRI Plant Information Network). As a tool, it can be used to help realize such policies. The DAIS does not provide data storage facilities, schema integration, distributed query processing, distributed applications or cooperative processing. Rather, DAIS is complementary to these functions and can be used with other software that does provide these functions. This project documented the requirements for the DAIS. These requirements are the basis for design of the DAIS specifications. The key requirements for a DAIS are: Uniform access to heterogeneous utility data systems, remote update; coexistence with local data systems; local autonomy ; Security and access restriction enforcement; OSI compatibility; open architecture and extensibility; and operating platform independence.

  4. Method for Accessing Distributed Heterogeneous Databases

    NASA Technical Reports Server (NTRS)

    Jacobs, B. E.

    1984-01-01

    A scenario of relational, hierarchial, and network data bases is presented and a distributed access view integrated data base system (DAVID) is described for uniformly accessing data bases which are heterogeneous and physically distributed. The DAVID system is based on data base logic so that the relational approach is generalized to the heterogeneous approach. The global data manager is explained as are global data manipulation languages which can operate on all the data bases and can query the data dictionary and the data directory.

  5. Enhanced DIII-D Data Management Through a Relational Database

    NASA Astrophysics Data System (ADS)

    Burruss, J. R.; Peng, Q.; Schachter, J.; Schissel, D. P.; Terpstra, T. B.

    2000-10-01

    A relational database is being used to serve data about DIII-D experiments. The database is optimized for queries across multiple shots, allowing for rapid data mining by SQL-literate researchers. The relational database relates different experiments and datasets, thus providing a big picture of DIII-D operations. Users are encouraged to add their own tables to the database. Summary physics quantities about DIII-D discharges are collected and stored in the database automatically. Meta-data about code runs, MDSplus usage, and visualization tool usage are collected, stored in the database, and later analyzed to improve computing. Documentation on the database may be accessed through programming languages such as C, Java, and IDL, or through ODBC compliant applications such as Excel and Access. A database-driven web page also provides a convenient means for viewing database quantities through the World Wide Web. Demonstrations will be given at the poster.

  6. Updating the Qweak Database: Maintenance and Accessibility

    NASA Astrophysics Data System (ADS)

    Gammill, Matthew; Spayde, Damon T.

    2011-10-01

    The Qweak experiment at Thomas Jefferson National Accelerator Facility is being conducted by a collaboration representing over 25 universities and research institutions, and is an attempt to measure with very low total uncertainty, 4%, the weak nuclear charge of a proton through parity-violating elastic electron-proton scattering. The weak charge can be used to calculate the running Weinberg mixing angle. The Standard Model makes a confident prediction for the mixing angle at low energies, so divergence could point to physics beyond the Standard Model, while agreement will constrain new and existing models. The expected asymmetries are on the order of a few hundred parts per billion, so an exceptional quantity of data (2200 beam-hours) must be gathered. Storing and organizing this data presents a considerable challenge, which the Qweak database aims to satisfy. Tools to improve accessibility for researchers, efforts to improve efficiency, statistical and data quality checks, and ongoing expansion of the database will be discussed. Research funded by a grant from the NSF.

  7. Open-access dielectric elastomer material database

    NASA Astrophysics Data System (ADS)

    Vertechy, R.; Fontana, M.; Stiubianu, G.; Cazacu, M.

    2014-03-01

    Dielectric Elastomer Transducers (DETs) are deformable capacitors that can be used as sensors, actuators and generators. The design of effective and optimized DETs requires the knowledge of a set of relevant properties of the employed Dielectric Elastomer (DE) material, which make it possible to accurately predict their electromechanical dynamic behavior. In this context, an open-access database for DE materials has been created with the aim of providing the practicing engineer with the essential information for the design and optimization of new kinds of DET. Among the electrical properties, dielectric susceptibility, dielectric strength and conductivity are considered along with their dependence on mechanical strain. As regards mechanical behavior, experimental stress-strain curves are provided to predict hyperelasticity, plasticity, viscosity, Mullins effect and mechanical rupture. Properties of commercial elastomeric membranes have been entered in the database and made available to the research community. This paper describes the instrumentations, experimental setups and procedures that have been employed for the characterization of the considered DE materials. To provide an example, the experimental data acquired for a commercially available natural rubber membrane (OPPO Band Red 8012) are presented.

  8. datOZ: scientific databases readily accessible over the WWW.

    NASA Astrophysics Data System (ADS)

    Ortiz, P. F.

    datOZ: a tool designed to create scientific database systems accessible over the WWW is presented. datOZ can create customized database systems for a variety of scientific applications, (but oriented towards astronomy), keeping the same interface structure and philosophy for all the databases it creates. From the user's point of view, datOZ creates platform-independent databases with multilingual capabilities, which makes data accessible to any user with a connection to the Internet around the world. Some features of the databases created with datOZ include full data retrieval of individual database elements (DBE), partial data retrieval for a user-selected set of DBE's, the possibility of generating graphs with the data selected, and to cross-correlate the data with other databases created with the system. datOZ's databases can contain images, movies, hyper-links, and any other multimedia-type of information.

  9. Web interfaces to relational databases

    NASA Technical Reports Server (NTRS)

    Carlisle, W. H.

    1996-01-01

    This reports on a project to extend the capabilities of a Virtual Research Center (VRC) for NASA's Advanced Concepts Office. The work was performed as part of NASA's 1995 Summer Faculty Fellowship program and involved the development of a prototype component of the VRC - a database system that provides data creation and access services within a room of the VRC. In support of VRC development, NASA has assembled a laboratory containing the variety of equipment expected to be used by scientists within the VRC. This laboratory consists of the major hardware platforms, SUN, Intel, and Motorola processors and their most common operating systems UNIX, Windows NT, Windows for Workgroups, and Macintosh. The SPARC 20 runs SUN Solaris 2.4, an Intel Pentium runs Windows NT and is installed on a different network from the other machines in the laboratory, a Pentium PC runs Windows for Workgroups, two Intel 386 machines run Windows 3.1, and finally, a PowerMacintosh and a Macintosh IIsi run MacOS.

  10. Database and Related Activities in Japan

    NASA Astrophysics Data System (ADS)

    Murakami, Izumi; Kato, Daiji; Kato, Masatoshi; Sakaue, Hiroyuki A.; Kato, Takako; Ding, Xiaobin; Morita, Shigeru; Kitajima, Masashi; Koike, Fumihiro; Nakamura, Nobuyuki; Sakamoto, Naoki; Sasaki, Akira; Skobelev, Igor; Tsuchida, Hidetsugu; Ulantsev, Artemiy; Watanabe, Tetsuya; Yamamoto, Norimasa

    2011-05-01

    We have constructed and made available atomic and molecular (AM) numerical databases on collision processes such as electron-impact excitation and ionization, recombination and charge transfer of atoms and molecules relevant for plasma physics, fusion research, astrophysics, applied-science plasma, and other related areas. The retrievable data is freely accessible via the internet. We also work on atomic data evaluation and constructing collisional-radiative models for spectroscopic plasma diagnostics. Recently we have worked on Fe ions and W ions theoretically and experimentally. The atomic data and collisional-radiative models for these ions are examined and applied to laboratory plasmas. A visible M1 transition of W26+ ion is identified at 389.41 nm by EBIT experiments and theoretical calculations. We have small non-retrievable databases in addition to our main database. Recently we evaluated photo-absorption cross sections for 9 atoms and 23 molecules and we present them as a new database. We established a new association "Forum of Atomic and Molecular Data and Their Applications" to exchange information among AM data producers, data providers and data users in Japan and we hope this will help to encourage AM data activities in Japan.

  11. The Steward Observatory asteroid relational database

    NASA Technical Reports Server (NTRS)

    Sykes, Mark V.; Alvarezdelcastillo, Elizabeth M.

    1992-01-01

    The Steward Observatory Asteroid Relational Database (SOARD) was created as a flexible tool for undertaking studies of asteroid populations and sub-populations, to probe the biases intrinsic to asteroid databases, to ascertain the completeness of data pertaining to specific problems, to aid in the development of observational programs, and to develop pedagogical materials. To date SOARD has compiled an extensive list of data available on asteroids and made it accessible through a single menu-driven database program. Users may obtain tailored lists of asteroid properties for any subset of asteroids or output files which are suitable for plotting spectral data on individual asteroids. A browse capability allows the user to explore the contents of any data file. SOARD offers, also, an asteroid bibliography containing about 13,000 references. The program has online help as well as user and programmer documentation manuals. SOARD continues to provide data to fulfill requests by members of the astronomical community and will continue to grow as data is added to the database and new features are added to the program.

  12. Brain Tumor Database, a free relational database for collection and analysis of brain tumor patient information.

    PubMed

    Bergamino, Maurizio; Hamilton, David J; Castelletti, Lara; Barletta, Laura; Castellan, Lucio

    2015-03-01

    In this study, we describe the development and utilization of a relational database designed to manage the clinical and radiological data of patients with brain tumors. The Brain Tumor Database was implemented using MySQL v.5.0, while the graphical user interface was created using PHP and HTML, thus making it easily accessible through a web browser. This web-based approach allows for multiple institutions to potentially access the database. The BT Database can record brain tumor patient information (e.g. clinical features, anatomical attributes, and radiological characteristics) and be used for clinical and research purposes. Analytic tools to automatically generate statistics and different plots are provided. The BT Database is a free and powerful user-friendly tool with a wide range of possible clinical and research applications in neurology and neurosurgery. The BT Database graphical user interface source code and manual are freely available at http://tumorsdatabase.altervista.org. PMID:25784642

  13. Tao of Gateway: Providing Internet Access to Licensed Databases.

    ERIC Educational Resources Information Center

    McClellan, Gregory A.; Garrison, William V.

    1997-01-01

    Illustrates an approach for providing networked access to licensed databases over the Internet by positioning the library between patron and vendor. Describes how the gateway systems and database connection servers work and discusses how treatment of security has evolved with the introduction of the World Wide Web. Outlines plans to reimplement…

  14. Automating Relational Database Design for Microcomputer Users.

    ERIC Educational Resources Information Center

    Pu, Hao-Che

    1991-01-01

    Discusses issues involved in automating the relational database design process for microcomputer users and presents a prototype of a microcomputer-based system (RA, Relation Assistant) that is based on expert systems technology and helps avoid database maintenance problems. Relational database design is explained and the importance of easy input…

  15. Web Access to Electronic Journals and Databases in ARL Libraries

    ERIC Educational Resources Information Center

    Caudle, Dana M.; Schmitz, Cecilia M.

    2007-01-01

    Libraries are investing heavily in an increasing number of electronic journals and providing access to them through their websites. We set out to determine if ARL academic libraries offer the same options on their websites to access electronic journals and databases. Using a checklist, we evaluated the websites for the presence of A-Z lists, links…

  16. Migration of legacy mumps applications to relational database servers.

    PubMed

    O'Kane, K C

    2001-07-01

    An extended implementation of the Mumps language is described that facilitates vendor neutral migration of legacy Mumps applications to SQL-based relational database servers. Implemented as a compiler, this system translates Mumps programs to operating system independent, standard C code for subsequent compilation to fully stand-alone, binary executables. Added built-in functions and support modules extend the native hierarchical Mumps database with access to industry standard, networked, relational database management servers (RDBMS) thus freeing Mumps applications from dependence upon vendor specific, proprietary, unstandardized database models. Unlike Mumps systems that have added captive, proprietary RDMBS access, the programs generated by this development environment can be used with any RDBMS system that supports common network access protocols. Additional features include a built-in web server interface and the ability to interoperate directly with programs and functions written in other languages. PMID:11501636

  17. Relational Database Design in Information Science Education.

    ERIC Educational Resources Information Center

    Brooks, Terrence A.

    1985-01-01

    Reports on database management system (dbms) applications designed by library school students for university community at University of Iowa. Three dbms design issues are examined: synthesis of relations, analysis of relations (normalization procedure), and data dictionary usage. Database planning prior to automation using data dictionary approach…

  18. The relational database system of KM3NeT

    NASA Astrophysics Data System (ADS)

    Albert, Arnauld; Bozza, Cristiano

    2016-04-01

    The KM3NeT Collaboration is building a new generation of neutrino telescopes in the Mediterranean Sea. For these telescopes, a relational database is designed and implemented for several purposes, such as the centralised management of accounts, the storage of all documentation about components and the status of the detector and information about slow control and calibration data. It also contains information useful during the construction and the data acquisition phases. Highlights in the database schema, storage and management are discussed along with design choices that have impact on performances. In most cases, the database is not accessed directly by applications, but via a custom designed Web application server.

  19. Starbase Data Tables: An ASCII Relational Database for Unix

    NASA Astrophysics Data System (ADS)

    Roll, John

    2011-11-01

    Database management is an increasingly important part of astronomical data analysis. Astronomers need easy and convenient ways of storing, editing, filtering, and retrieving data about data. Commercial databases do not provide good solutions for many of the everyday and informal types of database access astronomers need. The Starbase database system with simple data file formatting rules and command line data operators has been created to answer this need. The system includes a complete set of relational and set operators, fast search/index and sorting operators, and many formatting and I/O operators. Special features are included to enhance the usefulness of the database when manipulating astronomical data. The software runs under UNIX, MSDOS and IRAF.

  20. Access to distributed marine databases on the Baltic Sea

    NASA Astrophysics Data System (ADS)

    Sokolov, A.; Axe, P.; Bock, S.; Kaitala, S.; Manscher, O. H.; Rodriguez-Medina, M.; Olsonen, R.; Priha, I.; Tikka, K.

    2012-04-01

    Baltic Nest Institute, Stockholm University (Sweden) in cooperation with Department of Bioscience/DCE, National Centre for Environment and Energy, Aarhus University (Denmark), Leibniz Institute for Baltic Sea Research (Germany), Finnish Environment Institute, Finnish Meteorological Institute and Swedish Meteorological and Hydrological Institute developed a data assessment system, aimed at providing tools for online analysis of marine environmental data (temperature, salinity, chemical properties) from distributed collection of databases on the Baltic Sea. Such approach allows users to have fast access to the most recent data from all major data providers and providers remain in control of their data. The system contains a web data portal, which provides concurrent access to distributed marine databases and presents information in a unified way. Two client programs use the data portal and provide tools to analyse the data. The DAS - Data Assimilation System (http://nest.su.se/das/) accesses databases through the data portal and allow analysing the raw data and creating gridded data, which can be used as initial fields for 3D hydrodynamic models. A decision support system Nest (http://nest.su.se/nest/) developed and maintained at the Stockholm University as a tool to support decision-making at international negotiations regarding the Baltic Sea environment also uses the data portal to access marine data, provide access to the raw data and perform time-series analysis. The data portal designed to output data in a common format (CSV) for further post-processing using other software. It makes the system open to develop another client programs for data analysis.

  1. MIMIC-III, a freely accessible critical care database

    PubMed Central

    Johnson, Alistair E.W.; Pollard, Tom J.; Shen, Lu; Lehman, Li-wei H.; Feng, Mengling; Ghassemi, Mohammad; Moody, Benjamin; Szolovits, Peter; Anthony Celi, Leo; Mark, Roger G.

    2016-01-01

    MIMIC-III (‘Medical Information Mart for Intensive Care’) is a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital. Data includes vital signs, medications, laboratory measurements, observations and notes charted by care providers, fluid balance, procedure codes, diagnostic codes, imaging reports, hospital length of stay, survival data, and more. The database supports applications including academic and industrial research, quality improvement initiatives, and higher education coursework. PMID:27219127

  2. MIMIC-III, a freely accessible critical care database.

    PubMed

    Johnson, Alistair E W; Pollard, Tom J; Shen, Lu; Lehman, Li-Wei H; Feng, Mengling; Ghassemi, Mohammad; Moody, Benjamin; Szolovits, Peter; Celi, Leo Anthony; Mark, Roger G

    2016-01-01

    MIMIC-III ('Medical Information Mart for Intensive Care') is a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital. Data includes vital signs, medications, laboratory measurements, observations and notes charted by care providers, fluid balance, procedure codes, diagnostic codes, imaging reports, hospital length of stay, survival data, and more. The database supports applications including academic and industrial research, quality improvement initiatives, and higher education coursework. PMID:27219127

  3. Techniques to Access Databases and Integrate Data for Hydrologic Modeling

    SciTech Connect

    Whelan, Gene; Tenney, Nathan D.; Pelton, Mitchell A.; Coleman, Andre M.; Ward, Duane L.; Droppo, James G.; Meyer, Philip D.; Dorow, Kevin E.; Taira, Randal Y.

    2009-06-17

    This document addresses techniques to access and integrate data for defining site-specific conditions and behaviors associated with ground-water and surface-water radionuclide transport applicable to U.S. Nuclear Regulatory Commission reviews. Environmental models typically require input data from multiple internal and external sources that may include, but are not limited to, stream and rainfall gage data, meteorological data, hydrogeological data, habitat data, and biological data. These data may be retrieved from a variety of organizations (e.g., federal, state, and regional) and source types (e.g., HTTP, FTP, and databases). Available data sources relevant to hydrologic analyses for reactor licensing are identified and reviewed. The data sources described can be useful to define model inputs and parameters, including site features (e.g., watershed boundaries, stream locations, reservoirs, site topography), site properties (e.g., surface conditions, subsurface hydraulic properties, water quality), and site boundary conditions, input forcings, and extreme events (e.g., stream discharge, lake levels, precipitation, recharge, flood and drought characteristics). Available software tools for accessing established databases, retrieving the data, and integrating it with models were identified and reviewed. The emphasis in this review was on existing software products with minimal required modifications to enable their use with the FRAMES modeling framework. The ability of four of these tools to access and retrieve the identified data sources was reviewed. These four software tools were the Hydrologic Data Acquisition and Processing System (HDAPS), Integrated Water Resources Modeling System (IWRMS) External Data Harvester, Data for Environmental Modeling Environmental Data Download Tool (D4EM EDDT), and the FRAMES Internet Database Tools. The IWRMS External Data Harvester and the D4EM EDDT were identified as the most promising tools based on their ability to access and

  4. Data dictionary model for relational databases

    SciTech Connect

    Seesing, P.R.

    1983-10-01

    Data Dictionary is an important tool in information engineering, especially when the data is maintained in relational structures. Using the formal concepts from which relational DBMS technology is derived, it is possible to construct a meta-informational dictionary to model relational database. This general model can be used to evaluate the design of existing and planned databases, as well as modeling business or scientific data. Such a dictionary model is described and its potential uses and benefits are explored with emphasis on integrity constraints. Issues related to the balancing of such formal conceptualization against real-world operations are presented.

  5. Midcontinent Interactive Digital Carbon Atlas and Relational Database (MIDCARB)

    SciTech Connect

    Timothy R. Carr; Scott W. White

    2002-06-01

    This annual report describes progress of the project entitled ''Midcontinent Interactive Digital Carbon Atlas and Relational Database (MIDCARB)''. This project, funded by the Department of Energy, is a cooperative project that assembles a consortium of five states (Indiana, Illinois, Kansas, Kentucky and Ohio) to construct an online distributed Relational Database Management System (RDBMS) and Geographic Information System (GIS) covering aspects of carbon dioxide geologic sequestration (http://www.midcarb.org). The system links the five states in the consortium into a coordinated regional database system consisting of datasets useful to industry, regulators and the public. The project is working to provide advanced distributed computing solutions to link database servers across the five states into a single system where data is maintained at the local level but is accessed through a single Web portal and can be queried, assembled, analyzed and displayed. Each individual state has strengths in data gathering, data manipulation and data display, including GIS mapping, custom application development, web development, and database design. Sharing of expertise provides the critical mass of technical expertise to improve CO{sub 2} databases and data access in all states. This project improves the flow of data across servers in the five states and increases the amount and quality of available digital data. The MIDCARB project is developing improved online tools to provide real-time display and analyze CO{sub 2} sequestration data. The system links together data from sources, sinks and transportation within a spatial database that can be queried online. Visualization of high quality and current data can assist decision makers by providing access to common sets of high quality data in a consistent manner.

  6. Table Access Protocol Applied to the SIMBAD Database

    NASA Astrophysics Data System (ADS)

    Mantelet, G.; Wenger, M.; Michel, L.

    2012-09-01

    We have implemented in the SIMBAD service the Table Access Protocol (TAP), a standard of the Virtual Observatory defining a protocol for accessing astronomical catalogs and database tables using queries written in the Astronomical Data Query Language (ADQL), another VO standard. Implementing TAP requires several steps: the definition of a database schema with the data exposed to the users, the translation of ADQL queries into regular SQL language performing the queries in SIMBAD, and the implementation of the Universal Worker Service (UWS) standard to manage asynchronous queries, useful for long queries, either by their duration or their output size. These standards were implemented as much as possible in a generic way, allowing them to be reused in other services, as it has already been done in the database generator SAADA. The ADQL to SQL translator uses callbacks to implement the specific routines for a given service. All these libraries have been designed as autonomous packages, easy to reuse with very few specific developments. The whole development is in the Java language.

  7. HEDS - EPA DATABASE SYSTEM FOR PUBLIC ACCESS TO HUMAN EXPOSURE DATA

    EPA Science Inventory

    Human Exposure Database System (HEDS) is an Internet-based system developed to provide public access to human-exposure-related data from studies conducted by EPA's National Exposure Research Laboratory (NERL). HEDS was designed to work with the EPA Office of Research and Devel...

  8. PSSARD: protein sequence-structure analysis relational database.

    PubMed

    Guruprasad, Kunchur; Srikanth, K; Babu, A V N

    2005-09-15

    We have implemented a relational database comprising a representative dataset of amino acid sequences and their associated secondary structure. The representative amino acid sequences were selected according to the PDB_SELECT program by choosing proteins corresponding to protein crystal structure data deposited in the protein data bank that share less than 25% overall pair-wise sequence identity. The secondary structure was extracted from the protein data bank website. The information content in the database includes the protein description, PDB code, crystal structure resolution, total number of amino acid residues in the protein chain, amino acid sequence, secondary structure conformation and its summary. The database is freely accessible from the website mentioned below and is useful to query on any of the above fields. The database is particularly useful to quickly retrieve amino acid sequences that are compatible to any super-secondary structure conformation from several proteins simultaneously. PMID:16054209

  9. A relational database of transcription factors.

    PubMed Central

    Ghosh, D

    1990-01-01

    Recent advances in the understanding of eukaryotic gene regulation have produced an extensive body of transcriptionally-related sequence information in the biological literature, and have created a need for computing structures that organize and manage this information. The 'relational model' represents an approach that is finding increasing application in the design of biological databases. This report describes the compilation of information regarding eukaryotic transcription factors, the organization of this information into five tables, the computational applications of the resultant relational database that are of theoretical as well as experimental interest, and possible avenues of further development. PMID:2186365

  10. Using BITNET to access the National Library of Medicine databases.

    PubMed Central

    Hsieh, R K; Gamboa, C A

    1992-01-01

    An ongoing developmental project is described that uses the National Library of Medicine (NLM) GRATEFUL MED software on the BITNET network to access the NLM databases. The objective of the project is to improve biomedical communication capabilities to support health professionals in countries where international telecommunication services are limited. After a successful demonstration of the concept, the system was assembled and tested by the University of Chile and NLM. The full impact of this project will be measured at a later time. This paper describes the concept and testing of the system in Latin American countries. PMID:1422503

  11. Generic Entity Resolution in Relational Databases

    NASA Astrophysics Data System (ADS)

    Sidló, Csaba István

    Entity Resolution (ER) covers the problem of identifying distinct representations of real-world entities in heterogeneous databases. We consider the generic formulation of ER problems (GER) with exact outcome. In practice, input data usually resides in relational databases and can grow to huge volumes. Yet, typical solutions described in the literature employ standalone memory resident algorithms. In this paper we utilize facilities of standard, unmodified relational database management systems (RDBMS) to enhance the efficiency of GER algorithms. We study and revise the problem formulation, and propose practical and efficient algorithms optimized for RDBMS external memory processing. We outline a real-world scenario and demonstrate the advantage of algorithms by performing experiments on insurance customer data.

  12. VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

    NASA Technical Reports Server (NTRS)

    Roussopoulos, N.; Sellis, Timos

    1992-01-01

    One of biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental database access method, VIEWCACHE, provides such an interface for accessing distributed data sets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image data sets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate distributed database search.

  13. A new relational database structure and online interface for the HITRAN database

    NASA Astrophysics Data System (ADS)

    Hill, Christian; Gordon, Iouli E.; Rothman, Laurence S.; Tennyson, Jonathan

    2013-11-01

    A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described.

  14. VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

    NASA Technical Reports Server (NTRS)

    Roussopoulos, N.; Sellis, Timos

    1993-01-01

    One of the biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental data base access method, VIEWCACHE, provides such an interface for accessing distributed datasets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image datasets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate database search.

  15. On Relations between Current Global Volcano Databases

    NASA Astrophysics Data System (ADS)

    Newhall, C. G.; Siebert, L.; Sparks, S.

    2009-12-01

    information in the VRF and VOGRIPA, based on geologic records and written history, is updated by WOVOdat and current monitoring. ● For event trees that estimate probabilities of both eruptions and their effects, WOVOdat, VRF, and VOGRIPA will all be co-contributors. Collectively, these databases will enable new studies of relations between tectonics, magma generation and transport, degassing, eruptions, and eruption aftermaths, and better probabilistic eruption forecasts and dynamic hazard and risk assessments; fragility curves; and cost-benefit analysis of mitigation decisions.

  16. Databases related to Large Igneous Provinces

    NASA Astrophysics Data System (ADS)

    Ernst, Richard; Pisarevsky, Sergei

    2015-04-01

    Large Igneous Provinces (LIPs) represent large volume (>0.1 Mkm3; often above >1 Mkm3), mainly mafic (-ultramafic) magmatic events of intraplate affinity in both continental and oceanic settings, and are typically of short duration (<5 m.y.) or consist of multiple short pulses over a maximum of a few 10s of m.y. Silicic, carbonatite and kimberlite magmatism may be associated. The young LIP record is dominated by continental flood basalts and oceanic plateaus, but Proterozoic LIPs have typically lost their flood basalt component during erosion, thus exposing the plumbing system of mafic (-ultramafic) dykes, sills and layered intrusions. LIPs occur at a rate of about 1 every 20-30 m.y. back through the Proterozoic, and Archean analogues are also recognized. The LIP record is growing as more events are recognized and the size of known LIPs (even those of those of Mesozoic age) is increasing through targeted U-Pb geochronology. We review databases related to this fast moving field. The LIPs Commission (www.largeigneousprovinces.org) of IAVCEI ongoingly highlights new insights and events through the "LIP of the Month" series. A global 1:5M scale global LIPs ArcGIS database is under construction through Industry and government funded projects (e.g. www.supercontinent.org) and will form a framework for additional thematic databases related to LIPs, including geochemistry, geochronology, and paleomagnetism (GPMDB, MAGIC). LIP databases provide useful constraints for global Precambrian paleogeographic reconstructions, a context for understanding some global and regional environmental changes, and a useful framework for resource exploration (mineral and hydrocarbon). One of the most important aspects of this global LIPs ArcGIS database is that it is integrating data on the volcanic component of LIPs (both flood basalts, and associated ultramafic and silicic volcanism) with data on the plumbing system component in order to develop an understanding of LIPs as an integrated

  17. Exploiting relational database technology in a GIS

    NASA Astrophysics Data System (ADS)

    Batty, Peter

    1992-05-01

    All systems for managing data face common problems such as backup, recovery, auditing, security, data integrity, and concurrent update. Other challenges include the ability to share data easily between applications and to distribute data across several computers, whereas continuing to manage the problems already mentioned. Geographic information systems are no exception, and need to tackle all these issues. Standard relational database-management systems (RDBMSs) provide many features to help solve the issues mentioned so far. This paper describes how the IBM geoManager product approaches these issues by storing all its geographic data in a standard RDBMS in order to take advantage of such features. Areas in which standard RDBMS functions need to be extended are highlighted, and the way in which geoManager does this is explained. The performance implications of storing all data in the relational database are discussed. An important distinction is made between the storage and management of geographic data and the manipulation and analysis of geographic data, which needs to be made when considering the applicability of relational database technology to GIS.

  18. MIDCONTINENT INTERACTIVE DIGITAL CARBON ATLAS AND RELATIONAL DATABASE (MIDCARB)

    SciTech Connect

    Timothy R. Carr; Scott W. White

    2003-07-01

    This annual report describes progress in the second year of the three-year project entitled ''Midcontinent Interactive Digital Carbon Atlas and Relational Database (MIDCARB)''. This project, funded by the Department of Energy, is a cooperative project that assembles a consortium of five states (Indiana, Illinois, Kansas, Kentucky and Ohio) to construct an online distributed Relational Database Management System (RDBMS) and Geographic Information System (GIS) covering aspects of carbon dioxide geologic sequestration (http://www.midcarb.org). The system links the five states in the consortium into a coordinated regional database system consisting of datasets useful to industry, regulators and the public. The project is providing advanced distributed computing solutions to link database servers across the five states into a single system where data is maintained at the local level but is accessed through a single Web portal and can be queried, assembled, analyzed and displayed. Each individual state has strengths in data gathering, data manipulation and data display, including GIS mapping, custom application development, web development, and database design. Sharing of expertise provides the critical mass of technical expertise to improve CO{sub 2} databases and data access in all states. This project improves the flow of data across servers in the five states and increases the amount and quality of available digital data. Data is being assembled to analyze CO{sub 2} sequestration potential from a single object (e.g., power plant or well) to a region and across geographic boundaries. The MIDCARB system is robust and capable of being updated from multiple sources on a daily basis. The MIDCARB project has developed improved online tools to provide real-time display and analysis of CO{sub 2} sequestration data. The MIDCARB project is a functional template for distributed data systems to address CO{sub 2} sequestration and other natural resource issues that cross the

  19. Short Fiction on Film: A Relational DataBase.

    ERIC Educational Resources Information Center

    May, Charles

    Short Fiction on Film is a database that was created and will run on DataRelator, a relational database manager created by Bill Finzer for the California State Department of Education in 1986. DataRelator was designed for use in teaching students database management skills and to provide teachers with examples of how a database manager might be…

  20. A review of accessibility of administrative healthcare databases in the Asia-Pacific region

    PubMed Central

    Milea, Dominique; Azmi, Soraya; Reginald, Praveen; Verpillat, Patrice; Francois, Clement

    2015-01-01

    Objective We describe and compare the availability and accessibility of administrative healthcare databases (AHDB) in several Asia-Pacific countries: Australia, Japan, South Korea, Taiwan, Singapore, China, Thailand, and Malaysia. Methods The study included hospital records, reimbursement databases, prescription databases, and data linkages. Databases were first identified through PubMed, Google Scholar, and the ISPOR database register. Database custodians were contacted. Six criteria were used to assess the databases and provided the basis for a tool to categorise databases into seven levels ranging from least accessible (Level 1) to most accessible (Level 7). We also categorised overall data accessibility for each country as high, medium, or low based on accessibility of databases as well as the number of academic articles published using the databases. Results Fifty-four administrative databases were identified. Only a limited number of databases allowed access to raw data and were at Level 7 [Medical Data Vision EBM Provider, Japan Medical Data Centre (JMDC) Claims database and Nihon-Chouzai Pharmacy Claims database in Japan, and Medicare, Pharmaceutical Benefits Scheme (PBS), Centre for Health Record Linkage (CHeReL), HealthLinQ, Victorian Data Linkages (VDL), SA-NT DataLink in Australia]. At Levels 3–6 were several databases from Japan [Hamamatsu Medical University Database, Medi-Trend, Nihon University School of Medicine Clinical Data Warehouse (NUSM)], Australia [Western Australia Data Linkage (WADL)], Taiwan [National Health Insurance Research Database (NHIRD)], South Korea [Health Insurance Review and Assessment Service (HIRA)], and Malaysia [United Nations University (UNU)-Casemix]. Countries were categorised as having a high level of data accessibility (Australia, Taiwan, and Japan), medium level of accessibility (South Korea), or a low level of accessibility (Thailand, China, Malaysia, and Singapore). In some countries, data may be available but

  1. Optics Toolbox: An Intelligent Relational Database System For Optical Designers

    NASA Astrophysics Data System (ADS)

    Weller, Scott W.; Hopkins, Robert E.

    1986-12-01

    designer as he interacted with a customer for the first time: asking the right questions, forming conclusions, and making suggestions. With these objectives in mind, we have developed the Optics Toolbox. Optics Toolbox is actually two programs in one: it is a powerful relational database system with twenty-one search parameters, four search modes, and multi-database support, as well as a first-order optical design expert system with a rule interpreter which has full access to the relational database. The system schematic is shown in Figure 1.

  2. The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies

    PubMed Central

    Cserhati, Matyas F.; Pandey, Sanjit; Beaudoin, James J.; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S.

    2015-01-01

    We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33 017 407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. Database URL: http://nntc-dcc.unmc.edu PMID:26228431

  3. Remote access to ACNUC nucleotide and protein sequence databases at PBIL.

    PubMed

    Gouy, Manolo; Delmotte, Stéphane

    2008-04-01

    The ACNUC biological sequence database system provides powerful and fast query and extraction capabilities to a variety of nucleotide and protein sequence databases. The collection of ACNUC databases served by the Pôle Bio-Informatique Lyonnais includes the EMBL, GenBank, RefSeq and UniProt nucleotide and protein sequence databases and a series of other sequence databases that support comparative genomics analyses: HOVERGEN and HOGENOM containing families of homologous protein-coding genes from vertebrate and prokaryotic genomes, respectively; Ensembl and Genome Reviews for analyses of prokaryotic and of selected eukaryotic genomes. This report describes the main features of the ACNUC system and the access to ACNUC databases from any internet-connected computer. Such access was made possible by the definition of a remote ACNUC access protocol and the implementation of Application Programming Interfaces between the C, Python and R languages and this communication protocol. Two retrieval programs for ACNUC databases, Query_win, with a graphical user interface and raa_query, with a command line interface, are also described. Altogether, these bioinformatics tools provide users with either ready-to-use means of querying remote sequence databases through a variety of selection criteria, or a simple way to endow application programs with an extensive access to these databases. Remote access to ACNUC databases is open to all and fully documented (http://pbil.univ-lyon1.fr/databases/acnuc/acnuc.html). PMID:17825976

  4. Teaching Case: Adapting the Access Northwind Database to Support a Database Course

    ERIC Educational Resources Information Center

    Dyer, John N.; Rogers, Camille

    2015-01-01

    A common problem encountered when teaching database courses is that few large illustrative databases exist to support teaching and learning. Most database textbooks have small "toy" databases that are chapter objective specific, and thus do not support application over the complete domain of design, implementation and management concepts…

  5. The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies.

    PubMed

    Cserhati, Matyas F; Pandey, Sanjit; Beaudoin, James J; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S

    2015-01-01

    We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33,017,407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. PMID:26228431

  6. Normalizing records data for relational databases

    SciTech Connect

    Seesing, P.R.

    1991-09-01

    When relational database management systems (RDBMS) replace traditionally programmed computer systems, managers and users are often confronted with a barrage of strange terminology and concepts. It is the intent of this paper (and workshop) to demystify some of the ideals surrounding RDBMS technology. After all, these systems were marketed to the computer community as tools for end-user'' development of computer applications. This paper describes how to manipulate RDBMS structures to create concise, linkable tables of unique facts, events, or concepts via a process called normalization. The three primary rules of normalization are covered in considerable detail. Additional rules of normalization are also briefly presented because they are sometimes necessary for certain groupings of information. Some of the more technical details of the process of normalization have been simplified or excluded in order to provide the essential concepts to a wide audience. 7 refs., 1 figs.

  7. Normalizing records data for relational databases

    SciTech Connect

    Seesing, P.R.

    1991-09-01

    When relational database management systems (RDBMS) replace traditionally programmed computer systems, managers and users are often confronted with a barrage of strange terminology and concepts. It is the intent of this paper (and workshop) to demystify some of the ideals surrounding RDBMS technology. After all, these systems were marketed to the computer community as tools for ``end-user`` development of computer applications. This paper describes how to manipulate RDBMS structures to create concise, linkable tables of unique facts, events, or concepts via a process called normalization. The three primary rules of normalization are covered in considerable detail. Additional rules of normalization are also briefly presented because they are sometimes necessary for certain groupings of information. Some of the more technical details of the process of normalization have been simplified or excluded in order to provide the essential concepts to a wide audience. 7 refs., 1 figs.

  8. Accessing the BIOSIS Previews Database in Clinical Psychology.

    ERIC Educational Resources Information Center

    Piotrowski, Chris; Perdue, Bob

    The efficacy of using the BIOSIS Previews database as an online information retrieval tool in clinical psychology was investigated in a study conducted at the University of West Florida. Recognizing the importance of multi-database searching strategies when seeking comprehensive results, this study compared the citation output of this…

  9. Performance assessment of EMR systems based on post-relational database.

    PubMed

    Yu, Hai-Yan; Li, Jing-Song; Zhang, Xiao-Guang; Tian, Yu; Suzuki, Muneou; Araki, Kenji

    2012-08-01

    Post-relational databases provide high performance and are currently widely used in American hospitals. As few hospital information systems (HIS) in either China or Japan are based on post-relational databases, here we introduce a new-generation electronic medical records (EMR) system called Hygeia, which was developed with the post-relational database Caché and the latest platform Ensemble. Utilizing the benefits of a post-relational database, Hygeia is equipped with an "integration" feature that allows all the system users to access data-with a fast response time-anywhere and at anytime. Performance tests of databases in EMR systems were implemented in both China and Japan. First, a comparison test was conducted between a post-relational database, Caché, and a relational database, Oracle, embedded in the EMR systems of a medium-sized first-class hospital in China. Second, a user terminal test was done on the EMR system Izanami, which is based on the identical database Caché and operates efficiently at the Miyazaki University Hospital in Japan. The results proved that the post-relational database Caché works faster than the relational database Oracle and showed perfect performance in the real-time EMR system. PMID:21503741

  10. Full-Text Linking: Affiliated versus Nonaffiliated Access in a Free Database.

    ERIC Educational Resources Information Center

    Grogg, Jill E.; Andreadis, Debra K.; Kirk, Rachel A.

    2002-01-01

    Presents a comparison of access to full-text articles from a free bibliographic database (PubSCIENCE) for affiliated and unaffiliated users. Found that affiliated users had access to more full-text articles than unaffiliated users had, and that both types of users could increase their level of access through additional searching and greater…

  11. Performance related issues in distributed database systems

    NASA Technical Reports Server (NTRS)

    Mukkamala, Ravi

    1991-01-01

    The key elements of research performed during the year long effort of this project are: Investigate the effects of heterogeneity in distributed real time systems; Study the requirements to TRAC towards building a heterogeneous database system; Study the effects of performance modeling on distributed database performance; and Experiment with an ORACLE based heterogeneous system.

  12. Converting a legacy system database into relational format to enhance query efficiency.

    PubMed

    Prather, J C; Lobach, D F; Hales, J W; Hage, M L; Fehrs, S J; Hammond, W E

    1995-01-01

    The analysis of clinical data collected over time can provide important insight into the health care process. Unfortunately, much of the electronic clinical data that exists today is stored in legacy systems, making it difficult to access and share the information. An approach is needed to improve the accessibility of electronic data stored in legacy system databases. In this study, a legacy database is converted into a relational format in the personal computer environment. The impact of such a conversion on query performance is evaluated, and issues that need to be considered when converting a legacy system database are identified. PMID:8563305

  13. SkyDOT: a publicly accessible variability database, containing multiple sky surveys and real-time data

    SciTech Connect

    Starr, D. L.; Wozniak, P. R.; Vestrand, W. T.

    2002-01-01

    SkyDOT (Sky Database for Objects in Time-Domain) is a Virtual Observatory currently comprised of data from the RAPTOR, ROTSE I, and OGLE I1 survey projects. This makes it a very large time domain database. In addition, the RAPTOR project provides SkyDOT with real-time variability data as well as stereoscopic information. With its web interface, we believe SkyDOT will be a very useful tool for both astronomers, and the public. Our main task has been to construct an efficient relational database containing all existing data, while handling a real-time inflow of data. We also provide a useful web interface allowing easy access to both astronomers and the public. Initially, this server will allow common searches, specific queries, and access to light curves. In the future we will include machine learning classification tools and access to spectral information.

  14. Experience in running relational databases on clustered storage

    NASA Astrophysics Data System (ADS)

    Gaspar Aparicio, Ruben; Potocky, Miroslav

    2015-12-01

    For past eight years, CERN IT Database group has based its backend storage on NAS (Network-Attached Storage) architecture, providing database access via NFS (Network File System) protocol. In last two and half years, our storage has evolved from a scale-up architecture to a scale-out one. This paper describes our setup and a set of functionalities providing key features to other services like Database on Demand [1] or CERN Oracle backup and recovery service. It also outlines possible trend of evolution that, storage for databases could follow.

  15. The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility.

    PubMed

    Charoute, Hicham; Nahili, Halima; Abidi, Omar; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Barakat, Abdelhamid

    2014-03-01

    National and ethnic mutation databases provide comprehensive information about genetic variations reported in a population or an ethnic group. In this paper, we present the Moroccan Genetic Disease Database (MGDD), a catalogue of genetic data related to diseases identified in the Moroccan population. We used the PubMed, Web of Science and Google Scholar databases to identify available articles published until April 2013. The Database is designed and implemented on a three-tier model using Mysql relational database and the PHP programming language. To date, the database contains 425 mutations and 208 polymorphisms found in 301 genes and 259 diseases. Most Mendelian diseases in the Moroccan population follow autosomal recessive mode of inheritance (74.17%) and affect endocrine, nutritional and metabolic physiology. The MGDD database provides reference information for researchers, clinicians and health professionals through a user-friendly Web interface. Its content should be useful to improve researches in human molecular genetics, disease diagnoses and design of association studies. MGDD can be publicly accessed at http://mgdd.pasteur.ma. PMID:23860041

  16. The KTOI Ecosystem Project Relational Database : a Report Prepared by Statistical Consulting Services for KTOI Describing the Key Components and Specifications of the KTOI Relational Database.

    SciTech Connect

    Shafii, Bahman

    2009-09-24

    Data are the central focus of any research project. Their collection and analysis are crucial to meeting project goals, testing scientific hypotheses, and drawing relevant conclusions. Typical research projects often devote the majority of their resources to the collection, storage and analysis of data. Therefore, issues related to data quality should be of foremost concern. Data quality issues are even more important when conducting multifaceted studies involving several teams of researchers. Without the use of a standardized protocol, for example, independent data collection carried out by separate research efforts can lead to inconsistencies, confusion and errors throughout the larger project. A database management system can be utilized to help avoid all of the aforementioned problems. The centralization of data into a common relational unit, i.e. a relational database, shifts the responsibility for data quality and maintenance from multiple individuals to a single database manager, thus allowing data quality issues to be assessed and corrected in a timely manner. The database system also provides an easy mechanism for standardizing data components, such as variable names and values uniformly across all segments of a project. This is particularly an important issue when data are collected on a number of biological/physical response and explanatory variables from various locations and times. The database system can integrate all segments of a large study into one unit, while providing oversight and accessibility to the data collection process. The quality of all data collected is uniformly maintained and compatibility between research efforts ensured. While the physical database would exist in a central location, access will not be physically limited. Advanced database interfaces are created to operate over the internet utilizing a Web-based relational database, allowing project members to access their data from virtually anywhere. These interfaces provide users

  17. Technical Aspects of Interfacing MUMPS to an External SQL Relational Database Management System

    PubMed Central

    Kuzmak, Peter M.; Walters, Richard F.; Penrod, Gail

    1988-01-01

    This paper describes an interface connecting InterSystems MUMPS (M/VX) to an external relational DBMS, the SYBASE Database Management System. The interface enables MUMPS to operate in a relational environment and gives the MUMPS language full access to a complete set of SQL commands. MUMPS generates SQL statements as ASCII text and sends them to the RDBMS. The RDBMS executes the statements and returns ASCII results to MUMPS. The interface suggests that the language features of MUMPS make it an attractive tool for use in the relational database environment. The approach described in this paper separates MUMPS from the relational database. Positioning the relational database outside of MUMPS promotes data sharing and permits a number of different options to be used for working with the data. Other languages like C, FORTRAN, and COBOL can access the RDBMS database. Advanced tools provided by the relational database vendor can also be used. SYBASE is an advanced high-performance transaction-oriented relational database management system for the VAX/VMS and UNIX operating systems. SYBASE is designed using a distributed open-systems architecture, and is relatively easy to interface with MUMPS.

  18. Building Access for Digital Images: Databases, Meta-data, Interfaces.

    ERIC Educational Resources Information Center

    Smith, Steven D.

    1999-01-01

    When providing access to digital images, there are three elements to consider: structure, location, and appearance. These considerations are illustrated with two examples--a book and a photograph collection. Each of the elements is then described in detail. (AEF)

  19. The Network Configuration of an Object Relational Database Management System

    NASA Technical Reports Server (NTRS)

    Diaz, Philip; Harris, W. C.

    2000-01-01

    The networking and implementation of the Oracle Database Management System (ODBMS) requires developers to have knowledge of the UNIX operating system as well as all the features of the Oracle Server. The server is an object relational database management system (DBMS). By using distributed processing, processes are split up between the database server and client application programs. The DBMS handles all the responsibilities of the server. The workstations running the database application concentrate on the interpretation and display of data.

  20. Development and Operation of a Database Machine for Online Access and Update of a Large Database.

    ERIC Educational Resources Information Center

    Rush, James E.

    1980-01-01

    Reviews the development of a fault tolerant database processor system which replaced OCLC's conventional file system. A general introduction to database management systems and the operating environment is followed by a description of the hardware selection, software processes, and system characteristics. (SW)

  1. Web-Accessible Database of hsp65 Sequences from Mycobacterium Reference Strains▿†

    PubMed Central

    Dai, Jianli; Chen, Yuansha; Lauzardo, Michael

    2011-01-01

    Mycobacteria include a large number of pathogens. Identification to species level is important for diagnoses and treatments. Here, we report the development of a Web-accessible database of the hsp65 locus sequences (http://msis.mycobacteria.info) from 149 out of 150 Mycobacterium species/subspecies. This database can serve as a reference for identifying Mycobacterium species. PMID:21450960

  2. End-Users/Public Access. Reprints from the Best of "ONLINE" [and]"DATABASE."

    ERIC Educational Resources Information Center

    Online, Inc., Weston, CT.

    Reprints of 20 articles pertaining to the topics of end-users and public access appear in this volume, which is one in a series of volumes of reprints from "ONLINE" and "DATABASE" magazines. Edited for information professionals who use electronically distributed databases, these articles address such topics as: (1) managing a compact disc…

  3. Open-Access Metabolomics Databases for Natural Product Research: Present Capabilities and Future Potential

    PubMed Central

    Johnson, Sean R.; Lange, Bernd Markus

    2015-01-01

    Various databases have been developed to aid in assigning structures to spectral peaks observed in metabolomics experiments. In this review article, we discuss the utility of currently available open-access spectral and chemical databases for natural products discovery. We also provide recommendations on how the research community can contribute to further improvements. PMID:25789275

  4. DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS TO DATABASES FOR BUILDING STRUCTURE-TOXICITY PREDICTION MODELS

    EPA Science Inventory

    DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction Models
    Ann M. Richard
    US Environmental Protection Agency, Research Triangle Park, NC, USA

    Distributed: Decentralized set of standardized, field-delimited databases,...

  5. Crystallography Open Database – an open-access collection of crystal structures

    PubMed Central

    Gražulis, Saulius; Chateigner, Daniel; Downs, Robert T.; Yokochi, A. F. T.; Quirós, Miguel; Lutterotti, Luca; Manakova, Elena; Butkus, Justas; Moeck, Peter; Le Bail, Armel

    2009-01-01

    The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal–organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ∼80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality. PMID:22477773

  6. An Introduction to Database Structure and Database Machines.

    ERIC Educational Resources Information Center

    Detweiler, Karen

    1984-01-01

    Enumerates principal management objectives of database management systems (data independence, quality, security, multiuser access, central control) and criteria for comparison (response time, size, flexibility, other features). Conventional database management systems, relational databases, and database machines used for backend processing are…

  7. Implementing Graph Pattern Queries on a Relational Database

    SciTech Connect

    Kaplan, I L; Abdulla, G M; Brugger, S T; Kohn, S R

    2007-12-26

    When a graph database is implemented on top of a relational database, queries in the graph query language are translated into relational SQL queries. Graph pattern queries are an important feature of a graph query language. Translating graph pattern queries into single SQL statements results in very poor query performance. By taking into account the pattern query structure and generating multiple SQL statements, pattern query performance can be dramatically improved. The performance problems encountered with the single SQL statements generated for pattern queries reflects a problem in the SQL query planner and optimizer. Addressing this problem would allow relational databases to better support semantic graph databases. Relational database systems that provide good support for graph databases may also be more flexible platforms for data warehouses.

  8. World Wide Web platform-independent access to biomedical text/image databases

    NASA Astrophysics Data System (ADS)

    Long, L. Rodney; Goh, Gin-Hua; Neve, Leif; Thoma, George R.

    1998-07-01

    The biomedical digital library of the future is expected to provide access to stores of biomedical database information containing text and images. Developing efficient methods for accessing such databases is a research effort at the Lister Hill National Center for Biomedical Communications of the National Library of Medicine. In this paper we examine issues in providing access to databases across the Web and describe a tool we have developed: the Web-based Medical Information Retrieval System (WebMIRS). We address a number of critical issues, including preservation of data integrity, efficient database design, access to documentation, quality of query and results interfaces, capability to export results to other software, and exploitation of multimedia data. WebMIRS is implemented as a Java applet that allows database access to text and to associated image data, without requiring any user software beyond a standard Web browser. The applet implementation allows WebMIRS to run on any hardware platform (such as PCs, the Macintosh, or Unix machines) which supports a Java-enabled Web browser, such as Netscape or Internet Explorer. WebMIRS is being tested on text/x-ray image databases created from the National Health and Nutrition Examination Surveys (NHANES) data collected by the National Center for Health Statistics.

  9. Cross: An OWL Wrapper for Reasoning on Relational Databases

    NASA Astrophysics Data System (ADS)

    Champin, Pierre-Antoine; Houben, Geert-Jan; Thiran, Philippe

    One of the challenges of the Semantic Web is to integrate the huge amount of information already available on the standard Web, usually stored in relational databases. In this paper, we propose a formalization of a logic model of relational databases, and a transformation of that model into OWL, a Semantic Web language. This transformation is implemented in Cross, as an open-source prototype. We prove a relation between the notion of legal database state and the consistency of the corresponding OWL knowledge base. We then show how that transformation can prove useful to enhance databases, and integrate them in the Semantic Web.

  10. The NASA ADS Abstract Service and the Distributed Astronomy Digital Library [and] Project Soup: Comparing Evaluations of Digital Collection Efforts [and] Cross-Organizational Access Management: A Digital Library Authentication and Authorization Architecture [and] BibRelEx: Exploring Bibliographic Databases by Visualization of Annotated Content-based Relations [and] Semantics-Sensitive Retrieval for Digital Picture Libraries [and] Encoded Archival Description: An Introduction and Overview.

    ERIC Educational Resources Information Center

    Kurtz, Michael J.; Eichorn, Guenther; Accomazzi, Alberto; Grant, Carolyn S.; Demleitner, Markus; Murray, Stephen S.; Jones, Michael L. W.; Gay, Geri K.; Rieger, Robert H.; Millman, David; Bruggemann-Klein, Anne; Klein, Rolf; Landgraf, Britta; Wang, James Ze; Li, Jia; Chan, Desmond; Wiederhold, Gio; Pitti, Daniel V.

    1999-01-01

    Includes six articles that discuss a digital library for astronomy; comparing evaluations of digital collection efforts; cross-organizational access management of Web-based resources; searching scientific bibliographic databases based on content-based relations between documents; semantics-sensitive retrieval for digital picture libraries; and…

  11. Strategy for a transparent, accessible, and sustainable national claims database.

    PubMed

    Gelburd, Robin

    2015-03-01

    The article outlines the strategy employed by FAIR Health, Inc, an independent nonprofit, to maintain a national database of over 18 billion private health insurance claims to support consumer education, payer and provider operations, policy makers, and researchers with standard and customized data sets on an economically self-sufficient basis. It explains how FAIR Health conducts all operations in-house, including data collection, security, validation, information organization, product creation, and transmission, with a commitment to objectivity and reliability in data and data products. It also describes the data elements available to researchers and the diverse studies that FAIR Health data facilitate. PMID:26014305

  12. NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases

    PubMed Central

    Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

    2013-01-01

    RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments. PMID:23984425

  13. WWW-based access to object-oriented clinical databases: the KHOSPAD project.

    PubMed

    Pinciroli, F; Portoni, L; Combi, C; Violante, F F

    1998-09-01

    KHOSPAD is a project aiming at improving the quality of the process of patient care concerning general practitioner-patient-hospital relationships, using current information and networking technologies. The studied application field is a cardiology division, with hemodynamic laboratory and the population of PTCA patients. Data related to PTCA patients are managed by ARCADIA, an object-oriented database management system developed for the considered clinical setting. We defined a remotely accessible view of ARCADIA medical record, suitable for general practitioners (GPs) caring patients after PTCA, during the follow-up period. Using a PC, a modem and Internet, an authorized GP can consult remotely the medical records of his PTCA patients. Main features of the application are related to the management and display of complex data, specifically characterized by multimedia and temporal features, based on an object-oriented temporal data model. PMID:9861510

  14. Database of extended radiation maps and its access system

    NASA Astrophysics Data System (ADS)

    Verkhodanov, O. V.; Naiden, Ya. V.; Chernenkov, V. N.; Verkhodanova, N. V.

    2014-01-01

    We describe the architecture of the developed computing web server http://cmb.sao.ru allowing to synthesize the maps of extended radiation on the full sphere from the spherical harmonics in the GLESP pixelization grid, smooth them with the power beam pattern with various angular resolutions in the multipole space, and identify regions of the sky with given coordinates. We describe the server access and administration systems as well as the technique constructing the sky region maps, organized in Python in the Django web-application development framework.

  15. Relational Database for the Geology of the Northern Rocky Mountains - Idaho, Montana, and Washington

    USGS Publications Warehouse

    Causey, J. Douglas; Zientek, Michael L.; Bookstrom, Arthur A.; Frost, Thomas P.; Evans, Karl V.; Wilson, Anna B.; Van Gosen, Bradley S.; Boleneus, David E.; Pitts, Rebecca A.

    2008-01-01

    A relational database was created to prepare and organize geologic map-unit and lithologic descriptions for input into a spatial database for the geology of the northern Rocky Mountains, a compilation of forty-three geologic maps for parts of Idaho, Montana, and Washington in U.S. Geological Survey Open File Report 2005-1235. Not all of the information was transferred to and incorporated in the spatial database due to physical file limitations. This report releases that part of the relational database that was completed for that earlier product. In addition to descriptive geologic information for the northern Rocky Mountains region, the relational database contains a substantial bibliography of geologic literature for the area. The relational database nrgeo.mdb (linked below) is available in Microsoft Access version 2000, a proprietary database program. The relational database contains data tables and other tables used to define terms, relationships between the data tables, and hierarchical relationships in the data; forms used to enter data; and queries used to extract data.

  16. Open-access databases as unprecedented resources and drivers of cultural change in fisheries science

    SciTech Connect

    McManamay, Ryan A; Utz, Ryan

    2014-01-01

    Open-access databases with utility in fisheries science have grown exponentially in quantity and scope over the past decade, with profound impacts to our discipline. The management, distillation, and sharing of an exponentially growing stream of open-access data represents several fundamental challenges in fisheries science. Many of the currently available open-access resources may not be universally known among fisheries scientists. We therefore introduce many national- and global-scale open-access databases with applications in fisheries science and provide an example of how they can be harnessed to perform valuable analyses without additional field efforts. We also discuss how the development, maintenance, and utilization of open-access data are likely to pose technical, financial, and educational challenges to fisheries scientists. Such cultural implications that will coincide with the rapidly increasing availability of free data should compel the American Fisheries Society to actively address these problems now to help ease the forthcoming cultural transition.

  17. Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases.

    PubMed

    Stein, L D; Thierry-Mieg, J

    1998-12-01

    Much of the world's genomic data are available to the community through networked databases that are accessed via Web interfaces. Although this paradigm provides browse-level access and has greatly facilitated linking between databases, it does not provide any convenient mechanism for programmatically fetching and integrating data from diverse databases. We have created a library and an application programming interface (API) named AcePerl that provides simple, direct access to ACEDB databases from the Perl programming language. With this library, programmers and computer-savvy biologists can write software to pose complex queries on local and remote ACEDB databases, retrieve the data, integrate the results, and move data objects from one database to another. In addition, a set of Web scripts running on top of AcePerl provides Web-based browsing of any local or remote ACEDB database. AcePerl and the AceBrowser Web browser run on Unix systems and are available under a license that allows for unrestricted use and redistribution. Both packages can be downloaded from URL. A Microsoft Windows port of AcePerl is in the planning stages. PMID:9872985

  18. Building an Interoperable Relational Database for the National Deep Submergence Facility (NDSF)

    NASA Astrophysics Data System (ADS)

    Ferrini, V.; McCue, S.; Arko, R.

    2008-12-01

    The National Deep Submergence Facility (NDSF) operates the Human Occupied Vehicle (HOV) Alvin, the Remote Operated Vehicle (ROV) Jason 2, and the Autonomous Underwater Vehicle (AUV) Sentry. Data acquired with these platforms is provided both to the science party on each expedition, and to the Woods Hole Oceanographic Institution (WHOI) Data Library. Although several data sets are inventoried online, and some data are accessible, there has not yet been a coordinated effort to construct an interoperable NDSF database that can serve data to other data systems. We present on progress made with the creation of an NDSF relational database maintained at WHOI and developed through collaborative efforts with the Marine Geoscience Data System (MGDS). While our initial efforts focus on standardizing vehicle metadata and developing techniques for digitally acquiring metadata at sea, the creation of a relational database backend provides opportunities for improved data access and interoperability. Constructing the database using PostgresSQL, coupled with spatial database extensions (PostGIS), and an online GIS backend (MapServer), enables a searchable database and Open Geospatial Consortium (OGC) compliant map based web services (Web Map Service and Web Feature Service) that can be used to provide data access pathways through several programmatic interfaces.

  19. Evolution of grid-wide access to database resident information in ATLAS using Frontier

    NASA Astrophysics Data System (ADS)

    Barberis, D.; Bujor, F.; de Stefano, J.; Dewhurst, A. L.; Dykstra, D.; Front, D.; Gallas, E.; Gamboa, C. F.; Luehring, F.; Walker, R.

    2012-12-01

    The ATLAS experiment deployed Frontier technology worldwide during the initial year of LHC collision data taking to enable user analysis jobs running on the Worldwide LHC Computing Grid to access database resident data. Since that time, the deployment model has evolved to optimize resources, improve performance, and streamline maintenance of Frontier and related infrastructure. In this presentation we focus on the specific changes in the deployment and improvements undertaken, such as the optimization of cache and launchpad location, the use of RPMs for more uniform deployment of underlying Frontier related components, improvements in monitoring, optimization of fail-over, and an increasing use of a centrally managed database containing site specific information (for configuration of services and monitoring). In addition, analysis of Frontier logs has allowed us a deeper understanding of problematic queries and understanding of use cases. Use of the system has grown beyond user analysis and subsystem specific tasks such as calibration and alignment, extending into production processing areas, such as initial reconstruction and trigger reprocessing. With a more robust and tuned system, we are better equipped to satisfy the still growing number of diverse clients and the demands of increasingly sophisticated processing and analysis.

  20. Geneious plugins for the access of PlasmoDB and PiroplasmaDB databases.

    PubMed

    Ma, Charles; Gunther, Svenja; Cooke, Brian; Coppel, Ross L

    2013-04-01

    The bioinformatics software, Geneious, provides a useful platform for researchers to retrieve and analyse genomic and functional genomics information. However, the main databases that the software is able to access are hosted by NCBI (National Center for Biotechnology Information). The databases of EuPathDB (Eukaryotic Pathogen Database Resources), such as PlasmoDB and PiroplasmaDB, collect more specific and detailed information about eukaryotic pathogens than those kept in NCBI databases. Two plugins for Geneious, one for PlasmaDB and one for PiroplasmaDB were developed. When installed, users can use search facilities to find and import gene and protein sequences from the EuPathDB databases. Users can then use the functions of Geneious to process the sequence information. When information unique to PlasmoDB and PiroplasmaDB is required, the user can access results linked with the gene/protein sequence via the default web browser. The plugins are freely available from the Victorian Bioinformatics Consortium website. The plugins can be modified to access any of the databases of EuPathDB. PMID:23183102

  1. Advanced technologies for scalable ATLAS conditions database access on the grid

    NASA Astrophysics Data System (ADS)

    Basset, R.; Canali, L.; Dimitrov, G.; Girone, M.; Hawkings, R.; Nevski, P.; Valassi, A.; Vaniachine, A.; Viegas, F.; Walker, R.; Wong, A.

    2010-04-01

    During massive data reprocessing operations an ATLAS Conditions Database application must support concurrent access from numerous ATLAS data processing jobs running on the Grid. By simulating realistic work-flow, ATLAS database scalability tests provided feedback for Conditions Db software optimization and allowed precise determination of required distributed database resources. In distributed data processing one must take into account the chaotic nature of Grid computing characterized by peak loads, which can be much higher than average access rates. To validate database performance at peak loads, we tested database scalability at very high concurrent jobs rates. This has been achieved through coordinated database stress tests performed in series of ATLAS reprocessing exercises at the Tier-1 sites. The goal of database stress tests is to detect scalability limits of the hardware deployed at the Tier-1 sites, so that the server overload conditions can be safely avoided in a production environment. Our analysis of server performance under stress tests indicates that Conditions Db data access is limited by the disk I/O throughput. An unacceptable side-effect of the disk I/O saturation is a degradation of the WLCG 3D Services that update Conditions Db data at all ten ATLAS Tier-1 sites using the technology of Oracle Streams. To avoid such bottlenecks we prototyped and tested a novel approach for database peak load avoidance in Grid computing. Our approach is based upon the proven idea of pilot job submission on the Grid: instead of the actual query, an ATLAS utility library sends to the database server a pilot query first.

  2. Constructing a Geology Ontology Using a Relational Database

    NASA Astrophysics Data System (ADS)

    Hou, W.; Yang, L.; Yin, S.; Ye, J.; Clarke, K.

    2013-12-01

    In geology community, the creation of a common geology ontology has become a useful means to solve problems of data integration, knowledge transformation and the interoperation of multi-source, heterogeneous and multiple scale geological data. Currently, human-computer interaction methods and relational database-based methods are the primary ontology construction methods. Some human-computer interaction methods such as the Geo-rule based method, the ontology life cycle method and the module design method have been proposed for applied geological ontologies. Essentially, the relational database-based method is a reverse engineering of abstracted semantic information from an existing database. The key is to construct rules for the transformation of database entities into the ontology. Relative to the human-computer interaction method, relational database-based methods can use existing resources and the stated semantic relationships among geological entities. However, two problems challenge the development and application. One is the transformation of multiple inheritances and nested relationships and their representation in an ontology. The other is that most of these methods do not measure the semantic retention of the transformation process. In this study, we focused on constructing a rule set to convert the semantics in a geological database into a geological ontology. According to the relational schema of a geological database, a conversion approach is presented to convert a geological spatial database to an OWL-based geological ontology, which is based on identifying semantics such as entities, relationships, inheritance relationships, nested relationships and cluster relationships. The semantic integrity of the transformation was verified using an inverse mapping process. In a geological ontology, an inheritance and union operations between superclass and subclass were used to present the nested relationship in a geochronology and the multiple inheritances

  3. PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values.

    PubMed

    Toseland, Christopher P; McSparron, Helen; Davies, Matthew N; Flower, Darren R

    2006-01-01

    The Protein pK(a) Database (PPD) v1.0 provides a compendium of protein residue-specific ionization equilibria (pK(a) values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play key roles in the molecular mechanisms that underlie many biological phenomena, including protein folding and enzyme catalysis. The PPD serves as a general protein pK(a) archive and as a source of data that allows for the development and improvement of pK(a) prediction systems. The database is accessed through an HTML interface, which offers two fast, efficient search methods: an amino acid-based query and a Basic Local Alignment Search Tool search. Entries also give details of experimental techniques and links to other key databases, such as National Center for Biotechnology Information and the Protein Data Bank, providing the user with considerable background information. The database can be found at the following URL: http://www.jenner.ac.uk/PPD. PMID:16381845

  4. Database Access Manager for the Software Engineering Laboratory (DAMSEL) user's guide

    NASA Technical Reports Server (NTRS)

    1990-01-01

    Operating instructions for the Database Access Manager for the Software Engineering Laboratory (DAMSEL) system are presented. Step-by-step instructions for performing various data entry and report generation activities are included. Sample sessions showing the user interface display screens are also included. Instructions for generating reports are accompanied by sample outputs for each of the reports. The document groups the available software functions by the classes of users that may access them.

  5. The Politics of Information: Building a Relational Database To Support Decision-Making at a Public University.

    ERIC Educational Resources Information Center

    Friedman, Debra; Hoffman, Phillip

    2001-01-01

    Describes creation of a relational database at the University of Washington supporting ongoing academic planning at several levels and affecting the culture of decision making. Addresses getting started; sharing the database; questions, worries, and issues; improving access to high-demand courses; the advising function; management of instructional…

  6. Toward an Open-Access Global Database for Mapping, Control, and Surveillance of Neglected Tropical Diseases

    PubMed Central

    Hürlimann, Eveline; Schur, Nadine; Boutsika, Konstantina; Stensgaard, Anna-Sofie; Laserna de Himpsl, Maiti; Ziegelbauer, Kathrin; Laizer, Nassor; Camenzind, Lukas; Di Pasquale, Aurelio; Ekpo, Uwem F.; Simoonga, Christopher; Mushinge, Gabriel; Saarnak, Christopher F. L.; Utzinger, Jürg; Kristensen, Thomas K.; Vounatsou, Penelope

    2011-01-01

    Background After many years of general neglect, interest has grown and efforts came under way for the mapping, control, surveillance, and eventual elimination of neglected tropical diseases (NTDs). Disease risk estimates are a key feature to target control interventions, and serve as a benchmark for monitoring and evaluation. What is currently missing is a georeferenced global database for NTDs providing open-access to the available survey data that is constantly updated and can be utilized by researchers and disease control managers to support other relevant stakeholders. We describe the steps taken toward the development of such a database that can be employed for spatial disease risk modeling and control of NTDs. Methodology With an emphasis on schistosomiasis in Africa, we systematically searched the literature (peer-reviewed journals and ‘grey literature’), contacted Ministries of Health and research institutions in schistosomiasis-endemic countries for location-specific prevalence data and survey details (e.g., study population, year of survey and diagnostic techniques). The data were extracted, georeferenced, and stored in a MySQL database with a web interface allowing free database access and data management. Principal Findings At the beginning of 2011, our database contained more than 12,000 georeferenced schistosomiasis survey locations from 35 African countries available under http://www.gntd.org. Currently, the database is expanded to a global repository, including a host of other NTDs, e.g. soil-transmitted helminthiasis and leishmaniasis. Conclusions An open-access, spatially explicit NTD database offers unique opportunities for disease risk modeling, targeting control interventions, disease monitoring, and surveillance. Moreover, it allows for detailed geostatistical analyses of disease distribution in space and time. With an initial focus on schistosomiasis in Africa, we demonstrate the proof-of-concept that the establishment and running of a

  7. Epistemonikos: a free, relational, collaborative, multilingual database of health evidence.

    PubMed

    Rada, Gabriel; Pérez, Daniel; Capurro, Daniel

    2013-01-01

    Epistemonikos (www.epistemonikos.org) is a free, multilingual database of the best available health evidence. This paper describes the design, development and implementation of the Epistemonikos project. Using several web technologies to store systematic reviews, their included articles, overviews of reviews and structured summaries, Epistemonikos is able to provide a simple and powerful search tool to access health evidence for sound decision making. Currently, Epistemonikos stores more than 115,000 unique documents and more than 100,000 relationships between documents. In addition, since its database is translated into 9 different languages, Epistemonikos ensures that non-English speaking decision-makers can access the best available evidence without language barriers. PMID:23920602

  8. Providing Access to Unique Information Sources: A Reusable Platform for Publishing Bibliographic Databases on the Web.

    ERIC Educational Resources Information Center

    Jantz, Ronald C.

    2000-01-01

    Discussion of digital library projects at Rutgers University focuses on publishing bibliographic databases on the Web to provide access to information sources not likely to be published elsewhere. Describes the reusable technology platform concept, bibliographic platform architecture, metadata approach, data entry, and managing the process.…

  9. A relational database application in support of integrated neuroscience research.

    PubMed

    Rudowsky, Ira; Kulyba, Olga; Kunin, Mikhail; Ogarodnikov, Dmitri; Raphan, Theodore

    2004-12-01

    The development of relational databases has significantly improved the performance of storage, search, and retrieval functions and has made it possible for applications that perform real-time data acquisition and analysis to interact with these types of databases. The purpose of this research was to develop a user interface for interaction between a data acquisition and analysis application and a relational database using the Oracle9i system. The overall system was designed to have an indexing capability that threads into the data acquisition and analysis programs. Tables were designed and relations within the database for indexing the files and information contained within the files were established. The system provides retrieval capabilities over a broad range of media, including analog, event, and video data types. The system's ability to interact with a data capturing program at the time of the experiment to create both multimedia files as well as the meta-data entries in the relational database avoids manual entries in the database and ensures data integrity and completeness for further interaction with the data by analysis applications. PMID:15657974

  10. [Construction of nervous system relative protein and gene secondary database].

    PubMed

    Wang, Pan; Chen, Xinhao; Liu, Xiangming

    2007-10-01

    Along with the rapid research of neural molecular biology, abundant data are produced so that the collection and coordination of high-throughout data about nervous system relative proteins and genes are imperative. Through analyzing the biological primary databases maintained by NCBI and RCSB as the main data source and designing a new data model, a local specialized secondary database is constructed, which mainly includes nucleotide sequences, protein sequences and protein structures, and is established on Sun Blade 2000 System and Oracle 9i. All programs are developed by Java technology. A method of web information automatic retrieval with XML is proposed for sequence data collection and submission to the database. JSP + JavaBean technology is used to support data promulgation on Internet. The establishment of this database provides an excellent platform for the research of neural molecular biology and the pathogenesis of related diseases. PMID:18027688

  11. ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.

    PubMed

    Zeng, Victor; Extavour, Cassandra G

    2012-01-01

    The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental

  12. A Generalized Relational Schema for an Integrated Clinical Patient Database

    PubMed Central

    Friedman, Carol; Hripcsak, George; Johnson, Stephen B.; Cimino, James J.; Clayton, Paul D.

    1990-01-01

    Patient data is central to a Clinical Information System (CIS). The organization of the data in a patient database is essential to the functioning of the system. If the CIS contains a medical decision support component, further requirements are imposed on the database. It must be capable of accurately representing a broad range of clinical information in coded form, and be organized for efficient retrievals by patient, time, and type of clinical term. This paper presents a generalized schema for a clinical patient database within the relational database model. The general design makes it possible to represent diverse clinical data in a standard structure and to organize the data so that it is densely clustered by patient and time.

  13. [Development of an anesthesia ledger using relational database].

    PubMed

    Hayashi, I; Mizoguchi, H; Fujiwara, M; Kato, H; Kawamura, J; Odashiro, M

    1993-08-01

    An anesthesia ledger was developed using relational database KIRI Ver3. This anesthesia database includes 33 items for input, for example patient's name, patient's I.D. number, data of operation, diagnosis, operative procedure, name of surgeon, name of anesthesiologists and so on. One can select data from displayed menu cards only by rolling down or rolling up the cursor at 19 items and can input numbers by keyboard at twelve items. Even a computer beginner can easily operate it after a minimal training. Only patient's name must be input by text style. We can construct this anesthesia database only by use of functions of KIRI Ver3 without programming. One can use this anesthesia ledger at any operative facilities by changing a part of database and a file of doctor's name. PMID:8366569

  14. Design and implementation of relational and spatial databases for petroleum-related information

    SciTech Connect

    Schneider, R.; Sepehrnoori, K.; Wang, M.

    1987-01-01

    A relational database has been defined and implemented which describes the attributes and entities of engineering, geological, regulatory, economic, and historical data associated with the petroleum industry. This relational model allows the user to view this database of information from many different perspectives. An entity-relationship model was used to design the various relations of the database, and a data dictionary was developed to define the attributes of the database. Using the data model and data dictionary developed for the relational database, a spatial database was implemented which allows the user to graphically view the spatial relationships between various attributes of the database as well as additional information which may be computed from those attributes.

  15. Selecting a Relational Database Management System for Library Automation Systems.

    ERIC Educational Resources Information Center

    Shekhel, Alex; O'Brien, Mike

    1989-01-01

    Describes the evaluation of four relational database management systems (RDBMSs) (Informix Turbo, Oracle 6.0 TPS, Unify 2000 and Relational Technology's Ingres 5.0) to determine which is best suited for library automation. The evaluation criteria used to develop a benchmark specifically designed to test RDBMSs for libraries are discussed. (CLB)

  16. A Blind Reversible Robust Watermarking Scheme for Relational Databases

    PubMed Central

    Chang, Chin-Chen; Nguyen, Thai-Son; Lin, Chia-Chen

    2013-01-01

    Protecting the ownership and controlling the copies of digital data have become very important issues in Internet-based applications. Reversible watermark technology allows the distortion-free recovery of relational databases after the embedded watermark data are detected or verified. In this paper, we propose a new, blind, reversible, robust watermarking scheme that can be used to provide proof of ownership for the owner of a relational database. In the proposed scheme, a reversible data-embedding algorithm, which is referred to as “histogram shifting of adjacent pixel difference” (APD), is used to obtain reversibility. The proposed scheme can detect successfully 100% of the embedded watermark data, even if as much as 80% of the watermarked relational database is altered. Our extensive analysis and experimental results show that the proposed scheme is robust against a variety of data attacks, for example, alteration attacks, deletion attacks, mix-match attacks, and sorting attacks. PMID:24223033

  17. SymbioGenomesDB: a database for the integration and access to knowledge on host–symbiont relationships

    PubMed Central

    Reyes-Prieto, Mariana; Vargas-Chávez, Carlos; Latorre, Amparo; Moya, Andrés

    2015-01-01

    Symbiotic relationships occur naturally throughout the tree of life, either in a commensal, mutualistic or pathogenic manner. The genomes of multiple organisms involved in symbiosis are rapidly being sequenced and becoming available, especially those from the microbial world. Currently, there are numerous databases that offer information on specific organisms or models, but none offer a global understanding on relationships between organisms, their interactions and capabilities within their niche, as well as their role as part of a system, in this case, their role in symbiosis. We have developed the SymbioGenomesDB as a community database resource for laboratories which intend to investigate and use information on the genetics and the genomics of organisms involved in these relationships. The ultimate goal of SymbioGenomesDB is to host and support the growing and vast symbiotic–host relationship information, to uncover the genetic basis of such associations. SymbioGenomesDB maintains a comprehensive organization of information on genomes of symbionts from diverse hosts throughout the Tree of Life, including their sequences, their metadata and their genomic features. This catalog of relationships was generated using computational tools, custom R scripts and manual integration of data available in public literature. As a highly curated and comprehensive systems database, SymbioGenomesDB provides web access to all the information of symbiotic organisms, their features and links to the central database NCBI. Three different tools can be found within the database to explore symbiosis-related organisms, their genes and their genomes. Also, we offer an orthology search for one or multiple genes in one or multiple organisms within symbiotic relationships, and every table, graph and output file is downloadable and easy to parse for further analysis. The robust SymbioGenomesDB will be constantly updated to cope with all the data being generated and included in major

  18. SymbioGenomesDB: a database for the integration and access to knowledge on host-symbiont relationships.

    PubMed

    Reyes-Prieto, Mariana; Vargas-Chávez, Carlos; Latorre, Amparo; Moya, Andrés

    2015-01-01

    Symbiotic relationships occur naturally throughout the tree of life, either in a commensal, mutualistic or pathogenic manner. The genomes of multiple organisms involved in symbiosis are rapidly being sequenced and becoming available, especially those from the microbial world. Currently, there are numerous databases that offer information on specific organisms or models, but none offer a global understanding on relationships between organisms, their interactions and capabilities within their niche, as well as their role as part of a system, in this case, their role in symbiosis. We have developed the SymbioGenomesDB as a community database resource for laboratories which intend to investigate and use information on the genetics and the genomics of organisms involved in these relationships. The ultimate goal of SymbioGenomesDB is to host and support the growing and vast symbiotic-host relationship information, to uncover the genetic basis of such associations. SymbioGenomesDB maintains a comprehensive organization of information on genomes of symbionts from diverse hosts throughout the Tree of Life, including their sequences, their metadata and their genomic features. This catalog of relationships was generated using computational tools, custom R scripts and manual integration of data available in public literature. As a highly curated and comprehensive systems database, SymbioGenomesDB provides web access to all the information of symbiotic organisms, their features and links to the central database NCBI. Three different tools can be found within the database to explore symbiosis-related organisms, their genes and their genomes. Also, we offer an orthology search for one or multiple genes in one or multiple organisms within symbiotic relationships, and every table, graph and output file is downloadable and easy to parse for further analysis. The robust SymbioGenomesDB will be constantly updated to cope with all the data being generated and included in major

  19. A High Speed Mobile Courier Data Access System That Processes Database Queries in Real-Time

    NASA Astrophysics Data System (ADS)

    Gatsheni, Barnabas Ndlovu; Mabizela, Zwelakhe

    A secure high-speed query processing mobile courier data access (MCDA) system for a Courier Company has been developed. This system uses the wireless networks in combination with wired networks for updating a live database at the courier centre in real-time by an offsite worker (the Courier). The system is protected by VPN based on IPsec. There is no system that we know of to date that performs the task for the courier as proposed in this paper.

  20. Mashup of Geo and Space Science Data Provided via Relational Databases in the Semantic Web

    NASA Astrophysics Data System (ADS)

    Ritschel, B.; Seelus, C.; Neher, G.; Iyemori, T.; Koyama, Y.; Yatagai, A. I.; Murayama, Y.; King, T. A.; Hughes, J. S.; Fung, S. F.; Galkin, I. A.; Hapgood, M. A.; Belehaki, A.

    2014-12-01

    The use of RDBMS for the storage and management of geo and space science data and/or metadata is very common. Although the information stored in tables is based on a data model and therefore well organized and structured, a direct mashup with RDF based data stored in triple stores is not possible. One solution of the problem consists in the transformation of the whole content into RDF structures and storage in triple stores. Another interesting way is the use of a specific system/service, such as e.g. D2RQ, for the access to relational database content as virtual, read only RDF graphs. The Semantic Web based -proof of concept- GFZ ISDC uses the triple store Virtuoso for the storage of general context information/metadata to geo and space science satellite and ground station data. There is information about projects, platforms, instruments, persons, product types, etc. available but no detailed metadata about the data granuals itself. Such important information, as e.g. start or end time or the detailed spatial coverage of a single measurement is stored in RDBMS tables of the ISDC catalog system only. In order to provide a seamless access to all available information about the granuals/data products a mashup of the different data resources (triple store and RDBMS) is necessary. This paper describes the use of D2RQ for a Semantic Web/SPARQL based mashup of relational databases used for ISDC data server but also for the access to IUGONET and/or ESPAS and further geo and space science data resources. RDBMS Relational Database Management System RDF Resource Description Framework SPARQL SPARQL Protocol And RDF Query Language D2RQ Accessing Relational Databases as Virtual RDF Graphs GFZ ISDC German Research Centre for Geosciences Information System and Data Center IUGONET Inter-university Upper Atmosphere Global Observation Network (Japanese project) ESPAS Near earth space data infrastructure for e-science (European Union funded project)

  1. Next generation database relational solutions for ATLAS distributed computing

    NASA Astrophysics Data System (ADS)

    Dimitrov, G.; Maeno, T.; Garonne, V.; Atlas Collaboration

    2014-06-01

    The ATLAS Distributed Computing (ADC) project delivers production tools and services for ATLAS offline activities such as data placement and data processing on the Grid. The system has been capable of sustaining with high efficiency the needed computing activities during the first run of LHC data taking, and has demonstrated flexibility in reacting promptly to new challenges. Databases are a vital part of the whole ADC system. The Oracle Relational Database Management System (RDBMS) has been addressing a majority of the ADC database requirements for many years. Much expertise was gained through the years and without a doubt will be used as a good foundation for the next generation PanDA (Production ANd Distributed Analysis) and DDM (Distributed Data Management) systems. In this paper we present the current production ADC database solutions and notably the planned changes on the PanDA system, and the next generation ATLAS DDM system called Rucio. Significant work was performed on studying different solutions to arrive at the best relational and physical database model for performance and scalability in order to be ready for deployment and operation in 2014.

  2. Database Relation Watermarking Resilient against Secondary Watermarking Attacks

    NASA Astrophysics Data System (ADS)

    Gupta, Gaurav; Pieprzyk, Josef

    There has been tremendous interest in watermarking multimedia content during the past two decades, mainly for proving ownership and detecting tamper. Digital fingerprinting, that deals with identifying malicious user(s), has also received significant attention. While extensive work has been carried out in watermarking of images, other multimedia objects still have enormous research potential. Watermarking database relations is one of the several areas which demand research focus owing to the commercial implications of database theft. Recently, there has been little progress in database watermarking, with most of the watermarking schemes modeled after the irreversible database watermarking scheme proposed by Agrawal and Kiernan. Reversibility is the ability to re-generate the original (unmarked) relation from the watermarked relation using a secret key. As explained in our paper, reversible watermarking schemes provide greater security against secondary watermarking attacks, where an attacker watermarks an already marked relation in an attempt to erase the original watermark. This paper proposes an improvement over the reversible and blind watermarking scheme presented in [5], identifying and eliminating a critical problem with the previous model. Experiments showing that the average watermark detection rate is around 91% even with attacker distorting half of the attributes. The current scheme provides security against secondary watermarking attacks.

  3. IntEnz, the integrated relational enzyme database

    PubMed Central

    Fleischmann, Astrid; Darsow, Michael; Degtyarenko, Kirill; Fleischmann, Wolfgang; Boyce, Sinéad; Axelsen, Kristian B.; Bairoch, Amos; Schomburg, Dietmar; Tipton, Keith F.; Apweiler, Rolf

    2004-01-01

    IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at http://www.ebi.ac.uk/intenz. PMID:14681451

  4. IntEnz, the integrated relational enzyme database.

    PubMed

    Fleischmann, Astrid; Darsow, Michael; Degtyarenko, Kirill; Fleischmann, Wolfgang; Boyce, Sinéad; Axelsen, Kristian B; Bairoch, Amos; Schomburg, Dietmar; Tipton, Keith F; Apweiler, Rolf

    2004-01-01

    IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at http://www.ebi.ac.uk/intenz. PMID:14681451

  5. Nuclear data made easily accessible through the Notre Dame Nuclear Database

    NASA Astrophysics Data System (ADS)

    Khouw, Timothy; Lee, Kevin; Fasano, Patrick; Mumpower, Matthew; Aprahamian, Ani

    2014-09-01

    In 1994, the NNDC revolutionized nuclear research by providing a colorful, clickable, searchable database over the internet. Over the last twenty years, web technology has evolved dramatically. Our project, the Notre Dame Nuclear Database, aims to provide a more comprehensive and broadly searchable interactive body of data. The database can be searched by an array of filters which includes metadata such as the facility where a measurement is made, the author(s), or date of publication for the datum of interest. The user interface takes full advantage of HTML, a web markup language, CSS (cascading style sheets to define the aesthetics of the website), and JavaScript, a language that can process complex data. A command-line interface is supported that interacts with the database directly on a user's local machine which provides single command access to data. This is possible through the use of a standardized API (application programming interface) that relies upon well-defined filtering variables to produce customized search results. We offer an innovative chart of nuclides utilizing scalable vector graphics (SVG) to deliver users an unsurpassed level of interactivity supported on all computers and mobile devices. We will present a functional demo of our database at the conference.

  6. Efficient hemodynamic event detection utilizing relational databases and wavelet analysis

    NASA Technical Reports Server (NTRS)

    Saeed, M.; Mark, R. G.

    2001-01-01

    Development of a temporal query framework for time-oriented medical databases has hitherto been a challenging problem. We describe a novel method for the detection of hemodynamic events in multiparameter trends utilizing wavelet coefficients in a MySQL relational database. Storage of the wavelet coefficients allowed for a compact representation of the trends, and provided robust descriptors for the dynamics of the parameter time series. A data model was developed to allow for simplified queries along several dimensions and time scales. Of particular importance, the data model and wavelet framework allowed for queries to be processed with minimal table-join operations. A web-based search engine was developed to allow for user-defined queries. Typical queries required between 0.01 and 0.02 seconds, with at least two orders of magnitude improvement in speed over conventional queries. This powerful and innovative structure will facilitate research on large-scale time-oriented medical databases.

  7. MapApp: A Java(TM) Applet for Accessing Geographic Databases

    NASA Astrophysics Data System (ADS)

    Haxby, W.; Carbotte, S.; Ryan, W. B.; OHara, S.

    2001-12-01

    MapApp (http://coast.ldeo.columbia.edu/help/MapApp.html) is a prototype Java(TM) applet that is intended to give easy and versatile access to geographic data sets through a web browser. It was developed initially to interface with the RIDGE Multibeam Synthesis. Subsequently, interfaces with other geophysical databases were added. At present, multibeam bathymetry grids, underway geophysics along ship tracks, and the LDEO Borehole Research Group's ODP well logging database are accessible through MapApp. We plan to add an interface with the Ridge Petrology Database in the near future. The central component of MapApp is a world physiographic map. Users may navigate around the map (zoom/pan) without waiting for HTTP requests to a remote server to be processed. A focus request loads image tiles from the server to compose a new map at the current viewing resolution. Areas in which multibeam grids are available may be focused to a pixel resolution of about 200 m. These areas may be identified by toggling a mask. Databases may be accessed through menus, and selected data objects may be loaded into MapApp by selecting items from tables. Once loaded, a bathymetry grid may be contoured or used to create bathymetric profiles; ship tracks and ODP sites may be overlain on the map and their geophysical data plotted in X-Y graphs. The advantage of applets over traditional web pages is that they permit dynamic interaction with data sets, while limiting time consuming interaction with a remote server. Users may customize the graphics display by modifying the scale, or the symbol or line characteristics of rendered data, contour interval, etc. The ease with which users can select areas, view the physiography of areas, and preview data sets and evaluate them for quality and applicability, makes MapApp a valuable tool for education and research.

  8. MINEs: Open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

    SciTech Connect

    Jeffryes, James G.; Colastani, Ricardo L.; Elbadawi-Sidhu, Mona; Kind, Tobias; Niehaus, Thomas D.; Broadbelt, Linda J.; Hanson, Andrew D.; Fiehn, Oliver; Tyo, Keith E. J.; Henry, Christopher S.

    2015-08-28

    Metabolomics have proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography–mass spectrometry (LC–MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and that new metabolites are seldom discovered in untargeted studies. These challenges require new approaches that consider compounds beyond those available in curated biochemistry databases. Here we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and common biochemical reactions. We utilize an algorithm called the Biochemical Network Integrated Computational Explorer (BNICE) and expert-curated reaction rules based on the Enzyme Commission classification system to propose the novel chemical structures and reactions that comprise MINE databases. Starting from the Kyoto Encyclopedia of Genes and Genomes (KEGG) COMPOUND database, the MINE contains over 571,000 compounds, of which 93% are not present in the PubChem database. However, these MINE compounds have on average higher structural similarity to natural products than compounds from KEGG or PubChem. MINE databases were able to propose annotations for 98.6% of a set of 667 MassBank spectra, 14% more than KEGG alone and equivalent to PubChem while returning far fewer candidates per spectra than PubChem (46 vs. 1715 median candidates). Application of MINEs to LC–MS accurate mass data enabled the identity of an unknown peak to be confidently predicted. MINE databases are freely accessible for non-commercial use via user-friendly web-tools at http://minedatabase.mcs.anl.gov and developer-friendly APIs. MINEs improve metabolomics peak identification as compared to general chemical databases whose results

  9. MINEs: Open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

    DOE PAGESBeta

    Jeffryes, James G.; Colastani, Ricardo L.; Elbadawi-Sidhu, Mona; Kind, Tobias; Niehaus, Thomas D.; Broadbelt, Linda J.; Hanson, Andrew D.; Fiehn, Oliver; Tyo, Keith E. J.; Henry, Christopher S.

    2015-08-28

    Metabolomics have proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography–mass spectrometry (LC–MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and that new metabolites are seldom discovered in untargeted studies. These challenges require new approaches that consider compounds beyond those available in curated biochemistry databases. Here we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likelymore » to occur based on known metabolites and common biochemical reactions. We utilize an algorithm called the Biochemical Network Integrated Computational Explorer (BNICE) and expert-curated reaction rules based on the Enzyme Commission classification system to propose the novel chemical structures and reactions that comprise MINE databases. Starting from the Kyoto Encyclopedia of Genes and Genomes (KEGG) COMPOUND database, the MINE contains over 571,000 compounds, of which 93% are not present in the PubChem database. However, these MINE compounds have on average higher structural similarity to natural products than compounds from KEGG or PubChem. MINE databases were able to propose annotations for 98.6% of a set of 667 MassBank spectra, 14% more than KEGG alone and equivalent to PubChem while returning far fewer candidates per spectra than PubChem (46 vs. 1715 median candidates). Application of MINEs to LC–MS accurate mass data enabled the identity of an unknown peak to be confidently predicted. MINE databases are freely accessible for non-commercial use via user-friendly web-tools at http://minedatabase.mcs.anl.gov and developer-friendly APIs. MINEs improve metabolomics peak identification as compared to general chemical databases whose

  10. Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections ▿

    PubMed Central

    O'Donnell, Kerry; Sutton, Deanna A.; Rinaldi, Michael G.; Sarver, Brice A. J.; Balajee, S. Arunmozhi; Schroers, Hans-Josef; Summerbell, Richard C.; Robert, Vincent A. R. G.; Crous, Pedro W.; Zhang, Ning; Aoki, Takayuki; Jung, Kyongyong; Park, Jongsun; Lee, Yong-Hwan; Kang, Seogchan; Park, Bongsoo; Geiser, David M.

    2010-01-01

    Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1α (EF-1α), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate's clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the

  11. Internet-accessible DNA sequence database for identifying fusaria from human and animal infections.

    PubMed

    O'Donnell, Kerry; Sutton, Deanna A; Rinaldi, Michael G; Sarver, Brice A J; Balajee, S Arunmozhi; Schroers, Hans-Josef; Summerbell, Richard C; Robert, Vincent A R G; Crous, Pedro W; Zhang, Ning; Aoki, Takayuki; Jung, Kyongyong; Park, Jongsun; Lee, Yong-Hwan; Kang, Seogchan; Park, Bongsoo; Geiser, David M

    2010-10-01

    Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1α (EF-1α), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate's clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the

  12. Data Model and Relational Database Design for Highway Runoff Water-Quality Metadata

    USGS Publications Warehouse

    Granato, Gregory E.; Tessler, Steven

    2001-01-01

    A National highway and urban runoff waterquality metadatabase was developed by the U.S. Geological Survey in cooperation with the Federal Highway Administration as part of the National Highway Runoff Water-Quality Data and Methodology Synthesis (NDAMS). The database was designed to catalog available literature and to document results of the synthesis in a format that would facilitate current and future research on highway and urban runoff. This report documents the design and implementation of the NDAMS relational database, which was designed to provide a catalog of available information and the results of an assessment of the available data. All the citations and the metadata collected during the review process are presented in a stratified metadatabase that contains citations for relevant publications, abstracts (or previa), and reportreview metadata for a sample of selected reports that document results of runoff quality investigations. The database is referred to as a metadatabase because it contains information about available data sets rather than a record of the original data. The database contains the metadata needed to evaluate and characterize how valid, current, complete, comparable, and technically defensible published and available information may be when evaluated for application to the different dataquality objectives as defined by decision makers. This database is a relational database, in that all information is ultimately linked to a given citation in the catalog of available reports. The main database file contains 86 tables consisting of 29 data tables, 11 association tables, and 46 domain tables. The data tables all link to a particular citation, and each data table is focused on one aspect of the information collected in the literature search and the evaluation of available information. This database is implemented in the Microsoft (MS) Access database software because it is widely used within and outside of government and is familiar to many

  13. BioSYNTHESIS: access to a knowledge network of health sciences databases.

    PubMed

    Broering, N C; Hylton, J S; Guttmann, R; Eskridge, D

    1991-04-01

    Users of the IAIMS Knowledge Network at the Georgetown University Medical Center have access to multiple in-house and external databases from a single point of entry through BioSYNTHESIS. The IAIMS project has developed a rich environment of biomedical information resources that represent a medical decision support system for campus physicians and students. The BioSYNTHESIS system is an information navigator that provides transparent access to a Knowledge Network of over a dozen databases. These multiple health sciences databases consist of bibliographic, informational, diagnostic, and research systems which reside on diverse computers such as DEC VAXs, SUN 490, AT&T 3B2s, Macintoshes, IBM PC/PS2s and the AT&T ISN and SYTEK network systems. Ethernet and TCP/IP protocols are used in the network architecture. BioSYNTHESIS also provides network links to the other campus libraries and to external institutions. As additional knowledge resources and technological advances have become available. BioSYNTHESIS has evolved from a two phase to a three phase program. Major components of the system including recent achievements and future plans are described. PMID:1661772

  14. Federated web-accessible clinical data management within an extensible neuroimaging database.

    PubMed

    Ozyurt, I Burak; Keator, David B; Wei, Dingying; Fennema-Notestine, Christine; Pease, Karen R; Bockholt, Jeremy; Grethe, Jeffrey S

    2010-12-01

    Managing vast datasets collected throughout multiple clinical imaging communities has become critical with the ever increasing and diverse nature of datasets. Development of data management infrastructure is further complicated by technical and experimental advances that drive modifications to existing protocols and acquisition of new types of research data to be incorporated into existing data management systems. In this paper, an extensible data management system for clinical neuroimaging studies is introduced: The Human Clinical Imaging Database (HID) and Toolkit. The database schema is constructed to support the storage of new data types without changes to the underlying schema. The complex infrastructure allows management of experiment data, such as image protocol and behavioral task parameters, as well as subject-specific data, including demographics, clinical assessments, and behavioral task performance metrics. Of significant interest, embedded clinical data entry and management tools enhance both consistency of data reporting and automatic entry of data into the database. The Clinical Assessment Layout Manager (CALM) allows users to create on-line data entry forms for use within and across sites, through which data is pulled into the underlying database via the generic clinical assessment management engine (GAME). Importantly, the system is designed to operate in a distributed environment, serving both human users and client applications in a service-oriented manner. Querying capabilities use a built-in multi-database parallel query builder/result combiner, allowing web-accessible queries within and across multiple federated databases. The system along with its documentation is open-source and available from the Neuroimaging Informatics Tools and Resource Clearinghouse (NITRC) site. PMID:20567938

  15. Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database

    PubMed Central

    Keator, David B.; Wei, Dingying; Fennema-Notestine, Christine; Pease, Karen R.; Bockholt, Jeremy; Grethe, Jeffrey S.

    2010-01-01

    Managing vast datasets collected throughout multiple clinical imaging communities has become critical with the ever increasing and diverse nature of datasets. Development of data management infrastructure is further complicated by technical and experimental advances that drive modifications to existing protocols and acquisition of new types of research data to be incorporated into existing data management systems. In this paper, an extensible data management system for clinical neuroimaging studies is introduced: The Human Clinical Imaging Database (HID) and Toolkit. The database schema is constructed to support the storage of new data types without changes to the underlying schema. The complex infrastructure allows management of experiment data, such as image protocol and behavioral task parameters, as well as subject-specific data, including demographics, clinical assessments, and behavioral task performance metrics. Of significant interest, embedded clinical data entry and management tools enhance both consistency of data reporting and automatic entry of data into the database. The Clinical Assessment Layout Manager (CALM) allows users to create on-line data entry forms for use within and across sites, through which data is pulled into the underlying database via the generic clinical assessment management engine (GAME). Importantly, the system is designed to operate in a distributed environment, serving both human users and client applications in a service-oriented manner. Querying capabilities use a built-in multi-database parallel query builder/result combiner, allowing web-accessible queries within and across multiple federated databases. The system along with its documentation is open-source and available from the Neuroimaging Informatics Tools and Resource Clearinghouse (NITRC) site. PMID:20567938

  16. The representation of manipulable solid objects in a relational database

    NASA Technical Reports Server (NTRS)

    Bahler, D.

    1984-01-01

    This project is concerned with the interface between database management and solid geometric modeling. The desirability of integrating computer-aided design, manufacture, testing, and management into a coherent system is by now well recognized. One proposed configuration for such a system uses a relational database management system as the central focus; the various other functions are linked through their use of a common data repesentation in the data manager, rather than communicating pairwise to integrate a geometric modeling capability with a generic relational data managemet system in such a way that well-formed questions can be posed and answered about the performance of the system as a whole. One necessary feature of any such system is simplification for purposes of anaysis; this and system performance considerations meant that a paramount goal therefore was that of unity and simplicity of the data structures used.

  17. Head-related transfer function database and its analyses

    NASA Astrophysics Data System (ADS)

    Xie, Bosun; Zhong, Xiaoli; Rao, Dan; Liang, Zhiqiang

    2007-06-01

    Based on the measurements from 52 Chinese subjects (26 males and 26 females), a high-spatial-resolution head-related transfer function (HRTF) database with corresponding anthropometric parameters is established. By using the database, cues relating to sound source localization, including interaural time difference (ITD), interaural level difference (ILD), and spectral features introduced by pinna, are analyzed. Moreover, the statistical relationship between ITD and anthropometric parameters is estimated. It is proved that the mean values of maximum ITD for male and female are significantly different, so are those for Chinese and western subjects. The difference in ITD is due to the difference in individual anthropometric parameters. It is further proved that the spectral features introduced by pinna strongly depend on individual; while at high frequencies (f ⩾ 5.5 kHz), HRTFs are left-right asymmetric. This work is instructive and helpful for the research on binaural hearing and applications on virtual auditory in future.

  18. Relational Database Design for Computer-Analyzed Medical Narrative

    PubMed Central

    Sager, N.; Chi, E.C.; Tick, L.J.; Lyman, M.

    1982-01-01

    A detailed analysis of the syntactic and semantic patterns of the narrative portions of patient records reveals surprising regularity in both regards. Building on these observed regularities, the NYU Linguistic String Project has programmed and tested a processor that accepts free text input and produces information-structured output, suitable for mapping (with some adjustments) into a database of the network or relational type. The first schema, a network design, was presented at the Fourth Annual Symposium on Computer Applications in Medical Care. This paper will describe the development of a relational data model which parallels the earlier CODASYL design. Experiments using SYSTEM R will be described and compared with similar experiments using DMS1100. The suitability of SQL for queries addressed to a database of natural language medical data is also discussed.

  19. DbAccess: Interactive Statistics and Graphics for Plasma Physics Databases

    SciTech Connect

    W. Davis; D. Mastrovito

    2003-10-09

    DbAccess is an X-windows application, written in IDL{reg_sign}, meeting many specialized statistical and graphical needs of NSTX [National Spherical Torus Experiment] plasma physicists, such as regression statistics and the analysis of variance. Flexible ''views'' and ''joins,'' which include options for complex SQL expressions, facilitate mixing data from different database tables. General Atomics Plot Objects add extensive graphical and interactive capabilities. An example is included for plasma confinement-time scaling analysis using a multiple linear regression least-squares power fit.

  20. TPP - An interactive database of cataclysmic variables and related objects

    NASA Astrophysics Data System (ADS)

    Kube, J.; Gänsicke, B. T.; Hoffmann, B.

    2002-01-01

    We introduce our interactive online catalogue of cataclysmic variables, historically dubbed TPP. Similar to the Downes et al. catalogue, we include all systems which have been -- even remotely -- mentioned as a cataclysmic variable. However, TPP is intended to include all the available published information on the listed systems, such as, e.g. orbital period, inclination, distance, primary and secondary masses, magnetic field strength, etc. A major difference to the established catalogues is that every member of the community can contribute information to the database. Technically speaking, the catalogue is contained in a MySQL database and accessed through a Perl script running on our web server. Hence, the user interface is displayed in the client's web browser. On July 30, 2001, our data base contained 1167 single objects with 4071 pieces of information drawn from 1958 different literature sources. Literature references are directly linked to the ADS abstract system, the arXive preprint server and the VSNET mail archive. You find TPP in the World Wide Web at TPP, where we also provide a complete user manual. TPP was made possible by using the free scripting language Perl and the free data base MySQL. A big ``thank you'' to the developers of these powerful tools and to the whole GNU community!

  1. 2016 update of the PRIDE database and its related tools

    PubMed Central

    Vizcaíno, Juan Antonio; Csordas, Attila; del-Toro, Noemi; Dianes, José A.; Griss, Johannes; Lavidas, Ilias; Mayer, Gerhard; Perez-Riverol, Yasset; Reisinger, Florian; Ternent, Tobias; Xu, Qing-Wei; Wang, Rui; Hermjakob, Henning

    2016-01-01

    The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development ‘PRIDE Cluster’ and ‘PRIDE Proteomes’, which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive. PMID:26527722

  2. An integrated database of wood-formation related genes in plants.

    PubMed

    Xu, Ting; Ma, Tao; Hu, Quanjun; Liu, Jianquan

    2015-01-01

    Wood, which consists mainly of plant cell walls, is an extremely important resource in daily lives. Genes whose products participate in the processes of cell wall and wood formation are therefore major subjects of plant science research. The Wood-Formation Related Genes database (WFRGdb, http://me.lzu.edu.cn/woodformation/) serves as a data resource center for genes involved in wood formation. To create this database, we collected plant genome data published in other online databases and predicted all cell wall and wood formation related genes using BLAST and HMMER. To date, 47 gene families and 33 transcription factors from 57 genomes (28 herbaceous, 22 woody and 7 non-vascular plants) have been covered and more than 122,000 genes have been checked and recorded. To provide easy access to these data, we have developed several search methods, which make it easy to download targeted genes or groups of genes free of charge in FASTA format. Sequence and phylogenetic analyses are also available online. WFRGdb brings together cell wall and wood formation related genes from all available plant genomes, and provides an integrative platform for gene inquiry, downloading and analysis. This database will therefore be extremely useful for those who focuses on cell wall and wood research. PMID:26078228

  3. Historical seismometry database project: A comprehensive relational database for historical seismic records

    NASA Astrophysics Data System (ADS)

    Bono, Andrea

    2007-01-01

    The recovery and preservation of the patrimony made of the instrumental registrations regarding the historical earthquakes is with no doubt a subject of great interest. This attention, besides being purely historical, must necessarily be also scientific. In fact, the availability of a great amount of parametric information on the seismic activity in a given area is a doubtless help to the seismologic researcher's activities. In this article the project of the Sismos group of the National Institute of Geophysics and Volcanology of Rome new database is presented. In the structure of the new scheme the matured experience of five years of activity is summarized. We consider it useful for those who are approaching to "recovery and reprocess" computer based facilities. In the past years several attempts on Italian seismicity have followed each other. It has almost never been real databases. Some of them have had positive success because they were well considered and organized. In others it was limited in supplying lists of events with their relative hypocentral standards. What makes this project more interesting compared to the previous work is the completeness and the generality of the managed information. For example, it will be possible to view the hypocentral information regarding a given historical earthquake; it will be possible to research the seismograms in raster, digital or digitalized format, the information on times of arrival of the phases in the various stations, the instrumental standards and so on. The relational modern logic on which the archive is based, allows the carrying out of all these operations with little effort. The database described below will completely substitute Sismos' current data bank. Some of the organizational principles of this work are similar to those that inspire the database for the real-time monitoring of the seismicity in use in the principal offices of international research. A modern planning logic in a distinctly historical

  4. A relational database of protein structures designed for flexible enquiries about conformation.

    PubMed

    Islam, S A; Sternberg, M J

    1989-03-01

    A relational database of protein structure has been developed to enable rapid and flexible enquiries about the occurrence of many aspects of protein architecture. The coordinates of 294 proteins from the Brookhaven Data Bank have been processed by standard computer programs to generate many additional terms that quantify aspects of protein structure. These terms include solvent accessibility, main-chain and side-chain dihedral angles, and secondary structure. In a relational database, the information is stored in tables with columns holding the different terms and rows holding the different entries for the terms. The different relational base tables store the information about the protein coordinate set, the different chains in the protein, the amino acid residues and ligands, the atomic coordinates, the salt bridges, the hydrogen bonds, the disulphide bridges and the close tertiary contacts. The database was established under ORACLE management system. Enquiries are constructed in ORACLE using SQL (structured query language) which is simple to use and alleviates the need for extensive computer programs. A single table can be searched for entries that meet various criteria, e.g. all protein solved to better than a given resolution. The power of the database occurs when several tables, or the entries in a single table, are cross-correlated. For example the dihedral angles of proline in the fourth position in an alpha-helix in high resolution structures can be rapidly obtained. The structural database provides a powerful tool to obtain empirical rules about protein conformation. This database of protein structures is part of a joint project between Birkbeck College and Leeds University to establish an integrated data resource of protein sequences and structures (ISIS) that encodes the complex patterns of residues and coordinates that define protein conformation. The entire data resource (ISIS) will provide a system to guide all areas of protein modelling including

  5. SPAM: A Canned Internet-Accessible Database of Interest to Solar Flare Researchers

    NASA Astrophysics Data System (ADS)

    Canfield, R. C.; Hudson, H. S.; Kiernan, E.; Metcalf, T. R.; Wulser, J.-P.

    1992-05-01

    We have established a searchable database, called SPAM (Spectroscopy and Polarimetry at Mees), which contains logs of observations made at Mees Solar Observatory (Haleakala, Maui). Of more general interest, the database also includes the Events List and Region Report from the Space Environment Laboratory (Boulder). Logs from YOHKOH are currently being added. Hence, SPAM can be used to determine, for example, whether Mees has vector magnetograms of a certain NOAA AR or whether YOHKOH has certain types of observations in specified time ranges. As well, it can be used to search the SEL database for flares with selected attributes. Included logs (and searchable attributes, in addition to date, day of year, and time) are: Mees Solar Observatory Log (instrument, NOAA AR, data type, observing setup), SEL Event List (NOAA AR, X-ray Class), SEL Region Report (NOAA AR), YOHKOH Orbit Summary, YOHKOH SXT Quiet Mode PFI Observations (latitude, longitude, X-ray and optical image size), YOHKOH Flare Observations (latitude, longitude, specific channel counts or ratios). SPAM runs on a Sun workstation at Mees Solar Observatory, and is available over Internet. Simply access (e.g., telnet) koa.ifa.hawaii.edu (128.171.167.1) from any vt100, Sun, or xterm emulator. Log on as spam (lower case); there is no password. New users are asked to read release notes and hints.

  6. NATIONAL CARBON SEQUESTRATION DATABASE AND GEOGRAPHIC INFORMATION SYSTEM (NATCARB) FORMER TITLE-MIDCONTINENT INTERACTIVE DIGITAL CARBON ATLAS AND RELATIONAL DATABASE (MIDCARB)

    SciTech Connect

    Timothy R. Carr

    2004-07-16

    This annual report describes progress in the third year of the three-year project entitled ''Midcontinent Interactive Digital Carbon Atlas and Relational Database (MIDCARB)''. The project assembled a consortium of five states (Indiana, Illinois, Kansas, Kentucky and Ohio) to construct an online distributed Relational Database Management System (RDBMS) and Geographic Information System (GIS) covering aspects of carbon dioxide (CO{sub 2}) geologic sequestration (http://www.midcarb.org). The system links the five states in the consortium into a coordinated regional database system consisting of datasets useful to industry, regulators and the public. The project has been extended and expanded as a ''NATional CARBon Sequestration Database and Geographic Information System (NATCARB)'' to provide national coverage across the Regional CO{sub 2} Partnerships, which currently cover 40 states (http://www.natcarb.org). Advanced distributed computing solutions link database servers across the five states and other publicly accessible servers (e.g., USGS) into a single system where data is maintained and enhanced at the local level but is accessed and assembled through a single Web portal and can be queried, assembled, analyzed and displayed. This project has improved the flow of data across servers and increased the amount and quality of available digital data. The online tools used in the project have improved in stability and speed in order to provide real-time display and analysis of CO{sub 2} sequestration data. The move away from direct database access to web access through eXtensible Markup Language (XML) has increased stability and security while decreasing management overhead. The MIDCARB viewer has been simplified to provide improved display and organization of the more than 125 layers and data tables that have been generated as part of the project. The MIDCARB project is a functional demonstration of distributed management of data systems that cross the boundaries

  7. NASA's Astromaterials Database: Enabling Research Through Increased Access to Sample Data, Metadata and Imagery

    NASA Technical Reports Server (NTRS)

    Evans, Cindy; Todd, Nancy

    2014-01-01

    The Astromaterials Acquisition & Curation Office at NASA's Johnson Space Center (JSC) is the designated facility for curating all of NASA's extraterrestrial samples. Today, the suite of collections includes the lunar samples from the Apollo missions, cosmic dust particles falling into the Earth's atmosphere, meteorites collected in Antarctica, comet and interstellar dust particles from the Stardust mission, asteroid particles from Japan's Hayabusa mission, solar wind atoms collected during the Genesis mission, and space-exposed hardware from several missions. To support planetary science research on these samples, JSC's Astromaterials Curation Office hosts NASA's Astromaterials Curation digital repository and data access portal [http://curator.jsc.nasa.gov/], providing descriptions of the missions and collections, and critical information about each individual sample. Our office is designing and implementing several informatics initiatives to better serve the planetary research community. First, we are re-hosting the basic database framework by consolidating legacy databases for individual collections and providing a uniform access point for information (descriptions, imagery, classification) on all of our samples. Second, we continue to upgrade and host digital compendia that summarize and highlight published findings on the samples (e.g., lunar samples, meteorites from Mars). We host high resolution imagery of samples as it becomes available, including newly scanned images of historical prints from the Apollo missions. Finally we are creating plans to collect and provide new data, including 3D imagery, point cloud data, micro CT data, and external links to other data sets on selected samples. Together, these individual efforts will provide unprecedented digital access to NASA's Astromaterials, enabling preservation of the samples through more specific and targeted requests, and supporting new planetary science research and collaborations on the samples.

  8. NATIONAL URBAN DATABASE AND ACCESS PORTAL TOOL (NUDAPT): FACILITATING ADVANCEMENTS IN URBAN METEOROLOGY AND CLIMATE MODELING WITH COMMUNITY-BASED URBAN DATABASES

    EPA Science Inventory

    We discuss the initial design and application of the National Urban Database and Access Portal Tool (NUDAPT). This new project is sponsored by the USEPA and involves collaborations and contributions from many groups from federal and state agencies, and from private and academic i...

  9. Development of a gene expression database and related analysis programs for evaluation of anticancer compounds.

    PubMed

    Ushijima, Masaru; Mashima, Tetsuo; Tomida, Akihiro; Dan, Shingo; Saito, Sakae; Furuno, Aki; Tsukahara, Satomi; Seimiya, Hiroyuki; Yamori, Takao; Matsuura, Masaaki

    2013-03-01

    Genome-wide transcriptional expression analysis is a powerful strategy for characterizing the biological activity of anticancer compounds. It is often instructive to identify gene sets involved in the activity of a given drug compound for comparison with different compounds. Currently, however, there is no comprehensive gene expression database and related application system that is; (i) specialized in anticancer agents; (ii) easy to use; and (iii) open to the public. To develop a public gene expression database of antitumor agents, we first examined gene expression profiles in human cancer cells after exposure to 35 compounds including 25 clinically used anticancer agents. Gene signatures were extracted that were classified as upregulated or downregulated after exposure to the drug. Hierarchical clustering showed that drugs with similar mechanisms of action, such as genotoxic drugs, were clustered. Connectivity map analysis further revealed that our gene signature data reflected modes of action of the respective agents. Together with the database, we developed analysis programs that calculate scores for ranking changes in gene expression and for searching statistically significant pathways from the Kyoto Encyclopedia of Genes and Genomes database in order to analyze the datasets more easily. Our database and the analysis programs are available online at our website (http://scads.jfcr.or.jp/db/cs/). Using these systems, we successfully showed that proteasome inhibitors are selectively classified as endoplasmic reticulum stress inducers and induce atypical endoplasmic reticulum stress. Thus, our public access database and related analysis programs constitute a set of efficient tools to evaluate the mode of action of novel compounds and identify promising anticancer lead compounds. PMID:23176546

  10. Complete OWL-DL Reasoning Using Relational Databases

    NASA Astrophysics Data System (ADS)

    Del Mar Roldan-Garcia, Maria; Aldana-Montes, Jose F.

    Real Semantic Web applications, such as biological tools, use large ontologies, that is, ontologies with a large number (millions) of instances. Due to the increasing development of such applications, it is necessary to provide scalable and efficient ontology querying and reasoning systems. DBOWL is a Persistent and Scalable OWL reasoner which stores ontologies and implements reasoning using a relational database. In this paper we present an extension of DBOWL that implements all inference rules for OWL-DL. Furthermore, we describe briefly the reasoning algorithms and their completeness proofs.

  11. Secure web-based access to radiology: forms and databases for fast queries

    NASA Astrophysics Data System (ADS)

    McColl, Roderick W.; Lane, Thomas J.

    2002-05-01

    Currently, Web-based access to mini-PACS or similar databases commonly utilizes either JavaScript, Java applets or ActiveX controls. Many sites do not permit applets or controls or other binary objects for fear of viruses or worms sent by malicious users. In addition, the typical CGI query mechanism requires several parameters to be sent with the http GET/POST request, which may identify the patient in some way; this in unacceptable for privacy protection. Also unacceptable are pages produced by server-side scripts which can be cached by the browser, since these may also contain sensitive information. We propose a simple mechanism for access to patient information, including images, which guarantees security of information, makes it impossible to bookmark the page, or to return to the page after some defined length of time. In addition, this mechanism is simple, therefore permitting rapid access without the need to initially download an interface such as an applet or control. In addition to image display, the design of the site allows the user to view and save movies of multi-phasic data, or to construct multi-frame datasets from entire series. These capabilities make the site attractive for research purposes such as teaching file preparation.

  12. Benchmarking NMR experiments: A relational database of protein pulse sequences

    NASA Astrophysics Data System (ADS)

    Senthamarai, Russell R. P.; Kuprov, Ilya; Pervushin, Konstantin

    2010-03-01

    Systematic benchmarking of multi-dimensional protein NMR experiments is a critical prerequisite for optimal allocation of NMR resources for structural analysis of challenging proteins, e.g. large proteins with limited solubility or proteins prone to aggregation. We propose a set of benchmarking parameters for essential protein NMR experiments organized into a lightweight (single XML file) relational database (RDB), which includes all the necessary auxiliaries (waveforms, decoupling sequences, calibration tables, setup algorithms and an RDB management system). The database is interfaced to the Spinach library ( http://spindynamics.org), which enables accurate simulation and benchmarking of NMR experiments on large spin systems. A key feature is the ability to use a single user-specified spin system to simulate the majority of deposited solution state NMR experiments, thus providing the (hitherto unavailable) unified framework for pulse sequence evaluation. This development enables predicting relative sensitivity of deposited implementations of NMR experiments, thus providing a basis for comparison, optimization and, eventually, automation of NMR analysis. The benchmarking is demonstrated with two proteins, of 170 amino acids I domain of αXβ2 Integrin and 440 amino acids NS3 helicase.

  13. Using concept maps on the World-Wide Web to access a curriculum database for problem-based learning.

    PubMed

    Patrick, T B; Worth, E R; Hardin, L E

    1996-01-01

    Development of medical school curriculum databases continues to be challenging. Representation of the instructional unit is becoming increasingly difficult due to characteristics of the problem-based learning (PBL) curricula. Curriculum databases may be used to store materials for the PBL curricula, and also to provide a delivery mechanism for those materials. However, in order to take advantage of the curriculum database as a tool for PBL, methods for accessing the curriculum database that are better suited to the information needs of students, faculty, and administrators must be developed. Concept maps are directed graph representations of conceptual relationships, and may be used to represent the content of a curriculum database. In this paper, we describe a Web application that uses Java-based concept maps was the user interface to a curriculum database. PMID:8947622

  14. TRENDS: A flight test relational database user's guide and reference manual

    NASA Technical Reports Server (NTRS)

    Bondi, M. J.; Bjorkman, W. S.; Cross, J. L.

    1994-01-01

    This report is designed to be a user's guide and reference manual for users intending to access rotocraft test data via TRENDS, the relational database system which was developed as a tool for the aeronautical engineer with no programming background. This report has been written to assist novice and experienced TRENDS users. TRENDS is a complete system for retrieving, searching, and analyzing both numerical and narrative data, and for displaying time history and statistical data in graphical and numerical formats. This manual provides a 'guided tour' and a 'user's guide' for the new and intermediate-skilled users. Examples for the use of each menu item within TRENDS is provided in the Menu Reference section of the manual, including full coverage for TIMEHIST, one of the key tools. This manual is written around the XV-15 Tilt Rotor database, but does include an appendix on the UH-60 Blackhawk database. This user's guide and reference manual establishes a referrable source for the research community and augments NASA TM-101025, TRENDS: The Aeronautical Post-Test, Database Management System, Jan. 1990, written by the same authors.

  15. Interface design challenges for single point access to diverse and dispersed science databases

    NASA Technical Reports Server (NTRS)

    Harberts, R. L.; Pfister, R. G.; Dobinson, E. R.

    1992-01-01

    Efforts to relate the diversity of terminology in science data bases in a logical way for information system interfaces are discussed. Attention is given to the NASA development of the Information Management System (V. 0 IMS), a prototypic common interface for accessing dispersed earth science data.

  16. MetaboLights: An Open-Access Database Repository for Metabolomics Data.

    PubMed

    Kale, Namrata S; Haug, Kenneth; Conesa, Pablo; Jayseelan, Kalaivani; Moreno, Pablo; Rocca-Serra, Philippe; Nainala, Venkata Chandrasekhar; Spicer, Rachel A; Williams, Mark; Li, Xuefei; Salek, Reza M; Griffin, Julian L; Steinbeck, Christoph

    2016-01-01

    MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user-friendly submission tools. PMID:27010336

  17. The CEBAF Element Database and Related Operational Software

    SciTech Connect

    Larrieu, Theodore; Slominski, Christopher; Keesee, Marie; Turner, Dennison; Joyce, Michele

    2015-09-01

    The newly commissioned 12GeV CEBAF accelerator relies on a flexible, scalable and comprehensive database to define the accelerator. This database delivers the configuration for CEBAF operational tools, including hardware checkout, the downloadable optics model, control screens, and much more. The presentation will describe the flexible design of the CEBAF Element Database (CED), its features and assorted use case examples.

  18. A web-based, relational database for studying glaciers in the Italian Alps

    NASA Astrophysics Data System (ADS)

    Nigrelli, G.; Chiarle, M.; Nuzzi, A.; Perotti, L.; Torta, G.; Giardino, M.

    2013-02-01

    Glaciers are among the best terrestrial indicators of climate change and thus glacier inventories have attracted a growing, worldwide interest in recent years. In Italy, the first official glacier inventory was completed in 1925 and 774 glacial bodies were identified. As the amount of data continues to increase, and new techniques become available, there is a growing demand for computer tools that can efficiently manage the collected data. The Research Institute for Geo-hydrological Protection of the National Research Council, in cooperation with the Departments of Computer Science and Earth Sciences of the University of Turin, created a database that provides a modern tool for storing, processing and sharing glaciological data. The database was developed according to the need of storing heterogeneous information, which can be retrieved through a set of web search queries. The database's architecture is server-side, and was designed by means of an open source software. The website interface, simple and intuitive, was intended to meet the needs of a distributed public: through this interface, any type of glaciological data can be managed, specific queries can be performed, and the results can be exported in a standard format. The use of a relational database to store and organize a large variety of information about Italian glaciers collected over the last hundred years constitutes a significant step forward in ensuring the safety and accessibility of such data. Moreover, the same benefits also apply to the enhanced operability for handling information in the future, including new and emerging types of data formats, such as geographic and multimedia files. Future developments include the integration of cartographic data, such as base maps, satellite images and vector data. The relational database described in this paper will be the heart of a new geographic system that will merge data, data attributes and maps, leading to a complete description of Italian glacial

  19. An Efficient Method for the Retrieval of Objects by Topological Relations in Spatial Database Systems.

    ERIC Educational Resources Information Center

    Lin, P. L.; Tan, W. H.

    2003-01-01

    Presents a new method to improve the performance of query processing in a spatial database. Experiments demonstrated that performance of database systems can be improved because both the number of objects accessed and number of objects requiring detailed inspection are much less than those in the previous approach. (AEF)

  20. Data model and relational database design for the New England Water-Use Data System (NEWUDS)

    USGS Publications Warehouse

    Tessler, Steven

    2001-01-01

    The New England Water-Use Data System (NEWUDS) is a database for the storage and retrieval of water-use data. NEWUDS can handle data covering many facets of water use, including (1) tracking various types of water-use activities (withdrawals, returns, transfers, distributions, consumptive-use, wastewater collection, and treatment); (2) the description, classification and location of places and organizations involved in water-use activities; (3) details about measured or estimated volumes of water associated with water-use activities; and (4) information about data sources and water resources associated with water use. In NEWUDS, each water transaction occurs unidirectionally between two site objects, and the sites and conveyances form a water network. The core entities in the NEWUDS model are site, conveyance, transaction/rate, location, and owner. Other important entities include water resources (used for withdrawals and returns), data sources, and aliases. Multiple water-exchange estimates can be stored for individual transactions based on different methods or data sources. Storage of user-defined details is accommodated for several of the main entities. Numerous tables containing classification terms facilitate detailed descriptions of data items and can be used for routine or custom data summarization. NEWUDS handles single-user and aggregate-user water-use data, can be used for large or small water-network projects, and is available as a stand-alone Microsoft? Access database structure. Users can customize and extend the database, link it to other databases, or implement the design in other relational database applications.

  1. For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases.

    PubMed

    Liljekvist, Mads Svane; Andresen, Kristoffer; Pommergaard, Hans-Christian; Rosenberg, Jacob

    2015-01-01

    Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases' criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ's coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined. Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ. Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases

  2. Accessing Data Resources in the Mouse Phenome Database for Genetic Analysis of Murine Life Span and Health Span.

    PubMed

    Bogue, Molly A; Peters, Luanne L; Paigen, Beverly; Korstanje, Ron; Yuan, Rong; Ackert-Bicknell, Cheryl; Grubb, Stephen C; Churchill, Gary A; Chesler, Elissa J

    2016-02-01

    Understanding the source of genetic variation in aging and using this variation to define the molecular mechanisms of healthy aging require deep and broad quantification of a host of physiological, morphological, and behavioral endpoints. The murine model is a powerful system in which to understand the relations across age-related phenotypes and to identify research models with variation in life span and health span. The Jackson Laboratory Nathan Shock Center of Excellence in the Basic Biology of Aging has performed broad characterization of aging in genetically diverse laboratory mice and has placed these data, along with data from several other major aging initiatives, into the interactive Mouse Phenome Database. The data may be accessed and analyzed by researchers interested in finding mouse models for specific aging processes, age-related health and disease states, and for genetic analysis of aging variation and trait covariation. We expect that by placing these data in the hands of the aging community that there will be (a) accelerated genetic analyses of aging processes, (b) discovery of genetic loci regulating life span, (c) identification of compelling correlations between life span and susceptibility for age-related disorders, and (d) discovery of concordant genomic loci influencing life span and aging phenotypes between mouse and humans. PMID:25533306

  3. Accessing Data Resources in the Mouse Phenome Database for Genetic Analysis of Murine Life Span and Health Span

    PubMed Central

    Peters, Luanne L.; Paigen, Beverly; Korstanje, Ron; Yuan, Rong; Ackert-Bicknell, Cheryl; Grubb, Stephen C.; Churchill, Gary A.; Chesler, Elissa J.

    2016-01-01

    Understanding the source of genetic variation in aging and using this variation to define the molecular mechanisms of healthy aging require deep and broad quantification of a host of physiological, morphological, and behavioral endpoints. The murine model is a powerful system in which to understand the relations across age-related phenotypes and to identify research models with variation in life span and health span. The Jackson Laboratory Nathan Shock Center of Excellence in the Basic Biology of Aging has performed broad characterization of aging in genetically diverse laboratory mice and has placed these data, along with data from several other major aging initiatives, into the interactive Mouse Phenome Database. The data may be accessed and analyzed by researchers interested in finding mouse models for specific aging processes, age-related health and disease states, and for genetic analysis of aging variation and trait covariation. We expect that by placing these data in the hands of the aging community that there will be (a) accelerated genetic analyses of aging processes, (b) discovery of genetic loci regulating life span, (c) identification of compelling correlations between life span and susceptibility for age-related disorders, and (d) discovery of concordant genomic loci influencing life span and aging phenotypes between mouse and humans. PMID:25533306

  4. FACILITATING ADVANCED URBAN METEOROLOGY AND AIR QUALITY MODELING CAPABILITIES WITH HIGH RESOLUTION URBAN DATABASE AND ACCESS PORTAL TOOLS

    EPA Science Inventory

    Information of urban morphological features at high resolution is needed to properly model and characterize the meteorological and air quality fields in urban areas. We describe a new project called National Urban Database with Access Portal Tool, (NUDAPT) that addresses this nee...

  5. For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases

    PubMed Central

    Andresen, Kristoffer; Pommergaard, Hans-Christian; Rosenberg, Jacob

    2015-01-01

    Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases’ criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ’s coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined. Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ. Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical

  6. Managing Large Scale Project Analysis Teams through a Web Accessible Database

    NASA Technical Reports Server (NTRS)

    O'Neil, Daniel A.

    2008-01-01

    Large scale space programs analyze thousands of requirements while mitigating safety, performance, schedule, and cost risks. These efforts involve a variety of roles with interdependent use cases and goals. For example, study managers and facilitators identify ground-rules and assumptions for a collection of studies required for a program or project milestone. Task leaders derive product requirements from the ground rules and assumptions and describe activities to produce needed analytical products. Disciplined specialists produce the specified products and load results into a file management system. Organizational and project managers provide the personnel and funds to conduct the tasks. Each role has responsibilities to establish information linkages and provide status reports to management. Projects conduct design and analysis cycles to refine designs to meet the requirements and implement risk mitigation plans. At the program level, integrated design and analysis cycles studies are conducted to eliminate every 'to-be-determined' and develop plans to mitigate every risk. At the agency level, strategic studies analyze different approaches to exploration architectures and campaigns. This paper describes a web-accessible database developed by NASA to coordinate and manage tasks at three organizational levels. Other topics in this paper cover integration technologies and techniques for process modeling and enterprise architectures.

  7. miSolRNA: A tomato micro RNA relational database

    PubMed Central

    2010-01-01

    Background The economic importance of Solanaceae plant species is well documented and tomato has become a model for functional genomics studies. In plants, important processes are regulated by microRNAs (miRNA). Description We describe here a data base integrating genetic map positions of miRNA-targeted genes, their expression profiles and their relations with quantitative fruit metabolic loci and yield associated traits. miSolRNA provides a metadata source to facilitate the construction of hypothesis aimed at defining physiological modes of action of regulatory process underlying the metabolism of the tomato fruit. Conclusions The MiSolRNA database allows the simple extraction of metadata for the proposal of new hypothesis concerning possible roles of miRNAs in the regulation of tomato fruit metabolism. It permits i) to map miRNAs and their predicted target sites both on expressed (SGN-UNIGENES) and newly annotated sequences (BAC sequences released), ii) to co-locate any predicted miRNA-target interaction with metabolic QTL found in tomato fruits, iii) to retrieve expression data of target genes in tomato fruit along their developmental period and iv) to design further experiments for unresolved questions in complex trait biology based on the use of genetic materials that have been proven to be a useful tools for map-based cloning experiments in Solanaceae plant species. PMID:21059227

  8. Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration

    PubMed Central

    Gražulis, Saulius; Daškevič, Adriana; Merkys, Andrius; Chateigner, Daniel; Lutterotti, Luca; Quirós, Miguel; Serebryanaya, Nadezhda R.; Moeck, Peter; Downs, Robert T.; Le Bail, Armel

    2012-01-01

    Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge. PMID:22070882

  9. SchizConnect: Mediating neuroimaging databases on schizophrenia and related disorders for large-scale integration.

    PubMed

    Wang, Lei; Alpert, Kathryn I; Calhoun, Vince D; Cobia, Derin J; Keator, David B; King, Margaret D; Kogan, Alexandr; Landis, Drew; Tallis, Marcelo; Turner, Matthew D; Potkin, Steven G; Turner, Jessica A; Ambite, Jose Luis

    2016-01-01

    SchizConnect (www.schizconnect.org) is built to address the issues of multiple data repositories in schizophrenia neuroimaging studies. It includes a level of mediation--translating across data sources--so that the user can place one query, e.g. for diffusion images from male individuals with schizophrenia, and find out from across participating data sources how many datasets there are, as well as downloading the imaging and related data. The current version handles the Data Usage Agreements across different studies, as well as interpreting database-specific terminologies into a common framework. New data repositories can also be mediated to bring immediate access to existing datasets. Compared with centralized, upload data sharing models, SchizConnect is a unique, virtual database with a focus on schizophrenia and related disorders that can mediate live data as information is being updated at each data source. It is our hope that SchizConnect can facilitate testing new hypotheses through aggregated datasets, promoting discovery related to the mechanisms underlying schizophrenic dysfunction. PMID:26142271

  10. RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database.

    PubMed

    Field, Helen I; Fenyö, David; Beavis, Ronald C

    2002-01-01

    RADARS, a rapid, automated, data archiving and retrieval software system for high-throughput proteomic mass spectral data processing and storage, is described. The majority of mass spectrometer data files are compatible with RADARS, for consistent processing. The system automatically takes unprocessed data files, identifies proteins via in silico database searching, then stores the processed data and search results in a relational database suitable for customized reporting. The system is robust, used in 24/7 operation, accessible to multiple users of an intranet through a web browser, may be monitored by Virtual Private Network, and is secure. RADARS is scalable for use on one or many computers, and is suited to multiple processor systems. It can incorporate any local database in FASTA format, and can search protein and DNA databases online. A key feature is a suite of visualisation tools (many available gratis), allowing facile manipulation of spectra, by hand annotation, reanalysis, and access to all procedures. We also described the use of Sonar MS/MS, a novel, rapid search engine requiring 40 MB RAM per process for searches against a genomic or EST database translated in all six reading frames. RADARS reduces the cost of analysis by its efficient algorithms: Sonar MS/MS can identifiy proteins without accurate knowledge of the parent ion mass and without protein tags. Statistical scoring methods provide close-to-expert accuracy and brings robust data analysis to the non-expert user. PMID:11788990

  11. Relational Databases: A Transparent Framework for Encouraging Biology Students to Think Informatically

    ERIC Educational Resources Information Center

    Rice, Michael; Gladstone, William; Weir, Michael

    2004-01-01

    We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a…

  12. Simple Logic for Big Problems: An Inside Look at Relational Databases.

    ERIC Educational Resources Information Center

    Seba, Douglas B.; Smith, Pat

    1982-01-01

    Discusses database design concept termed "normalization" (process replacing associations between data with associations in two-dimensional tabular form) which results in formation of relational databases (they are to computers what dictionaries are to spoken languages). Applications of the database in serials control and complex systems are noted.…

  13. Displaying bias in sampling effort of data accessed from biodiversity databases using ignorance maps

    PubMed Central

    2015-01-01

    Abstract Background Open-access biodiversity databases including mainly citizen science data make temporally and spatially extensive species’ observation data available to a wide range of users. Such data have limitations however, which include: sampling bias in favour of recorder distribution, lack of survey effort assessment, and lack of coverage of the distribution of all organisms. These limitations are not always recorded, while any technical assessment or scientific research based on such data should include an evaluation of the uncertainty of its source data and researchers should acknowledge this information in their analysis. The here proposed maps of ignorance are a critical and easy way to implement a tool to not only visually explore the quality of the data, but also to filter out unreliable results. New information I present simple algorithms to display ignorance maps as a tool to report the spatial distribution of the bias and lack of sampling effort across a study region. Ignorance scores are expressed solely based on raw data in order to rely on the fewest assumptions possible. Therefore there is no prediction or estimation involved. The rationale is based on the assumption that it is appropriate to use species groups as a surrogate for sampling effort because it is likely that an entire group of species observed by similar methods will share similar bias. Simple algorithms are then used to transform raw data into ignorance scores scaled 0-1 that are easily comparable and scalable. Because of the need to perform calculations over big datasets, simplicity is crucial for web-based implementations on infrastructures for biodiversity information. With these algorithms, any infrastructure for biodiversity information can offer a quality report of the observations accessed through them. Users can specify a reference taxonomic group and a time frame according to the research question. The potential of this tool lies in the simplicity of its algorithms

  14. The Virtual Skeleton Database: An Open Access Repository for Biomedical Research and Collaboration

    PubMed Central

    Bonaretti, Serena; Pfahrer, Marcel; Niklaus, Roman; Büchler, Philippe

    2013-01-01

    Background Statistical shape models are widely used in biomedical research. They are routinely implemented for automatic image segmentation or object identification in medical images. In these fields, however, the acquisition of the large training datasets, required to develop these models, is usually a time-consuming process. Even after this effort, the collections of datasets are often lost or mishandled resulting in replication of work. Objective To solve these problems, the Virtual Skeleton Database (VSD) is proposed as a centralized storage system where the data necessary to build statistical shape models can be stored and shared. Methods The VSD provides an online repository system tailored to the needs of the medical research community. The processing of the most common image file types, a statistical shape model framework, and an ontology-based search provide the generic tools to store, exchange, and retrieve digital medical datasets. The hosted data are accessible to the community, and collaborative research catalyzes their productivity. Results To illustrate the need for an online repository for medical research, three exemplary projects of the VSD are presented: (1) an international collaboration to achieve improvement in cochlear surgery and implant optimization, (2) a population-based analysis of femoral fracture risk between genders, and (3) an online application developed for the evaluation and comparison of the segmentation of brain tumors. Conclusions The VSD is a novel system for scientific collaboration for the medical image community with a data-centric concept and semantically driven search option for anatomical structures. The repository has been proven to be a useful tool for collaborative model building, as a resource for biomechanical population studies, or to enhance segmentation algorithms. PMID:24220210

  15. Relational database for the space plasma data collected by the SACI-1 mission

    NASA Astrophysics Data System (ADS)

    de Fatima Mattiello Francisco, Maria; Angelo da Costa F. Neri, Jose; Pereira, Romualdo A., Jr.

    1997-09-01

    The study of the space plasma environment is the goal of the experiments named: PLASMEX, ORCAS, MAGNEX and PHOTO. They constitute the payload of the first small Brazilian satellite for scientific applications (SACI-1). The SACI-1 is a low earth polar orbit satellite which shall be launched as China- Brazil Earth Resource Satellite (CBERS) piggyback, by the Chinese launcher Long March IV, in the beginning of 1998. All the space plasma data measured by the SACI-1 payload will be received and archived in the SACI-1 Ground Station by a software system which uses the relational data modeling to build the system database. Focusing on the space plasma data base, this article describes the Ground Station software facilities such as: quick-looks of the SACI-1 remote sensing data and the data access in raw form from the investigators, via Internet.

  16. DDRprot: a database of DNA damage response-related proteins

    PubMed Central

    Andrés-León, Eduardo; Cases, Ildefonso; Arcas, Aida; Rojas, Ana M.

    2016-01-01

    The DNA Damage Response (DDR) signalling network is an essential system that protects the genome’s integrity. The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. For each particular DDR protein, we present detailed information about its function. If involved in post-translational modifications (PTMs) with each other, we depict the position of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins. All this information is linked to the original publication from where it was obtained. Phylogenetic information is also shown, including time of emergence and conservation across 47 selected species, family trees and sequence alignments of homologues. The DDRprot database can be queried by different criteria: pathways, species, evolutionary age or involvement in (PTM). Sequence searches using hidden Markov models can be also used. Database URL: http://ddr.cbbio.es. PMID:27577567

  17. DDRprot: a database of DNA damage response-related proteins.

    PubMed

    Andrés-León, Eduardo; Cases, Ildefonso; Arcas, Aida; Rojas, Ana M

    2016-01-01

    The DNA Damage Response (DDR) signalling network is an essential system that protects the genome's integrity. The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. For each particular DDR protein, we present detailed information about its function. If involved in post-translational modifications (PTMs) with each other, we depict the position of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins. All this information is linked to the original publication from where it was obtained. Phylogenetic information is also shown, including time of emergence and conservation across 47 selected species, family trees and sequence alignments of homologues. The DDRprot database can be queried by different criteria: pathways, species, evolutionary age or involvement in (PTM). Sequence searches using hidden Markov models can be also used.Database URL: http://ddr.cbbio.es. PMID:27577567

  18. Evaluating parallel relational databases for medical data analysis.

    SciTech Connect

    Rintoul, Mark Daniel; Wilson, Andrew T.

    2012-03-01

    Hospitals have always generated and consumed large amounts of data concerning patients, treatment and outcomes. As computers and networks have permeated the hospital environment it has become feasible to collect and organize all of this data. This raises naturally the question of how to deal with the resulting mountain of information. In this report we detail a proof-of-concept test using two commercially available parallel database systems to analyze a set of real, de-identified medical records. We examine database scalability as data sizes increase as well as responsiveness under load from multiple users.

  19. Glia Open Access Database (GOAD): A comprehensive gene expression encyclopedia of glia cells in health and disease.

    PubMed

    Holtman, Inge R; Noback, Michiel; Bijlsma, Marieke; Duong, Kim N; van der Geest, Marije A; Ketelaars, Peer T; Brouwer, Nieske; Vainchtein, Ilia D; Eggen, Bart J L; Boddeke, Hendrikus W G M

    2015-09-01

    Recently, the number of genome-wide transcriptome profiles of pure populations of glia cells has drastically increased, resulting in an unprecedented amount of data that offer opportunities to study glia phenotypes and functions in health and disease. To make genome-wide transcriptome data easily accessible, we developed the Glia Open Access Database (GOAD), available via www.goad.education. GOAD contains a collection of previously published and unpublished transcriptome data, including datasets from isolated microglia, astrocytes and oligodendrocytes both at homeostatic and pathological conditions. It contains an intuitive web-based interface that consists of three features that enable searching, browsing, analyzing, and downloading of the data. The first feature is differential gene expression (DE) analysis that provides genes that are significantly up and down-regulated with the associated fold changes and p-values between two conditions of interest. In addition, an interactive Venn diagram is generated to illustrate the overlap and differences between several DE gene lists. The second feature is quantitative gene expression (QE) analysis, to investigate which genes are expressed in a particular glial cell type and to what degree. The third feature is a search utility, which can be used to find a gene of interest and depict its expression in all available expression data sets by generating a gene card. In addition, quality guidelines and relevant concepts for transcriptome analysis are discussed. Finally, GOAD is discussed in relation to several online transcriptome tools developed in neuroscience and immunology. In conclusion, GOAD is a unique platform to facilitate integration of bioinformatics in glia biology. PMID:25808223

  20. Development of a Relational Database for Learning Management Systems

    ERIC Educational Resources Information Center

    Deperlioglu, Omer; Sarpkaya, Yilmaz; Ergun, Ertugrul

    2011-01-01

    In today's world, Web-Based Distance Education Systems have a great importance. Web-based Distance Education Systems are usually known as Learning Management Systems (LMS). In this article, a database design, which was developed to create an educational institution as a Learning Management System, is described. In this sense, developed Learning…

  1. An Analysis of the Vulnerability of Global Drinking Water Access to Climate-related Hazards

    NASA Astrophysics Data System (ADS)

    Elliott, M.; Banerjee, O.; Christenson, E.; Holcomb, D.; Hamrick, L.; Bartram, J.

    2014-12-01

    Global drinking water access targets are formulated around "sustainable access." Global climate change (GCC) and associated hazards threaten the sustainability of drinking water supply. Extensive literature exists on the impacts of GCC on precipitation and water resources. However, the literature lacks a credible analysis of the vulnerability of global drinking water access. This research reports on an analysis of the current vulnerability of drinking water access due to three climate-related hazardous events: cyclone, drought and flood. An ArcGIS database was built incorporating the following: population density, hazardous event frequency, drinking water technologies in use and adaptive capacity. Two global grids were incorporated first: (1) LandScanTM global population distribution; and (2) frequency of cyclone, drought and flood from ~1980-2000 from Columbia University Center for Hazards Risk Research (CHRR). Population density was used to characterize cells as urban or rural and country-level urban/rural drinking water technologies in use were added based on the WHO/UNICEF Joint Monitoring Programme data. Expert assessment of the resilience of each technology to each hazardous event based on WHO/DFID Vision 2030 were quantified and added to the database. Finally, country-level adaptive capacity was drawn from the "readiness" parameter of the Global Adaptation Index (GaIn). ArcGIS Model Builder and Python were used to automate the addition of datasets. This presentation will report on the results of this analysis, the first credible attempt to assess the vulnerability of global drinking water access to climate-related hazardous events. This analysis has yielded country-level scores and maps displaying the ranking of exposure score (for flood, drought, cyclone, and all three in aggregate) and the corresponding country-level vulnerability scores and rankings incorporating the impact of drinking water technologies and adaptive capacity (Figure 1).

  2. ExpoCastDB: A Publicly Accessible Database for Observational Exposure Data

    EPA Science Inventory

    The application of environmental informatics tools for human health risk assessment will require the development of advanced exposure information technology resources. Exposure data for chemicals is often not readily accessible. There is a pressing need for easily accessible, che...

  3. Electronic Journals in Aggregated Collections: Providing Access through the Catalog and a Cold Fusion Database

    ERIC Educational Resources Information Center

    Anderson, Sue

    2005-01-01

    Patrons in academic libraries want convenient 24-hour access to full-text journals in a rapid, convenient manner. They want "anytime, anywhere" access to information and they do not want to enter a library to obtain it. This article describes how Eastern Washington University Libraries provide access to full-text journals through several…

  4. Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease

    PubMed Central

    Moskalev, Alexey; Chernyagina, Elizaveta; de Magalhães, João Pedro; Barardo, Diogo; Thoppil, Harikrishnan; Shaposhnikov, Mikhail; Budovsky, Arie; Fraifeld, Vadim E.; Garazha, Andrew; Tsvetkov, Vasily; Bronovitsky, Evgeny; Bogomolov, Vladislav; Scerbacov, Alexei; Kuryan, Oleg; Gurinovich, Roman; Jellen, Leslie C.; Kennedy, Brian; Mamoshina, Polina; Dobrovolskaya, Evgeniya; Aliper, Alex; Kaminsky, Dmitry; Zhavoronkov, Alex

    2015-01-01

    As the level of interest in aging research increases, there is a growing number of geroprotectors, or therapeutic interventions that aim to extend the healthy lifespan and repair or reduce aging-related damage in model organisms and, eventually, in humans. There is a clear need for a manually-curated database of geroprotectors to compile and index their effects on aging and age-related diseases and link these effects to relevant studies and multiple biochemical and drug databases. Here, we introduce the first such resource, Geroprotectors (http://geroprotectors.org). Geroprotectors is a public, rapidly explorable database that catalogs over 250 experiments involving over 200 known or candidate geroprotectors that extend lifespan in model organisms. Each compound has a comprehensive profile complete with biochemistry, mechanisms, and lifespan effects in various model organisms, along with information ranging from chemical structure, side effects, and toxicity to FDA drug status. These are presented in a visually intuitive, efficient framework fit for casual browsing or in-depth research alike. Data are linked to the source studies or databases, providing quick and convenient access to original data. The Geroprotectors database facilitates cross-study, cross-organism, and cross-discipline analysis and saves countless hours of inefficient literature and web searching. Geroprotectors is a one-stop, knowledge-sharing, time-saving resource for researchers seeking healthy aging solutions. PMID:26342919

  5. Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase

    PubMed Central

    2009-01-01

    Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as

  6. A Quantitative Analysis of the Extrinsic and Intrinsic Turnover Factors of Relational Database Support Professionals

    ERIC Educational Resources Information Center

    Takusi, Gabriel Samuto

    2010-01-01

    This quantitative analysis explored the intrinsic and extrinsic turnover factors of relational database support specialists. Two hundred and nine relational database support specialists were surveyed for this research. The research was conducted based on Hackman and Oldham's (1980) Job Diagnostic Survey. Regression analysis and a univariate ANOVA…

  7. Alternatives to relational database: comparison of NoSQL and XML approaches for clinical data storage.

    PubMed

    Lee, Ken Ka-Yin; Tang, Wai-Choi; Choi, Kup-Sze

    2013-04-01

    Clinical data are dynamic in nature, often arranged hierarchically and stored as free text and numbers. Effective management of clinical data and the transformation of the data into structured format for data analysis are therefore challenging issues in electronic health records development. Despite the popularity of relational databases, the scalability of the NoSQL database model and the document-centric data structure of XML databases appear to be promising features for effective clinical data management. In this paper, three database approaches--NoSQL, XML-enabled and native XML--are investigated to evaluate their suitability for structured clinical data. The database query performance is reported, together with our experience in the databases development. The results show that NoSQL database is the best choice for query speed, whereas XML databases are advantageous in terms of scalability, flexibility and extensibility, which are essential to cope with the characteristics of clinical data. While NoSQL and XML technologies are relatively new compared to the conventional relational database, both of them demonstrate potential to become a key database technology for clinical data management as the technology further advances. PMID:23177219

  8. ARCTOS: a relational database relating specimens, specimen-based science, and archival documentation

    USGS Publications Warehouse

    Jarrell, Gordon H.; Ramotnik, Cindy A.; McDonald, D.L.

    2010-01-01

    Data are preserved when they are perpetually discoverable, but even in the Information Age, discovery of legacy data appropriate to particular investigations is uncertain. Secure Internet storage is necessary but insufficient. Data can be discovered only when they are adequately described, and visibility increases markedly if the data are related to other data that are receiving usage. Such relationships can be built within (1) the framework of a relational database, or (1) they can be built among separate resources, within the framework of the Internet. Evolving primarily around biological collections, Arctos is a database that does both of these tasks. It includes data structures for a diversity of specimen attributes, essentially all collection-management tasks, plus literature citations, project descriptions, etc. As a centralized collaboration of several university museums, Arctos is an ideal environment for capitalizing on the many relationships that often exist between items in separate collections. Arctos is related to NIH’s DNA-sequence repository (GenBank) with record-to-record reciprocal linkages, and it serves data to several discipline-specific web portals, including the Global Biodiversity Information Network (GBIF). The University of Alaska Museum’s paleontological collection is Arctos’s recent extension beyond the constraints of neontology. With about 1.3 million cataloged items, additional collections are being added each year.

  9. HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server.

    PubMed

    Hardison, Ross C; Chui, David H K; Giardine, Belinda; Riemer, Cathy; Patrinos, George P; Anagnou, Nicholas; Miller, Webb; Wajcman, Henri

    2002-03-01

    We have constructed a relational database of hemoglobin variants and thalassemia mutations, called HbVar, which can be accessed on the web at http://globin.cse.psu.edu. Extensive information is recorded for each variant and mutation, including a description of the variant and associated pathology, hematology, electrophoretic mobility, methods of isolation, stability information, ethnic occurrence, structure studies, functional studies, and references. The initial information was derived from books by Dr. Titus Huisman and colleagues [Huisman et al., 1996, 1997, 1998]. The current database is updated regularly with the addition of new data and corrections to previous data. Queries can be formulated based on fields in the database. Tables of common categories of variants, such as all those involving the alpha1-globin gene (HBA1) or all those that result in high oxygen affinity, are maintained by automated queries on the database. Users can formulate more precise queries, such as identifying "all beta-globin variants associated with instability and found in Scottish populations." This new database should be useful for clinical diagnosis as well as in fundamental studies of hemoglobin biochemistry, globin gene regulation, and human sequence variation at these loci. PMID:11857738

  10. Visual Access to Visual Images: The UC Berkeley Image Database Project.

    ERIC Educational Resources Information Center

    Besser, Howard

    1990-01-01

    Discusses the problem of access in managing image collections and describes a prototype system for the University of California Berkeley which would include the University Art Museum, Architectural Slide Library, Geography Department's Map Library and Lowie Museum of Anthropology photographs. The system combines an online public access catalog…

  11. Accessibility and Usability of Web-Based Library Databases for Non-Visual Users.

    ERIC Educational Resources Information Center

    Byerley, Suzanne L.; Chambers, Mary Beth

    2002-01-01

    Examined the accessibility of two Web-based abstracting and indexing services by blind users using screen-reading programs based on guidelines from the Rehabilitation Act of 1973 and Web Content Accessibility Guidelines by the WWW Consortium. Suggests Web developers need to conduct usability testing and librarians need to be aware of accessibility…

  12. Implementing UNCRPD - Barrier Free Access to Buildings in NRW - Database and Signet "NRW Inklusiv".

    PubMed

    Bühler, Christian; Borosch, Roland; Servos, Gertrud

    2015-01-01

    UNCRD [1] has reemphasized the relevance of barrier free accessibility to infrastructures. Article 9 deals with accessibility of the manmade environment including buildings. Although accessibility has been required by people with disabilities for decades the existing built infrastructure often lacks adequate accessibility. If at all, it addresses requirements for users of wheelchairs but not for users with sensory or cognitive challenges. In this paper the development of a survey and publication of data from buildings is reported. The methodology is based on user participation and inclusion and follows a civil society approach, embedded in the overall strategy for inclusion in North Rhine-Westphalia (Germany). The internet portal presenting the information to the public is a first step to improve accessibility. An award on this data basis is proposed as incentive. PMID:26294518

  13. Real time access to commercial microwave link data: Details of the data acquisition software, the database and its web frontend

    NASA Astrophysics Data System (ADS)

    Keis, Felix; Chwala, Christian; Kunstmann, Harald

    2015-04-01

    Using commercial microwave link networks for precipitation estimation has become popular in the last years. Acquiring the necessary data from the network operators is however still difficult. Usually, data is provided to researches with large temporal delay and at irregular basis. Driven by the demand to facilitate this data accessibility, a custom acquisition software for microwave links has been developed in joint cooperation with our industry partner Ericsson. It is capable of recording data from a great number of microwave links simultaneously and of forwarding the data instantaneously to a newly established KIT-internal database. It makes use of the Simple Network Management Protocol (SNMP) and collects the transmitter and receiver power levels via asynchronous SNMP requests. The software is currently in its first operational test phase, recording data from several hundred Ericsson microwave links in southern Germany. Furthermore the software is used to acquire data with 1 Hz temporal resolution from four microwave links operated by the skiing resort in Garmisch-Partenkirchen. For convenient accessibility of this amount of data we have developed a web frontend for the emerging microwave link database. It provides dynamic real time visualization and basic processing of the recorded transmitter and receiver power levels. Here we will present details of the custom data acquisition software with focus on the design of the KIT microwave link database and on the specifically developed web frontend.

  14. Locally weighted regression for accessing a database containing wheat grain NIR transmission spectra and grain quality parameters

    NASA Astrophysics Data System (ADS)

    Archibald, Douglas D.; Funk, David B.; Barton, Franklin E., II

    1999-01-01

    Networks of NIR transmission spectrometers operating in the range 850 to 1050 nm are used worldwide to determine wheat grain quality parameters such as protein content. These instrumental system often require maintenance of calibrations for each grain class, and updating of calibrations for each crop year. In order to facilitate annual updates nd eliminate the need for multiple wheat class calibration models, this laboratory is pursuing a modeling strategy that uses locally weighted regression (LWR) to access a spectral database. With LWR, the calibration model defines the procedure to access the database and calculate the prediction, and this model can potentially remain the same for all classes and crop years. Incorporation of new sample variation is accomplished by new additions to the spectral database. Details are presented on development of an NIR model for determination of protein in multiple wheat-classes using the LWR approach with Y- distance weighting. This model is compared with a linear partial least-squares regression model spanning the same diverse set of samples. Initial steps were taken to validate these models with spectra measured on seven instruments at two remote locations.

  15. Record Linkage system in a complex relational database - MINPHIS example.

    PubMed

    Achimugu, Philip; Soriyan, Abimbola; Oluwagbemi, Oluwatolani; Ajayi, Anu

    2010-01-01

    In the health sector, record linkage is of paramount importance as clinical data can be distributed across different data repositories leading to duplication. Record Linkage is the process of tracking duplicate records that actually refers to the same entity. This paper proposes a fast and efficient method for duplicates detection within the healthcare domain. The first step is to standardize the data in the database using SQL. The second is to match similar pair records, and third step is to organize records into match and non-match status. The system was developed in Unified Modeling Language and Java. In the batch analysis of 31, 177 "supposedly" distinct identities, our method isolates 25, 117 true unique records and 6, 060 suspected duplicates using a healthcare system called MINPHIS (Made in Nigeria Primary Healthcare Information System) as the test bed. PMID:20841859

  16. Age-Related Differences in Lexical Access Relate to Speech Recognition in Noise.

    PubMed

    Carroll, Rebecca; Warzybok, Anna; Kollmeier, Birger; Ruigendijk, Esther

    2016-01-01

    Vocabulary size has been suggested as a useful measure of "verbal abilities" that correlates with speech recognition scores. Knowing more words is linked to better speech recognition. How vocabulary knowledge translates to general speech recognition mechanisms, how these mechanisms relate to offline speech recognition scores, and how they may be modulated by acoustical distortion or age, is less clear. Age-related differences in linguistic measures may predict age-related differences in speech recognition in noise performance. We hypothesized that speech recognition performance can be predicted by the efficiency of lexical access, which refers to the speed with which a given word can be searched and accessed relative to the size of the mental lexicon. We tested speech recognition in a clinical German sentence-in-noise test at two signal-to-noise ratios (SNRs), in 22 younger (18-35 years) and 22 older (60-78 years) listeners with normal hearing. We also assessed receptive vocabulary, lexical access time, verbal working memory, and hearing thresholds as measures of individual differences. Age group, SNR level, vocabulary size, and lexical access time were significant predictors of individual speech recognition scores, but working memory and hearing threshold were not. Interestingly, longer accessing times were correlated with better speech recognition scores. Hierarchical regression models for each subset of age group and SNR showed very similar patterns: the combination of vocabulary size and lexical access time contributed most to speech recognition performance; only for the younger group at the better SNR (yielding about 85% correct speech recognition) did vocabulary size alone predict performance. Our data suggest that successful speech recognition in noise is mainly modulated by the efficiency of lexical access. This suggests that older adults' poorer performance in the speech recognition task may have arisen from reduced efficiency in lexical access; with an

  17. Age-Related Differences in Lexical Access Relate to Speech Recognition in Noise

    PubMed Central

    Carroll, Rebecca; Warzybok, Anna; Kollmeier, Birger; Ruigendijk, Esther

    2016-01-01

    Vocabulary size has been suggested as a useful measure of “verbal abilities” that correlates with speech recognition scores. Knowing more words is linked to better speech recognition. How vocabulary knowledge translates to general speech recognition mechanisms, how these mechanisms relate to offline speech recognition scores, and how they may be modulated by acoustical distortion or age, is less clear. Age-related differences in linguistic measures may predict age-related differences in speech recognition in noise performance. We hypothesized that speech recognition performance can be predicted by the efficiency of lexical access, which refers to the speed with which a given word can be searched and accessed relative to the size of the mental lexicon. We tested speech recognition in a clinical German sentence-in-noise test at two signal-to-noise ratios (SNRs), in 22 younger (18–35 years) and 22 older (60–78 years) listeners with normal hearing. We also assessed receptive vocabulary, lexical access time, verbal working memory, and hearing thresholds as measures of individual differences. Age group, SNR level, vocabulary size, and lexical access time were significant predictors of individual speech recognition scores, but working memory and hearing threshold were not. Interestingly, longer accessing times were correlated with better speech recognition scores. Hierarchical regression models for each subset of age group and SNR showed very similar patterns: the combination of vocabulary size and lexical access time contributed most to speech recognition performance; only for the younger group at the better SNR (yielding about 85% correct speech recognition) did vocabulary size alone predict performance. Our data suggest that successful speech recognition in noise is mainly modulated by the efficiency of lexical access. This suggests that older adults’ poorer performance in the speech recognition task may have arisen from reduced efficiency in lexical access

  18. Government databases and public health research: facilitating access in the public interest.

    PubMed

    Adams, Carolyn; Allen, Judy

    2014-06-01

    Access to datasets of personal health information held by government agencies is essential to support public health research and to promote evidence-based public health policy development. Privacy legislation in Australia allows the use and disclosure of such information for public health research. However, access is not always forthcoming in a timely manner and the decision-making process undertaken by government data custodians is not always transparent. Given the public benefit in research using these health information datasets, this article suggests that it is time to recognise a right of access for approved research and that the decisions, and decision-making processes, of government data custodians should be subject to increased scrutiny. The article concludes that researchers should have an avenue of external review where access to information has been denied or unduly delayed. PMID:25087372

  19. A Parallel Relational Database Management System Approach to Relevance Feedback in Information Retrieval.

    ERIC Educational Resources Information Center

    Lundquist, Carol; Frieder, Ophir; Holmes, David O.; Grossman, David

    1999-01-01

    Describes a scalable, parallel, relational database-drive information retrieval engine. To support portability across a wide range of execution environments, all algorithms adhere to the SQL-92 standard. By incorporating relevance feedback algorithms, accuracy is enhanced over prior database-driven information retrieval efforts. Presents…

  20. The relational clinical database: a possible solution to the star wars in registry systems.

    PubMed

    Michels, D K; Zamieroski, M

    1990-12-01

    In summary, having data from other service areas available in a relational clinical database could resolve many of the problems existing in today's registry systems. Uniting sophisticated information systems into a centralized database system could definitely be a corporate asset in managing the bottom line. PMID:10108501

  1. Keeping Track of Our Treasures: Managing Historical Data with Relational Database Software.

    ERIC Educational Resources Information Center

    Gutmann, Myron P.; And Others

    1989-01-01

    Describes the way a relational database management system manages a large historical data collection project. Shows that such databases are practical to construct. States that the programing tasks involved are not for beginners, but the rewards of having data organized are worthwhile. (GG)

  2. Automating testbed documentation and database access using World Wide Web (WWW) tools

    NASA Technical Reports Server (NTRS)

    Ames, Charles; Auernheimer, Brent; Lee, Young H.

    1994-01-01

    A method for providing uniform transparent access to disparate distributed information systems was demonstrated. A prototype testing interface was developed to access documentation and information using publicly available hypermedia tools. The prototype gives testers a uniform, platform-independent user interface to on-line documentation, user manuals, and mission-specific test and operations data. Mosaic was the common user interface, and HTML (Hypertext Markup Language) provided hypertext capability.

  3. An Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated wi...

  4. High Database Prices and Their Impact on Information Access: Is There a Solution?

    ERIC Educational Resources Information Center

    Nelson, Michael L.

    1987-01-01

    Recent trends in the pricing of online database systems are described and their impact on searcher behavior and satisfaction is discussed. A design is proposed for a major research project that would use data gathered by the Information Market Indicators to assess the feasibility of a price-based solution. (CLB)

  5. Online Searching of Bibliographic Databases: Microcomputer Access to National Information Systems.

    ERIC Educational Resources Information Center

    Coons, Bill

    This paper describes the range and scope of various information databases available for technicians, researchers, and managers employed in forestry and the forest products industry. Availability of information on reports of field and laboratory research, business trends, product prices, and company profiles through national distributors of…

  6. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  7. Relational-database model for improving quality assurance and process control in a composite manufacturing environment

    NASA Astrophysics Data System (ADS)

    Gentry, Jeffery D.

    2000-05-01

    A relational database is a powerful tool for collecting and analyzing the vast amounts of inner-related data associated with the manufacture of composite materials. A relational database contains many individual database tables that store data that are related in some fashion. Manufacturing process variables as well as quality assurance measurements can be collected and stored in database tables indexed according to lot numbers, part type or individual serial numbers. Relationships between manufacturing process and product quality can then be correlated over a wide range of product types and process variations. This paper presents details on how relational databases are used to collect, store, and analyze process variables and quality assurance data associated with the manufacture of advanced composite materials. Important considerations are covered including how the various types of data are organized and how relationships between the data are defined. Employing relational database techniques to establish correlative relationships between process variables and quality assurance measurements is then explored. Finally, the benefits of database techniques such as data warehousing, data mining and web based client/server architectures are discussed in the context of composite material manufacturing.

  8. Biofuel Database

    National Institute of Standards and Technology Data Gateway

    Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

  9. Progress in the GEOROC Database - Fast and Simple Access to Analytical Data by Precompilation

    NASA Astrophysics Data System (ADS)

    Sarbas, B.

    2001-12-01

    The geochemical database GEOROC of the Max-Planck-Institut fuer Chemie in Mainz http://georoc.mpch-mainz.gwdg.de includes the published chemical analyses of samples from Oceanic Islands, Convergent Margins, and Large Igneous Provinces. As a whole, the database comprises about 77,000 whole-rock, 35,000 mineral and 3,000 inclusion analyses published in about 2,800 papers (status Sept. 2001). For the individual tectonic settings, the following numbers of analyses are available: Oceanic Islands - 25,000 whole rocks, 14,000 minerals, 1,500 inclusions Convergent Margins - 20,000 whole rocks, 9,000 minerals, 500 inclusions Large Igneous Provinces - 32,000 whole rocks, 12,000 minerals, 1500 inclusions. Data entry is complete for samples from Oceanic Islands and Oceanic Large Igneous Provinces. Newly published papers are added regularly. Among the Continental Flood Basalts, which comprise 25,000 whole-rock and 12,000 mineral analyses, large and nearly complete datasets are available for the Columbia River, Deccan, Karoo, Paraná, and Siberian Plateau Basalts. Data for Convergent Margins have been added to the database most recently. The database includes, for instance, for the Honshu Arc 3,300, for the Izu-Bonin Arc 1,550, for the Mariana Arc 1,800, for the Kurile Arc 1,400, for the Aleutian Arc 1,500, for the Cascades 500, for the Andes 1,600, for the Lesser Antilles 1,100, and for the Tonga Arc 1,400 whole-rock analyses. For many localities, huge numbers of analyses (more than 2000) are included in the GEOROC database. The selection and compilation of such substantial datasets proved to be difficult and time-consuming when using the web interface of the database. Therefore, we are building precompiled datasets that include all published whole-rock analyses and a fixed set of location and sample metadata for the respective locations. These precompiled datasets are stored as Excel files and can be downloaded easily and rapidly. If multiple element analyses exist for a

  10. Large-Scale 1:1 Computing Initiatives: An Open Access Database

    ERIC Educational Resources Information Center

    Richardson, Jayson W.; McLeod, Scott; Flora, Kevin; Sauers, Nick J.; Kannan, Sathiamoorthy; Sincar, Mehmet

    2013-01-01

    This article details the spread and scope of large-scale 1:1 computing initiatives around the world. What follows is a review of the existing literature around 1:1 programs followed by a description of the large-scale 1:1 database. Main findings include: 1) the XO and the Classmate PC dominate large-scale 1:1 initiatives; 2) if professional…

  11. Accessing, Mining, and Archiving an On-line Database -- The APS Catalog of the POSS I

    NASA Astrophysics Data System (ADS)

    Humphreys, R. M.; Cabanela, J. E.; Kriessler, J.

    2000-12-01

    The APS Catalog of the POSS I is an on-line database of over 100 million stars and galaxies (http://aps.umn.edu). A unique subset of this database with over 218,000 galaxies within 30 degrees of the North Galactic Pole, the MAPS-NGP, is now available at our web site. This diameter--selected catalog (>= 10 arcsec) is the deepest galaxy catalog constructed over such a large area of the sky (3000 sq. degrees). The MAPS-NGP includes many additional parameters for the galaxy images not available in the APS Catalog. Working with members of our computer science department, we have developed a morphological classifier for galaxies that divides our galaxy type into three classes -- early, intermediate, and late. We have applied data mining techniques to identify the most useful image parameters for input into a neural network and decision--tree based classifier pipeline. We are also archiving the APS Catalog for distribution to astronomical data centers including NASA's ADC and SIMBAD at CDS. The extragalactic subset will be integrated into the NASA/IPAC extragalactic database(NED). The MAPS-NGP has already been provided to NED. The APS is supported by NASA's Applied Information Systems Research Program.

  12. Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

    PubMed Central

    Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

    2015-01-01

    Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. PMID:25158685

  13. SQL is Dead; Long-live SQL: Relational Database Technology in Science Contexts

    NASA Astrophysics Data System (ADS)

    Howe, B.; Halperin, D.

    2014-12-01

    Relational databases are often perceived as a poor fit in science contexts: Rigid schemas, poor support for complex analytics, unpredictable performance, significant maintenance and tuning requirements --- these idiosyncrasies often make databases unattractive in science contexts characterized by heterogeneous data sources, complex analysis tasks, rapidly changing requirements, and limited IT budgets. In this talk, I'll argue that although the value proposition of typical relational database systems are weak in science, the core ideas that power relational databases have become incredibly prolific in open source science software, and are emerging as a universal abstraction for both big data and small data. In addition, I'll talk about two open source systems we are building to "jailbreak" the core technology of relational databases and adapt them for use in science. The first is SQLShare, a Database-as-a-Service system supporting collaborative data analysis and exchange by reducing database use to an Upload-Query-Share workflow with no installation, schema design, or configuration required. The second is Myria, a service that supports much larger scale data, complex analytics, and supports multiple back end systems. Finally, I'll describe some of the ways our collaborators in oceanography, astronomy, biology, fisheries science, and more are using these systems to replace script-based workflows for reasons of performance, flexibility, and convenience.

  14. Accessibility

    MedlinePlus

    ... www.nlm.nih.gov/medlineplus/accessibility.html MedlinePlus Accessibility To use the sharing features on this page, ... Subscribe to RSS Follow us Disclaimers Copyright Privacy Accessibility Quality Guidelines Viewers & Players MedlinePlus Connect for EHRs ...

  15. YAdumper: extracting and translating large information volumes from relational databases to structured flat files.

    PubMed

    Fernández, José M; Valencia, Alfonso

    2004-10-12

    Downloading the information stored in relational databases into XML and other flat formats is a common task in bioinformatics. This periodical dumping of information requires considerable CPU time, disk and memory resources. YAdumper has been developed as a purpose-specific tool to deal with the integral structured information download of relational databases. YAdumper is a Java application that organizes database extraction following an XML template based on an external Document Type Declaration. Compared with other non-native alternatives, YAdumper substantially reduces memory requirements and considerably improves writing performance. PMID:15117748

  16. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

    SciTech Connect

    Novichkov, Pavel S.; Ratnere, Igor; Wolf, Yuri I.; Koonin, Eugene V.; Dubchak, Inna

    2009-07-23

    The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov.

  17. Assessing barriers to health insurance and threats to equity in comparative perspective: The Health Insurance Access Database

    PubMed Central

    2012-01-01

    Background Typologies traditionally used for international comparisons of health systems often conflate many system characteristics. To capture policy changes over time and by service in health systems regulation of public and private insurance, we propose a database containing explicit, standardized indicators of policy instruments. Methods The Health Insurance Access Database (HIAD) will collect policy information for ten OECD countries, over a range of eight health services, from 1990–2010. Policy indicators were selected through a comprehensive literature review which identified policy instruments most likely to constitute barriers to health insurance, thus potentially posing a threat to equity. As data collection is still underway, we present here the theoretical bases and methodology adopted, with a focus on the rationale underpinning the study instruments. Results These harmonized data will allow the capture of policy changes in health systems regulation of public and private insurance over time and by service. The standardization process will permit international comparisons of systems’ performance with regards to health insurance access and equity. Conclusion This research will inform and feed the current debate on the future of health care in developed countries and on the role of the private sector in these changes. PMID:22551599

  18. Legacy2Drupal: Conversion of an existing relational oceanographic database to a Drupal 7 CMS

    NASA Astrophysics Data System (ADS)

    Work, T. T.; Maffei, A. R.; Chandler, C. L.; Groman, R. C.

    2011-12-01

    Content Management Systems (CMSs) such as Drupal provide powerful features that can be of use to oceanographic (and other geo-science) data managers. However, in many instances, geo-science data management offices have already designed and implemented customized schemas for their metadata. The NSF funded Biological Chemical and Biological Data Management Office (BCO-DMO) has ported an existing relational database containing oceanographic metadata, along with an existing interface coded in Cold Fusion middleware, to a Drupal 7 Content Management System. This is an update on an effort described as a proof-of-concept in poster IN21B-1051, presented at AGU2009. The BCO-DMO project has translated all the existing database tables, input forms, website reports, and other features present in the existing system into Drupal CMS features. The replacement features are made possible by the use of Drupal content types, CCK node-reference fields, a custom theme, and a number of other supporting modules. This presentation describes the process used to migrate content in the original BCO-DMO metadata database to Drupal 7, some problems encountered during migration, and the modules used to migrate the content successfully. Strategic use of Drupal 7 CMS features that enable three separate but complementary interfaces to provide access to oceanographic research metadata will also be covered: 1) a Drupal 7-powered user front-end; 2) REST-ful JSON web services (providing a Mapserver interface to the metadata and data; and 3) a SPARQL interface to a semantic representation of the repository metadata (this feeding a new faceted search capability currently under development). The existing BCO-DMO ontology, developed in collaboration with Rensselaer Polytechnic Institute's Tetherless World Constellation, makes strategic use of pre-existing ontologies and will be used to drive semantically-enabled faceted search capabilities planned for the site. At this point, the use of semantic

  19. Database of host-pathogen and related species interactions, and their global distribution

    PubMed Central

    Wardeh, Maya; Risley, Claire; McIntyre, Marie Kirsty; Setzkorn, Christian; Baylis, Matthew

    2015-01-01

    Interactions between species, particularly where one is likely to be a pathogen of the other, as well as the geographical distribution of species, have been systematically extracted from various web-based, free-access sources, and assembled with the accompanying evidence into a single database. The database attempts to answer questions such as what are all the pathogens of a host, and what are all the hosts of a pathogen, what are all the countries where a pathogen was found, and what are all the pathogens found in a country. Two datasets were extracted from the database, focussing on species interactions and species distribution, based on evidence published between 1950–2012. The quality of their evidence was checked and verified against well-known, alternative, datasets of pathogens infecting humans, domestic animals and wild mammals. The presented datasets provide a valuable resource for researchers of infectious diseases of humans and animals, including zoonoses. PMID:26401317

  20. Database of host-pathogen and related species interactions, and their global distribution.

    PubMed

    Wardeh, Maya; Risley, Claire; McIntyre, Marie Kirsty; Setzkorn, Christian; Baylis, Matthew

    2015-01-01

    Interactions between species, particularly where one is likely to be a pathogen of the other, as well as the geographical distribution of species, have been systematically extracted from various web-based, free-access sources, and assembled with the accompanying evidence into a single database. The database attempts to answer questions such as what are all the pathogens of a host, and what are all the hosts of a pathogen, what are all the countries where a pathogen was found, and what are all the pathogens found in a country. Two datasets were extracted from the database, focussing on species interactions and species distribution, based on evidence published between 1950-2012. The quality of their evidence was checked and verified against well-known, alternative, datasets of pathogens infecting humans, domestic animals and wild mammals. The presented datasets provide a valuable resource for researchers of infectious diseases of humans and animals, including zoonoses. PMID:26401317

  1. Development of a functional, internet-accessible department of surgery outcomes database.

    PubMed

    Newcomb, William L; Lincourt, Amy E; Gersin, Keith; Kercher, Kent; Iannitti, David; Kuwada, Tim; Lyons, Cynthia; Sing, Ronald F; Hadzikadic, Mirsad; Heniford, B Todd; Rucho, Susan

    2008-06-01

    The need for surgical outcomes data is increasing due to pressure from insurance companies, patients, and the need for surgeons to keep their own "report card". Current data management systems are limited by inability to stratify outcomes based on patients, surgeons, and differences in surgical technique. Surgeons along with research and informatics personnel from an academic, hospital-based Department of Surgery and a state university's Department of Information Technology formed a partnership to develop a dynamic, internet-based, clinical data warehouse. A five-component model was used: data dictionary development, web application creation, participating center education and management, statistics applications, and data interpretation. A data dictionary was developed from a list of data elements to address needs of research, quality assurance, industry, and centers of excellence. A user-friendly web interface was developed with menu-driven check boxes, multiple electronic data entry points, direct downloads from hospital billing information, and web-based patient portals. Data were collected on a Health Insurance Portability and Accountability Act-compliant server with a secure firewall. Protected health information was de-identified. Data management strategies included automated auditing, on-site training, a trouble-shooting hotline, and Institutional Review Board oversight. Real-time, daily, monthly, and quarterly data reports were generated. Fifty-eight publications and 109 abstracts have been generated from the database during its development and implementation. Seven national academic departments now use the database to track patient outcomes. The development of a robust surgical outcomes database requires a combination of clinical, informatics, and research expertise. Benefits of surgeon involvement in outcomes research include: tracking individual performance, patient safety, surgical research, legal defense, and the ability to provide accurate information

  2. NETMARK: A Schema-less Extension for Relational Databases for Managing Semi-structured Data Dynamically

    NASA Technical Reports Server (NTRS)

    Maluf, David A.; Tran, Peter B.

    2003-01-01

    Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object-oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK, is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword search of records spanning across both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high-throughput open database framework for managing, storing, and searching unstructured or semi-structured arbitrary hierarchal models, such as XML and HTML.

  3. EasyKSORD: A Platform of Keyword Search Over Relational Databases

    NASA Astrophysics Data System (ADS)

    Peng, Zhaohui; Li, Jing; Wang, Shan

    Keyword Search Over Relational Databases (KSORD) enables casual users to use keyword queries (a set of keywords) to search relational databases just like searching the Web, without any knowledge of the database schema or any need of writing SQL queries. Based on our previous work, we design and implement a novel KSORD platform named EasyKSORD for users and system administrators to use and manage different KSORD systems in a novel and simple manner. EasyKSORD supports advanced queries, efficient data-graph-based search engines, multiform result presentations, and system logging and analysis. Through EasyKSORD, users can search relational databases easily and read search results conveniently, and system administrators can easily monitor and analyze the operations of KSORD and manage KSORD systems much better.

  4. A fragile zero watermarking scheme to detect and characterize malicious modifications in database relations.

    PubMed

    Khan, Aihab; Husain, Syed Afaq

    2013-01-01

    We put forward a fragile zero watermarking scheme to detect and characterize malicious modifications made to a database relation. Most of the existing watermarking schemes for relational databases introduce intentional errors or permanent distortions as marks into the database original content. These distortions inevitably degrade the data quality and data usability as the integrity of a relational database is violated. Moreover, these fragile schemes can detect malicious data modifications but do not characterize the tempering attack, that is, the nature of tempering. The proposed fragile scheme is based on zero watermarking approach to detect malicious modifications made to a database relation. In zero watermarking, the watermark is generated (constructed) from the contents of the original data rather than introduction of permanent distortions as marks into the data. As a result, the proposed scheme is distortion-free; thus, it also resolves the inherent conflict between security and imperceptibility. The proposed scheme also characterizes the malicious data modifications to quantify the nature of tempering attacks. Experimental results show that even minor malicious modifications made to a database relation can be detected and characterized successfully. PMID:23818831

  5. A Fragile Zero Watermarking Scheme to Detect and Characterize Malicious Modifications in Database Relations

    PubMed Central

    Husain, Syed Afaq

    2013-01-01

    We put forward a fragile zero watermarking scheme to detect and characterize malicious modifications made to a database relation. Most of the existing watermarking schemes for relational databases introduce intentional errors or permanent distortions as marks into the database original content. These distortions inevitably degrade the data quality and data usability as the integrity of a relational database is violated. Moreover, these fragile schemes can detect malicious data modifications but do not characterize the tempering attack, that is, the nature of tempering. The proposed fragile scheme is based on zero watermarking approach to detect malicious modifications made to a database relation. In zero watermarking, the watermark is generated (constructed) from the contents of the original data rather than introduction of permanent distortions as marks into the data. As a result, the proposed scheme is distortion-free; thus, it also resolves the inherent conflict between security and imperceptibility. The proposed scheme also characterizes the malicious data modifications to quantify the nature of tempering attacks. Experimental results show that even minor malicious modifications made to a database relation can be detected and characterized successfully. PMID:23818831

  6. Sting_RDB: a relational database of structural parameters for protein analysis with support for data warehousing and data mining.

    PubMed

    Oliveira, S R M; Almeida, G V; Souza, K R R; Rodrigues, D N; Kuser-Falcão, P R; Yamagishi, M E B; Santos, E H; Vieira, F D; Jardine, J G; Neshich, G

    2007-01-01

    An effective strategy for managing protein databases is to provide mechanisms to transform raw data into consistent, accurate and reliable information. Such mechanisms will greatly reduce operational inefficiencies and improve one's ability to better handle scientific objectives and interpret the research results. To achieve this challenging goal for the STING project, we introduce Sting_RDB, a relational database of structural parameters for protein analysis with support for data warehousing and data mining. In this article, we highlight the main features of Sting_RDB and show how a user can explore it for efficient and biologically relevant queries. Considering its importance for molecular biologists, effort has been made to advance Sting_RDB toward data quality assessment. To the best of our knowledge, Sting_RDB is one of the most comprehensive data repositories for protein analysis, now also capable of providing its users with a data quality indicator. This paper differs from our previous study in many aspects. First, we introduce Sting_RDB, a relational database with mechanisms for efficient and relevant queries using SQL. Sting_rdb evolved from the earlier, text (flat file)-based database, in which data consistency and integrity was not guaranteed. Second, we provide support for data warehousing and mining. Third, the data quality indicator was introduced. Finally and probably most importantly, complex queries that could not be posed on a text-based database, are now easily implemented. Further details are accessible at the Sting_RDB demo web page: http://www.cbi.cnptia.embrapa.br/StingRDB. PMID:18058712

  7. Optimizing Parallel Access to the BaBar Database System Using CORBA Servers

    SciTech Connect

    Becla, Jacek

    2002-05-01

    The BaBar Experiment collected around 20 TB of data during its first 6 months of running. Now, after 18 months, data size exceeds 300 TB, and according to prognosis, it is a small fraction of the size of data coming in the next few months. In order to keep up with the data, significant effort was put into tuning the database system. It led to great performance improvements, as well as to inevitable system expansion--450 simultaneous processing nodes alone used for data reconstruction. It is believed, that further growth beyond 600 nodes will happen soon. In such an environment, many complex operations are executed simultaneously on hundreds of machines, putting a huge load on data servers and increasing network traffic. Introducing two CORBA servers halved startup time, and dramatically offloaded database servers: data servers as well as lock servers. The paper describes details of design and implementation of two servers recently introduced in the BaBar system: Conditions OID Server and Clustering Server. The first experience of using these servers is discussed. A discussion on a Collection Server for data analysis, currently being designed is included.

  8. ``STANDARD LIBRARY'': A relational database for the management of electron microprobe standards

    NASA Astrophysics Data System (ADS)

    Diamond, Larryn W.; Schmatz, Dirk; Würsten, Felix

    1994-05-01

    Laboratory collections of well-characterized solid materials are an indispensable basis for the calibration of quantitative electron microprobe analyses. The STANDARD LIBRARY database has been designed to manage the wide variety of information needed to characterize such standards, and to provide a rapid way by which these data can be accessed. In addition to physical storage information, STANDARD LIBRARY includes a full set of chemical and mineralogic characterization variables, and a set of variables specific to microprobe calibration (instrumental setup, standard homogeneity, etc.). Application programs for STANDARD LIBRARY provide a series of interactive screen views for database search, retrieval, and editing operations (including inventories). Search and inventory results can be written as UNIX data files, some of which are formatted to be read directly by the software that controls CAMECA SX50™ electron microprobes. The application programs are coded in OSL for the INGRES™ database-management system, and run within any environment that supports INGRES™ (e.g. UNIX, VMS, DOS, etc.). STANDARD LIBRARY has been generalized, however, such that only the physical storage structure of the database is dependent on the selected database-management system.

  9. Accessing Suicide-Related Information on the Internet: A Retrospective Observational Study of Search Behavior

    PubMed Central

    2013-01-01

    Background The Internet’s potential impact on suicide is of major public health interest as easy online access to pro-suicide information or specific suicide methods may increase suicide risk among vulnerable Internet users. Little is known, however, about users’ actual searching and browsing behaviors of online suicide-related information. Objective To investigate what webpages people actually clicked on after searching with suicide-related queries on a search engine and to examine what queries people used to get access to pro-suicide websites. Methods A retrospective observational study was done. We used a web search dataset released by America Online (AOL). The dataset was randomly sampled from all AOL subscribers’ web queries between March and May 2006 and generated by 657,000 service subscribers. Results We found 5526 search queries (0.026%, 5526/21,000,000) that included the keyword "suicide". The 5526 search queries included 1586 different search terms and were generated by 1625 unique subscribers (0.25%, 1625/657,000). Of these queries, 61.38% (3392/5526) were followed by users clicking on a search result. Of these 3392 queries, 1344 (39.62%) webpages were clicked on by 930 unique users but only 1314 of those webpages were accessible during the study period. Each clicked-through webpage was classified into 11 categories. The categories of the most visited webpages were: entertainment (30.13%; 396/1314), scientific information (18.31%; 240/1314), and community resources (14.53%; 191/1314). Among the 1314 accessed webpages, we could identify only two pro-suicide websites. We found that the search terms used to access these sites included “commiting suicide with a gas oven”, “hairless goat”, “pictures of murder by strangulation”, and “photo of a severe burn”. A limitation of our study is that the database may be dated and confined to mainly English webpages. Conclusions Searching or browsing suicide-related or pro-suicide webpages was

  10. Filling in the GAPS: evaluating completeness and coverage of open-access biodiversity databases in the United States

    DOE PAGESBeta

    Troia, Matthew J.; McManamay, Ryan A.

    2016-06-12

    Primary biodiversity data constitute observations of particular species at given points in time and space. Open-access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open-access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records frommore » the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). In this study, we aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well-surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov–Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well-surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well-surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional

  11. Filling in the GAPS: evaluating completeness and coverage of open-access biodiversity databases in the United States.

    PubMed

    Troia, Matthew J; McManamay, Ryan A

    2016-07-01

    Primary biodiversity data constitute observations of particular species at given points in time and space. Open-access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open-access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records from the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). We aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well-surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov-Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well-surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well-surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional sampling biases. This

  12. A Novel Approach: Chemical Relational Databases, and the Role of the ISSCAN Database on Assessing Chemical Carcinogenity

    EPA Science Inventory

    Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did no...

  13. Legacy2Drupal - Conversion of an existing oceanographic relational database to a semantically enabled Drupal content management system

    NASA Astrophysics Data System (ADS)

    Maffei, A. R.; Chandler, C. L.; Work, T.; Allen, J.; Groman, R. C.; Fox, P. A.

    2009-12-01

    Content Management Systems (CMSs) provide powerful features that can be of use to oceanographic (and other geo-science) data managers. However, in many instances, geo-science data management offices have previously designed customized schemas for their metadata. The WHOI Ocean Informatics initiative and the NSF funded Biological Chemical and Biological Data Management Office (BCO-DMO) have jointly sponsored a project to port an existing, relational database containing oceanographic metadata, along with an existing interface coded in Cold Fusion middleware, to a Drupal6 Content Management System. The goal was to translate all the existing database tables, input forms, website reports, and other features present in the existing system to employ Drupal CMS features. The replacement features include Drupal content types, CCK node-reference fields, themes, RDB, SPARQL, workflow, and a number of other supporting modules. Strategic use of some Drupal6 CMS features enables three separate but complementary interfaces that provide access to oceanographic research metadata via the MySQL database: 1) a Drupal6-powered front-end; 2) a standard SQL port (used to provide a Mapserver interface to the metadata and data; and 3) a SPARQL port (feeding a new faceted search capability being developed). Future plans include the creation of science ontologies, by scientist/technologist teams, that will drive semantically-enabled faceted search capabilities planned for the site. Incorporation of semantic technologies included in the future Drupal 7 core release is also anticipated. Using a public domain CMS as opposed to proprietary middleware, and taking advantage of the many features of Drupal 6 that are designed to support semantically-enabled interfaces will help prepare the BCO-DMO database for interoperability with other ecosystem databases.

  14. Data model and relational database design for the New Jersey Water-Transfer Data System (NJWaTr)

    USGS Publications Warehouse

    Tessler, Steven

    2003-01-01

    The New Jersey Water-Transfer Data System (NJWaTr) is a database design for the storage and retrieval of water-use data. NJWaTr can manage data encompassing many facets of water use, including (1) the tracking of various types of water-use activities (withdrawals, returns, transfers, distributions, consumptive-use, wastewater collection, and treatment); (2) the storage of descriptions, classifications and locations of places and organizations involved in water-use activities; (3) the storage of details about measured or estimated volumes of water associated with water-use activities; and (4) the storage of information about data sources and water resources associated with water use. In NJWaTr, each water transfer occurs unidirectionally between two site objects, and the sites and conveyances form a water network. The core entities in the NJWaTr model are site, conveyance, transfer/volume, location, and owner. Other important entities include water resource (used for withdrawals and returns), data source, permit, and alias. Multiple water-exchange estimates based on different methods or data sources can be stored for individual transfers. Storage of user-defined details is accommodated for several of the main entities. Many tables contain classification terms to facilitate the detailed description of data items and can be used for routine or custom data summarization. NJWaTr accommodates single-user and aggregate-user water-use data, can be used for large or small water-network projects, and is available as a stand-alone Microsoft? Access database. Data stored in the NJWaTr structure can be retrieved in user-defined combinations to serve visualization and analytical applications. Users can customize and extend the database, link it to other databases, or implement the design in other relational database applications.

  15. R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

    PubMed Central

    Rimet, Frédéric; Chaumeil, Philippe; Keck, François; Kermarrec, Lenaïg; Vasselon, Valentin; Kahlert, Maria; Franc, Alain; Bouchez, Agnès

    2016-01-01

    Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the

  16. R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring.

    PubMed

    Rimet, Frédéric; Chaumeil, Philippe; Keck, François; Kermarrec, Lenaïg; Vasselon, Valentin; Kahlert, Maria; Franc, Alain; Bouchez, Agnès

    2016-01-01

    Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the

  17. Database Technology in Digital Libraries.

    ERIC Educational Resources Information Center

    Preston, Carole; Lin, Binshan

    2002-01-01

    Reviews issues relating to database technology and digital libraries. Highlights include resource sharing; ongoing digital library projects; metadata; user interfaces; query processing; interoperability; data quality; copyright infringement; and managerial implications, including electronic versus printed materials, accessibility,…

  18. Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases

    PubMed Central

    Asamizu, Erika; Ichihara, Hisako; Nakaya, Akihiro; Nakamura, Yasukazu; Hirakawa, Hideki; Ishii, Takahiro; Tamura, Takuro; Fukami-Kobayashi, Kaoru; Nakajima, Yukari; Tabata, Satoshi

    2014-01-01

    The Plant Genome DataBase Japan (PGDBj, http://pgdbj.jp/?ln=en) is a portal website that aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search over the contents of the DBs. The three DBs are as follows. (i) The Ortholog DB, providing gene cluster information based on the amino acid sequence similarity. Over 500,000 amino acid sequences of 20 Viridiplantae species were subjected to reciprocal BLAST searches and clustered. Sequences from plant genome DBs (e.g. TAIR10 and RAP-DB) were also included in the cluster with a direct link to the original DB. (ii) The Plant Resource DB, integrating the SABRE DB, which provides cDNA and genome sequence resources accumulated and maintained in the RIKEN BioResource Center and National BioResource Projects. (iii) The DNA Marker DB, providing manually or automatically curated information of DNA markers, quantitative trait loci and related linkage maps, from the literature and external DBs. As the PGDBj targets various plant species, including model plants, algae, and crops important as food, fodder and biofuel, researchers in the field of basic biology as well as a wide range of agronomic fields are encouraged to perform searches using DNA sequences, gene names, traits and phenotypes of interest. The PGDBj will return the search results from the component DBs and various types of linked external DBs. PMID:24363285

  19. Functions and Relations: Some Applications from Database Management for the Teaching of Classroom Mathematics.

    ERIC Educational Resources Information Center

    Hauge, Sharon K.

    While functions and relations are important concepts in the teaching of mathematics, research suggests that many students lack an understanding and appreciation of these concepts. The present paper discusses an approach for teaching functions and relations that draws on the use of illustrations from database management. This approach has the…

  20. Electronic Databases.

    ERIC Educational Resources Information Center

    Williams, Martha E.

    1985-01-01

    Presents examples of bibliographic, full-text, and numeric databases. Also discusses how to access these databases online, aids to online retrieval, and several issues and trends (including copyright and downloading, transborder data flow, use of optical disc/videodisc technology, and changing roles in database generation and processing). (JN)

  1. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

    PubMed Central

    Mathelier, Anthony; Fornes, Oriol; Arenillas, David J.; Chen, Chih-yu; Denay, Grégoire; Lee, Jessica; Shi, Wenqiang; Shyr, Casper; Tan, Ge; Worsley-Hunt, Rebecca; Zhang, Allen W.; Parcy, François; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W.

    2016-01-01

    JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release. PMID:26531826

  2. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

    PubMed

    Mathelier, Anthony; Fornes, Oriol; Arenillas, David J; Chen, Chih-Yu; Denay, Grégoire; Lee, Jessica; Shi, Wenqiang; Shyr, Casper; Tan, Ge; Worsley-Hunt, Rebecca; Zhang, Allen W; Parcy, François; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W

    2016-01-01

    JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release. PMID:26531826

  3. Two MBASIC programs that write application programs for accessing a database

    NASA Technical Reports Server (NTRS)

    Smith, R. M.

    1976-01-01

    A method was desired to relieve the tedium of writing and testing application programs. Two utility programs were developed to produce application programs that perform relational operations on data. No coding is performed by the user.

  4. Benchmarking framework for myocardial tracking and deformation algorithms: an open access database.

    PubMed

    Tobon-Gomez, C; De Craene, M; McLeod, K; Tautz, L; Shi, W; Hennemuth, A; Prakosa, A; Wang, H; Carr-White, G; Kapetanakis, S; Lutz, A; Rasche, V; Schaeffter, T; Butakoff, C; Friman, O; Mansi, T; Sermesant, M; Zhuang, X; Ourselin, S; Peitgen, H-O; Pennec, X; Razavi, R; Rueckert, D; Frangi, A F; Rhode, K S

    2013-08-01

    In this paper we present a benchmarking framework for the validation of cardiac motion analysis algorithms. The reported methods are the response to an open challenge that was issued to the medical imaging community through a MICCAI workshop. The database included magnetic resonance (MR) and 3D ultrasound (3DUS) datasets from a dynamic phantom and 15 healthy volunteers. Participants processed 3D tagged MR datasets (3DTAG), cine steady state free precession MR datasets (SSFP) and 3DUS datasets, amounting to 1158 image volumes. Ground-truth for motion tracking was based on 12 landmarks (4 walls at 3 ventricular levels). They were manually tracked by two observers in the 3DTAG data over the whole cardiac cycle, using an in-house application with 4D visualization capabilities. The median of the inter-observer variability was computed for the phantom dataset (0.77 mm) and for the volunteer datasets (0.84 mm). The ground-truth was registered to 3DUS coordinates using a point based similarity transform. Four institutions responded to the challenge by providing motion estimates for the data: Fraunhofer MEVIS (MEVIS), Bremen, Germany; Imperial College London - University College London (IUCL), UK; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Inria-Asclepios project (INRIA), France. Details on the implementation and evaluation of the four methodologies are presented in this manuscript. The manually tracked landmarks were used to evaluate tracking accuracy of all methodologies. For 3DTAG, median values were computed over all time frames for the phantom dataset (MEVIS=1.20mm, IUCL=0.73 mm, UPF=1.10mm, INRIA=1.09 mm) and for the volunteer datasets (MEVIS=1.33 mm, IUCL=1.52 mm, UPF=1.09 mm, INRIA=1.32 mm). For 3DUS, median values were computed at end diastole and end systole for the phantom dataset (MEVIS=4.40 mm, UPF=3.48 mm, INRIA=4.78 mm) and for the volunteer datasets (MEVIS=3.51 mm, UPF=3.71 mm, INRIA=4.07 mm). For SSFP, median values were computed at end diastole and

  5. Problems underlying the use of referential integrity mechanisms in relational database management systems

    SciTech Connect

    Markowitz, V.M.

    1990-12-01

    Referential integrity is used in relational data-bases for expressing existence dependencies between tuples. Relational database management systems (RDBMS) provide diverse referential integrity capabilities. Thus, is some RDBMSs referential integrity constraints can be specified non-procedurally (declaratively), while in other RDBMSs they must be specified procedurally. Moreover, some RDBMSs restrict the class of allowed referential integrity constraints. We examine in this paper the main problems underlying the use of referential integrity mechanisms in three representative RDBMSs, DB2, SYBASE, and INGRES. 11 refs.

  6. Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

    ERIC Educational Resources Information Center

    Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

    2011-01-01

    Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

  7. Learning Relational Policies from Electronic Health Record Access Logs

    PubMed Central

    Malin, Bradley; Nyemba, Steve; Paulett, John

    2011-01-01

    Modern healthcare organizations (HCOs) are composed of complex dynamic teams to ensure clinical operations are executed in a quick and competent manner. At the same time, the fluid nature of such environments hinders administrators' efforts to define access control policies that appropriately balance patient privacy and healthcare functions. Manual efforts to define these policies are labor-intensive and error-prone, often resulting in systems that endow certain care providers with overly broad access to patients' medical records while restricting other providers from legitimate and timely use. In this work, we propose an alternative method to generate these policies by automatically mining usage patterns from electronic health record (EHR) systems. EHR systems are increasingly being integrated into clinical environments and our approach is designed to be generalizable across HCOs, thus assisting in the design and evaluation of local access control policies. Our technique, which is grounded in data mining and social network analysis theory, extracts a statistical model of the organization from the access logs of its EHRs. In doing so, our approach enables the review of predefined policies, as well as the discovery of unknown behaviors. We evaluate our approach with five months of access logs from the Vanderbilt University Medical Center and confirm the existence of stable social structures and intuitive business operations. Additionally, we demonstrate that there is significant turnover in the interactions between users in the HCO and that policies learned at the department level afford greater stability over time. PMID:21277996

  8. Veterans Affairs databases are accurate for gout-related health care utilization: a validation study

    PubMed Central

    2013-01-01

    Introduction The aim of this study was to assess the accuracy of Veterans Affairs (VA) databases for gout-related health care utilization. Methods This retrospective study utilized VA administrative and clinical databases. A random sample of gout patients with visits (outpatient, inpatient or emergent/urgent care) with or without the diagnosis of gout (International Classification of Diseases, ninth revision, common modification ICD-9-CM code of 274.x or 274.xx) at the Birmingham VA hospital was selected. A blinded abstractor performed a review of VA electronic health records for the documentation of gout or gout-related terms (gouty arthritis, tophaceous gout, tophus/tophi, acute gout, chronic gout, podagra, urate stones, urate or uric acid crystals and so on) in the chief complaint, history of present illness or assessment and plan for the visit; this constituted the gold standard for gout-related utilization. The accuracy of database-derived gout-related claims was assessed by calculating sensitivity, specificity, and positive and negative predictive values (PPV and NPV). Results Of 108 potential visits, 85 outpatient, inpatient or urgent care/emergency room visits to a health care provider (85 patients: 84 men and 1 woman with a mean age of 63 years) and retrievable data from medical records constituted the analyzed dataset. Administrative claims for gout-related utilization with ICD-9 code for gout were accurate with a PPV of 86%, specificity of 95%, sensitivity of 86% and NPV of 95%. Conclusions VA databases are accurate for gout-related visits. These findings support their use for studies of health services and outcome studies. It remains to be seen if these findings are generalizable to other settings and databases. PMID:24377421

  9. From Relationships to Relationship Marketing: Applying Database Technology to Public Relations.

    ERIC Educational Resources Information Center

    Petrison, Lisa A.; Wang, Paul

    1993-01-01

    Notes that advances in new technologies and uses of databases have expanded the definition of publics and increased the ability to target messages to narrower and narrower ranges of publics. Explores the implications of these developments for the public relations profession. (RS)

  10. Dynamic taxonomies applied to a web-based relational database for geo-hydrological risk mitigation

    NASA Astrophysics Data System (ADS)

    Sacco, G. M.; Nigrelli, G.; Bosio, A.; Chiarle, M.; Luino, F.

    2012-02-01

    In its 40 years of activity, the Research Institute for Geo-hydrological Protection of the Italian National Research Council has amassed a vast and varied collection of historical documentation on landslides, muddy-debris flows, and floods in northern Italy from 1600 to the present. Since 2008, the archive resources have been maintained through a relational database management system. The database is used for routine study and research purposes as well as for providing support during geo-hydrological emergencies, when data need to be quickly and accurately retrieved. Retrieval speed and accuracy are the main objectives of an implementation based on a dynamic taxonomies model. Dynamic taxonomies are a general knowledge management model for configuring complex, heterogeneous information bases that support exploratory searching. At each stage of the process, the user can explore or browse the database in a guided yet unconstrained way by selecting the alternatives suggested for further refining the search. Dynamic taxonomies have been successfully applied to such diverse and apparently unrelated domains as e-commerce and medical diagnosis. Here, we describe the application of dynamic taxonomies to our database and compare it to traditional relational database query methods. The dynamic taxonomy interface, essentially a point-and-click interface, is considerably faster and less error-prone than traditional form-based query interfaces that require the user to remember and type in the "right" search keywords. Finally, dynamic taxonomy users have confirmed that one of the principal benefits of this approach is the confidence of having considered all the relevant information. Dynamic taxonomies and relational databases work in synergy to provide fast and precise searching: one of the most important factors in timely response to emergencies.

  11. Exposing USGS sample collections for broader discovery and access: collaboration between ScienceBase, IEDA:SESAR, and Paleobiology Database

    NASA Astrophysics Data System (ADS)

    Hsu, L.; Bristol, S.; Lehnert, K. A.; Arko, R. A.; Peters, S. E.; Uhen, M. D.; Song, L.

    2014-12-01

    The U.S. Geological Survey (USGS) is an exemplar of the need for improved cyberinfrastructure for its vast holdings of invaluable physical geoscience data. Millions of discrete paleobiological and geological specimens lie in USGS warehouses and at the Smithsonian Institution. These specimens serve as the basis for many geologic maps and geochemical databases, and are a potential treasure trove of new scientific knowledge. The extent of this treasure is virtually unknown and inaccessible outside a small group of paleogeoscientists and geochemists. A team from the USGS, the Integrated Earth Data Applications (IEDA) facility, and the Paleobiology Database (PBDB) are working to expose information on paleontological and geochemical specimens for discovery by scientists and citizens. This project uses existing infrastructure of the System for Earth Sample Registration (SESAR) and PBDB, which already contains much of the fundamental data schemas that are necessary to accommodate USGS records. The project is also developing a new Linked Data interface for the USGS National Geochemical Database (NGDB). The International Geo Sample Number (IGSN) is the identifier that links samples between all systems. For paleontological specimens, SESAR and PBDB will be the primary repositories for USGS records, with a data syncing process to archive records within the USGS ScienceBase system. The process began with mapping the metadata fields necessary for USGS collections to the existing SESAR and PBDB data structures, while aligning them with the Observations & Measurements and Darwin Core standards. New functionality needed in SESAR included links to a USGS locality registry, fossil classifications, a spatial qualifier attribution for samples with sensitive locations, and acknowledgement of data and metadata licensing. The team is developing a harvesting mechanism to periodically transfer USGS records from within PBDB and SESAR to ScienceBase. For the NGDB, the samples are being

  12. dbPEC: a comprehensive literature-based database for preeclampsia related genes and phenotypes

    PubMed Central

    Uzun, Alper; Triche, Elizabeth W.; Schuster, Jessica; Dewan, Andrew T.; Padbury, James F.

    2016-01-01

    Preeclampsia is one of the most common causes of fetal and maternal morbidity and mortality in the world. We built a Database for Preeclampsia (dbPEC) consisting of the clinical features, concurrent conditions, published literature and genes associated with Preeclampsia. We included gene sets associated with severity, concurrent conditions, tissue sources and networks. The published scientific literature is the primary repository for all information documenting human disease. We used semantic data mining to retrieve and extract the articles pertaining to preeclampsia-associated genes and performed manual curation. We deposited the articles, genes, preeclampsia phenotypes and other supporting information into the dbPEC. It is publicly available and freely accessible. Previously, we developed a database for preterm birth (dbPTB) using a similar approach. Using the gene sets in dbPTB, we were able to successfully analyze a genome-wide study of preterm birth including 4000 women and children. We identified important genes and pathways associated with preterm birth that were not otherwise demonstrable using genome-wide approaches. dbPEC serves not only as a resources for genes and articles associated with preeclampsia, it is a robust source of gene sets to analyze a wide range of high-throughput data for gene set enrichment analysis. Database URL: http://ptbdb.cs.brown.edu/dbpec/ PMID:26946289

  13. Procedures for Writers in the Field of Adult Education: How To Make Your Writings More Consistently Accessible within Computerized Information Databases.

    ERIC Educational Resources Information Center

    Adrian, Judith Gwinn

    Educators who write documents or journal articles want to have their writing read and cited. To achieve this today, educators need to produce writings that are easily accessible through computerized searching (online and on compact disk) in databases. The trend toward end-users doing their own computerized information retrieval has caused database…

  14. DISTRIBUTED STRUCTURE-SEARCHABLE TOXICITY (DSSTOX) DATABASE NETWORK: MAKING PUBLIC TOXICITY DATA RESOURCES MORE ACCESSIBLE AND USABLE FOR DATA EXPLORATION AND SAR DEVELOPMENT

    EPA Science Inventory


    Distributed Structure-Searchable Toxicity (DSSTox) Database Network: Making Public Toxicity Data Resources More Accessible and U sable for Data Exploration and SAR Development

    Many sources of public toxicity data are not currently linked to chemical structure, are not ...

  15. Recent advances in the compilation of holocene relative Sea-level database in North America

    NASA Astrophysics Data System (ADS)

    Horton, B.; Vacchi, M.; Engelhart, S. E.; Nikitina, D.

    2015-12-01

    Reconstruction of relative sea level (RSL) has implications for investigation of crustal movements, calibration of earth rheology models and the reconstruction of ice sheets. In recent years, efforts were made to create RSL databases following a standardized methodology. These regional databases provided a framework for developing our understanding of the primary mechanisms of RSL change since the Last Glacial Maximum and a long-term baseline against which to gauge changes in sea-level during the 20th century and forecasts for the 21st. Here we present two quality-controlled Holocene RSL database compiled for North America. Along the Pacific coast of North America (British Columbia, Canada to California, USA), our re-evaluation of sea-level indicators from geological and archaeological investigations yield 841 RSL data-points mainly from salt and freshwater wetlands or adjacent estuarine sediment as well as from isolation basin. Along the Atlantic coast of North America (Hudson Bay, Canada to South Carolina, USA), we are currently compiling a database including more than 2000 RSL data-points from isolation basin, salt and freshwater wetlands, beach ridges and intratidal deposits. We outline the difficulties and solutions we made to compile databases in such different depostional environment. We address complex tectonics and the framework to compare such large variability of RSL data-point. We discuss the implications of our results for the glacio-isostatic adjustment (GIA) models in the two studied regions.

  16. An Object-Relational Ifc Storage Model Based on Oracle Database

    NASA Astrophysics Data System (ADS)

    Li, Hang; Liu, Hua; Liu, Yong; Wang, Yuan

    2016-06-01

    With the building models are getting increasingly complicated, the levels of collaboration across professionals attract more attention in the architecture, engineering and construction (AEC) industry. In order to adapt the change, buildingSMART developed Industry Foundation Classes (IFC) to facilitate the interoperability between software platforms. However, IFC data are currently shared in the form of text file, which is defective. In this paper, considering the object-based inheritance hierarchy of IFC and the storage features of different database management systems (DBMS), we propose a novel object-relational storage model that uses Oracle database to store IFC data. Firstly, establish the mapping rules between data types in IFC specification and Oracle database. Secondly, design the IFC database according to the relationships among IFC entities. Thirdly, parse the IFC file and extract IFC data. And lastly, store IFC data into corresponding tables in IFC database. In experiment, three different building models are selected to demonstrate the effectiveness of our storage model. The comparison of experimental statistics proves that IFC data are lossless during data exchange.

  17. Databases as an information service

    NASA Technical Reports Server (NTRS)

    Vincent, D. A.

    1983-01-01

    The relationship of databases to information services, and the range of information services users and their needs for information is explored and discussed. It is argued that for database information to be valuable to a broad range of users, it is essential that access methods be provided that are relatively unstructured and natural to information services users who are interested in the information contained in databases, but who are not willing to learn and use traditional structured query languages. Unless this ease of use of databases is considered in the design and application process, the potential benefits from using database systems may not be realized.

  18. Global search tool for the Advanced Photon Source Integrated Relational Model of Installed Systems (IRMIS) database.

    SciTech Connect

    Quock, D. E. R.; Cianciarulo, M. B.; APS Engineering Support Division; Purdue Univ.

    2007-01-01

    The Integrated Relational Model of Installed Systems (IRMIS) is a relational database tool that has been implemented at the Advanced Photon Source to maintain an updated account of approximately 600 control system software applications, 400,000 process variables, and 30,000 control system hardware components. To effectively display this large amount of control system information to operators and engineers, IRMIS was initially built with nine Web-based viewers: Applications Organizing Index, IOC, PLC, Component Type, Installed Components, Network, Controls Spares, Process Variables, and Cables. However, since each viewer is designed to provide details from only one major category of the control system, the necessity for a one-stop global search tool for the entire database became apparent. The user requirements for extremely fast database search time and ease of navigation through search results led to the choice of Asynchronous JavaScript and XML (AJAX) technology in the implementation of the IRMIS global search tool. Unique features of the global search tool include a two-tier level of displayed search results, and a database data integrity validation and reporting mechanism.

  19. The PIR-International databases.

    PubMed Central

    Barker, W C; George, D G; Mewes, H W; Pfeiffer, F; Tsugita, A

    1993-01-01

    PIR-International is an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. PIR-International is most noted for the Protein Sequence Database. This database originated in the early 1960's with the pioneering work of the late Margaret Dayhoff as a research tool for the study of protein evolution and intersequence relationships; it is maintained as a scientific resource, organized by biological concepts, using sequence homology as a guiding principle. PIR-International also maintains a number of other genomic, protein sequence, and sequence-related databases. The databases of PIR-International are made widely available. This paper briefly describes the architecture of the Protein Sequence Database, a number of other PIR-International databases, and mechanisms for providing access to and for distribution of these databases. PMID:8332528

  20. Monitoring of services with non-relational databases and map-reduce framework

    NASA Astrophysics Data System (ADS)

    Babik, M.; Souto, F.

    2012-12-01

    Service Availability Monitoring (SAM) is a well-established monitoring framework that performs regular measurements of the core site services and reports the corresponding availability and reliability of the Worldwide LHC Computing Grid (WLCG) infrastructure. One of the existing extensions of SAM is Site Wide Area Testing (SWAT), which gathers monitoring information from the worker nodes via instrumented jobs. This generates quite a lot of monitoring data to process, as there are several data points for every job and several million jobs are executed every day. The recent uptake of non-relational databases opens a new paradigm in the large-scale storage and distributed processing of systems with heavy read-write workloads. For SAM this brings new possibilities to improve its model, from performing aggregation of measurements to storing raw data and subsequent re-processing. Both SAM and SWAT are currently tuned to run at top performance, reaching some of the limits in storage and processing power of their existing Oracle relational database. We investigated the usability and performance of non-relational storage together with its distributed data processing capabilities. For this, several popular systems have been compared. In this contribution we describe our investigation of the existing non-relational databases suited for monitoring systems covering Cassandra, HBase and MongoDB. Further, we present our experiences in data modeling and prototyping map-reduce algorithms focusing on the extension of the already existing availability and reliability computations. Finally, possible future directions in this area are discussed, analyzing the current deficiencies of the existing Grid monitoring systems and proposing solutions to leverage the benefits of the non-relational databases to get more scalable and flexible frameworks.

  1. Scientific Meetings Database: A New Tool for CTBT-Related International Cooperation

    SciTech Connect

    Knapik, Jerzy F.; Girven, Mary L.

    1999-08-20

    The mission of international cooperation is defined in the Comprehensive Nuclear-Test-Ban Treaty (CTBT). Ways and means of implementation were the subject of discussion during the International Cooperation Workshop held in Vienna in November 1998, and during the Regional Workshop for CTBTO International Cooperation held in Cairo, Egypt in June 1999. In particular, a database of ''Scientific and Technical Meetings Directly or Indirectly Related to CTBT Verification-Related Technologies'' was developed by the CTBTO PrepCom/PTS/International Cooperation section and integrated into the organization's various web sites in cooperation with the U.S. Department of Energy CTBT Research and Development Program. This database, the structure and use of which is described in this paper/presentation is meant to assist the CTBT-related scientific community in identifying worldwide expertise in the CTBT verification-related technologies and should help experts, particularly those of less technologically advanced States Signatories, to strengthen contacts and to pursue international cooperation under the Tredy regime. Specific opportunities for international cooperation, in particular those provided by active participation in the use and further development of this database, are presented in this paper and/or presentation.

  2. Developing a Multicomponent Model of Nutritious Food Access and Related Implications for Community and Policy Practice

    PubMed Central

    FREEDMAN, DARCY A.; BLAKE, CHRISTINE E.; LIESE, ANGELA D.

    2014-01-01

    Access to nutritious foods is limited in disenfranchised communities in the United States. Policies are beginning to focus on improving nutritious food access in these contexts; yet, few theories are available to guide this work. We developed a conceptual model of nutritious food access based on the qualitative responses of food consumers in 2 different regions of the American South. Five domains (economic, service delivery, spatial–temporal, social, and personal) and related dimensions of nutritious food access were identified. The conceptual model provides practical guidance to researchers, policy makers, and practitioners working to improve nutritious food access in communities. PMID:24563605

  3. Compilation of Physicochemical and Toxicological Information About Hydraulic Fracturing-Related Chemicals (Draft Database)

    EPA Science Inventory

    The purpose of this product is to make accessible the information about the 1,173 hydraulic fracturing-related chemicals that were listed in the external review draft of the Hydraulic Fracturing Drinking Water Assessment that was released recently. The product consists of a serie...

  4. Engineering the object-relation database model in O-Raid

    NASA Technical Reports Server (NTRS)

    Dewan, Prasun; Vikram, Ashish; Bhargava, Bharat

    1989-01-01

    Raid is a distributed database system based on the relational model. O-raid is an extension of the Raid system and will support complex data objects. The design of O-Raid is evolutionary and retains all features of relational data base systems and those of a general purpose object-oriented programming language. O-Raid has several novel properties. Objects, classes, and inheritance are supported together with a predicate-base relational query language. O-Raid objects are compatible with C++ objects and may be read and manipulated by a C++ program without any 'impedance mismatch'. Relations and columns within relations may themselves be treated as objects with associated variables and methods. Relations may contain heterogeneous objects, that is, objects of more than one class in a certain column, which can individually evolve by being reclassified. Special facilities are provided to reduce the data search in a relation containing complex objects.

  5. Adding Hierarchical Objects to Relational Database General-Purpose XML-Based Information Managements

    NASA Technical Reports Server (NTRS)

    Lin, Shu-Chun; Knight, Chris; La, Tracy; Maluf, David; Bell, David; Tran, Khai Peter; Gawdiak, Yuri

    2006-01-01

    NETMARK is a flexible, high-throughput software system for managing, storing, and rapid searching of unstructured and semi-structured documents. NETMARK transforms such documents from their original highly complex, constantly changing, heterogeneous data formats into well-structured, common data formats in using Hypertext Markup Language (HTML) and/or Extensible Markup Language (XML). The software implements an object-relational database system that combines the best practices of the relational model utilizing Structured Query Language (SQL) with those of the object-oriented, semantic database model for creating complex data. In particular, NETMARK takes advantage of the Oracle 8i object-relational database model using physical-address data types for very efficient keyword searches of records across both context and content. NETMARK also supports multiple international standards such as WEBDAV for drag-and-drop file management and SOAP for integrated information management using Web services. The document-organization and -searching capabilities afforded by NETMARK are likely to make this software attractive for use in disciplines as diverse as science, auditing, and law enforcement.

  6. Relative Impact of Print and Database Products on Database Producer Expenses and Income--A Follow-Up.

    ERIC Educational Resources Information Center

    Williams, Martha E.

    1982-01-01

    Provides update to 13-year analysis of finances of major database producer noting actions taken to improve finances (decrease expenses, increase efficiency, develop new products, market strategies and services, change pricing scheme, omit print products, increase prices) and consequences of actions (revenue increase, connect hour increase). Five…

  7. A State Survey's Experience with the National Geothermal Database System: Lessons Learned to Improve Data Discovery, Access, and Stewardship

    NASA Astrophysics Data System (ADS)

    Hills, D. J.; Richard, S. M.

    2013-12-01

    State Geological Surveys in the U.S., in conjunction with the U.S. Geological Survey, have thousands of databases, directories, and 85,000+ geologic maps that collectively constitute a national geoscience data 'backbone' for research and practical applications. Much of this data has been at-risk in its current format or difficult to access. Organized by the Association of American State Geologists (AASG) with funding from the U.S. Department of Energy, the National Geothermal Data System (NGDS) has been able to make large quantities of geothermal-relevant geoscience data available to the public by creating a national, sustainable, distributed, and interoperable network of data providers. State Surveys or their equivalent have been instrumental to the success of the NGDS, but many have not had previous experience developing the necessary resources for credibility, sustainability, and interoperability beyond their area. The Geological Survey of Alabama (GSA) was no exception; here we expand upon some of the lessons the GSA has learned throughout this process, including a vision of a path forward. A major challenge that had to be overcome was the disconnect between interoperability requirements for the content models and the research interests of scientists providing the data. This was overcome by open and direct dialogue between the content developers and content providers. Although the iterative process could be frustrating at times, the result is a robust and thoroughly tested content model for geothermal data. This content model will provide an excellent starting point for other geoscience data content models. The greatest challenges the GSA encountered during the NGDS project were lack of standardization of our own data resources; lack of documentation; unknown quality of data; and lack of provenance of data. Moving forward, the GSA now has a model for stewardship of data, including what information and metadata should be collected to ensure future

  8. IPD: the Immuno Polymorphism Database.

    PubMed

    Robinson, James; Marsh, Steven G E

    2007-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer cell immunoglobulin-like receptors (KIRs); IPD-MHC, a database of sequences of the major histocompatibility complex (MHC) of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC, share the same database structure. PMID:18449992

  9. The Relationship between Searches Performed in Online Databases and the Number of Full-Text Articles Accessed: Measuring the Interaction between Database and E-Journal Collections

    ERIC Educational Resources Information Center

    Lamothe, Alain R.

    2011-01-01

    The purpose of this paper is to report the results of a quantitative analysis exploring the interaction and relationship between the online database and electronic journal collections at the J. N. Desmarais Library of Laurentian University. A very strong relationship exists between the number of searches and the size of the online database…

  10. Relating L versus P to Reversal versus Access and Their Combinatorial Structures

    NASA Astrophysics Data System (ADS)

    Ueno, Kenya

    Reversal complexity has been studied as a fundamental computational resource along with time and space complexity. We revisit it by contrasting with access complexity which we introduce in this study. First, we study the structure of space bounded reversal and access complexity classes. We characterize the complexity classes L, P and PSPACE in terms of space bounded reversal and access complexity classes. We also show that the difference between polynomial space bounded reversal and access complexity is related with the L versus P problem. Moreover, we introduce a theory of memory access patterns, which is an abstracted structure of the order of memory accesses during a random access computation, and extend the notion of reversal and access complexity for general random access computational models. Then, we give probabilistic analyses of reversal and access complexity for almost all memory access patterns. In particular, we prove that almost all memory access patterns have ω(log n) reversal complexity while all languages in L are computable within O(log n) reversal complexity.

  11. DB90: A Fortran Callable Relational Database Routine for Scientific and Engineering Computer Programs

    NASA Technical Reports Server (NTRS)

    Wrenn, Gregory A.

    2005-01-01

    This report describes a database routine called DB90 which is intended for use with scientific and engineering computer programs. The software is written in the Fortran 90/95 programming language standard with file input and output routines written in the C programming language. These routines should be completely portable to any computing platform and operating system that has Fortran 90/95 and C compilers. DB90 allows a program to supply relation names and up to 5 integer key values to uniquely identify each record of each relation. This permits the user to select records or retrieve data in any desired order.

  12. In-house access to PACS images and related data through World Wide Web

    NASA Astrophysics Data System (ADS)

    Mascarini, Christian; Ratib, Osman M.; Trayser, Gerhard; Ligier, Yves; Appel, R. D.

    1996-05-01

    The development of a hospital wide PACS is in progress at the University Hospital of Geneva and several archive modules are operational since 1992. This PACS is intended for wide distribution of images to clinical wards. As the PACS project and the number of archived images grow rapidly in the hospital, it was necessary to provide an easy, more widely accessible and convenient access to the PACS database for the clinicians in the different wards and clinical units of the hospital. An innovative solution has been developed using tools such as Netscape navigator and NCSA World Wide Web server as an alternative to conventional database query and retrieval software. These tools present the advantages of providing an user interface which is the same independently of the platform being used (Mac, Windows, UNIX, ...), and an easy integration of different types of documents (text, images, ...). A strict access control has been added to this interface. It allows user identification and access rights checking, as defined by the in-house hospital information system, before allowing the navigation through patient data records.

  13. Oceans of Data: In what ways can learning research inform the development of electronic interfaces and tools for use by students accessing large scientific databases?

    NASA Astrophysics Data System (ADS)

    Krumhansl, R. A.; Foster, J.; Peach, C. L.; Busey, A.; Baker, I.

    2012-12-01

    The practice of science and engineering is being revolutionized by the development of cyberinfrastructure for accessing near real-time and archived observatory data. Large cyberinfrastructure projects have the potential to transform the way science is taught in high school classrooms, making enormous quantities of scientific data available, giving students opportunities to analyze and draw conclusions from many kinds of complex data, and providing students with experiences using state-of-the-art resources and techniques for scientific investigations. However, online interfaces to scientific data are built by scientists for scientists, and their design can significantly impede broad use by novices. Knowledge relevant to the design of student interfaces to complex scientific databases is broadly dispersed among disciplines ranging from cognitive science to computer science and cartography and is not easily accessible to designers of educational interfaces. To inform efforts at bridging scientific cyberinfrastructure to the high school classroom, Education Development Center, Inc. and the Scripps Institution of Oceanography conducted an NSF-funded 2-year interdisciplinary review of literature and expert opinion pertinent to making interfaces to large scientific databases accessible to and usable by precollege learners and their teachers. Project findings are grounded in the fundamentals of Cognitive Load Theory, Visual Perception, Schemata formation and Universal Design for Learning. The Knowledge Status Report (KSR) presents cross-cutting and visualization-specific guidelines that highlight how interface design features can address/ ameliorate challenges novice high school students face as they navigate complex databases to find data, and construct and look for patterns in maps, graphs, animations and other data visualizations. The guidelines present ways to make scientific databases more broadly accessible by: 1) adjusting the cognitive load imposed by the user

  14. The development of a virtual database to provide on-line access to a large archive of clinical data.

    PubMed Central

    Stevens, L. E.; Huff, S. M.; Haug, P. J.

    1992-01-01

    The archival database of the HELP Hospital Information System at LDS Hospital is too large to be stored on line. The archival data are important for clinical and research applications. Demountable disk packs have been used to store the archival database. This method of storage has four significant disadvantages. A virtual database was developed to overcome the limitations of this data-management scheme. This virtual database enables the transparent use of appropriate low-cost network-based storage technology to provide on-line availability of the entire archive of clinical data. The virtual database successfully resolves the problems associated with disk packs, and opens the door to enhanced use of the data for clinical and research applications. PMID:1482943

  15. Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders

    PubMed Central

    Chen, Chong; Jiang, Yi; Xu, Chenyang; Liu, Xinting; Hu, Lin; Xiang, Yanbao; Chen, Qingshuang; Chen, Denghui; Li, Huanzheng; Xu, Xueqin; Tang, Shaohua

    2016-01-01

    Genetic skeletal disorders (GSD) involving the skeletal system arises through disturbances in the complex processes of skeletal development, growth and homeostasis and remain a diagnostic challenge because of their clinical heterogeneity and genetic variety. Over the past decades, tremendous effort platforms have been made to explore the complex heterogeneity, and massive new genes and mutations have been identified in different GSD, but the information supplied by literature is still limited and it is hard to meet the further needs of scientists and clinicians. In this study, combined with Nosology and Classification of genetic skeletal disorders, we developed the first comprehensive and annotated genetic skeletal disorders database, named ‘SkeletonGenetics’, which contains information about all GSD-related knowledge including 8225 mutations in 357 genes, with detailed information associated with 481 clinical diseases (2260 clinical phenotype) classified in 42 groups defined by molecular, biochemical and/or radiographic criteria from 1698 publications. Further annotations were performed to each entry including Gene Ontology, pathways analysis, protein–protein interaction, mutation annotations, disease–disease clustering and gene–disease networking. Furthermore, using concise search methods, intuitive graphical displays, convenient browsing functions and constantly updatable features, ‘SkeletonGenetics’ could serve as a central and integrative database for unveiling the genetic and pathways pre-dispositions of GSD. Database URL: http://101.200.211.232/skeletongenetics/ PMID:27580923

  16. Analyzing product test data in a relational database using SAS software

    SciTech Connect

    Orman, J.L.

    1991-01-01

    SAS software is being used to analyze product test data stored in an INGRES relational database. The database has been implemented at Allied-Signal in Kansas City on a Digital Equipment Corporation (DEC) VAX computer. The INGRES application development has been a joint project between Sandia National Laboratories and Allied-Signal. Application screens have been developed so that the user can query the database for selected data. Fourth generation language procedures are used to retrieve all data requested. FORTRAN and VAX/VMS DCL (DIGITAL Control Language) procedures are invoked from the application to create SAS data sets and dynamically build SAS programs that are executed to build custom reports or graphically display the retrieved test data along with control and specification limits. A retrieval screen has also been developed which invokes SAS software to calculate the mean and standard deviation of the retrieved data. These parameters are passed back into the application for display and may then be used as an aid in setting new control limits for future test runs. Screens have been developed to provide an interface for the user to select from a library of SAS programs, edit the selected program, and run the program with a user-defined SAS data set as input. This paper will give a brief description of the application screens and provide details of how information is passed between the application and SAS programs.

  17. Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders.

    PubMed

    Chen, Chong; Jiang, Yi; Xu, Chenyang; Liu, Xinting; Hu, Lin; Xiang, Yanbao; Chen, Qingshuang; Chen, Denghui; Li, Huanzheng; Xu, Xueqin; Tang, Shaohua

    2016-01-01

    Genetic skeletal disorders (GSD) involving the skeletal system arises through disturbances in the complex processes of skeletal development, growth and homeostasis and remain a diagnostic challenge because of their clinical heterogeneity and genetic variety. Over the past decades, tremendous effort platforms have been made to explore the complex heterogeneity, and massive new genes and mutations have been identified in different GSD, but the information supplied by literature is still limited and it is hard to meet the further needs of scientists and clinicians. In this study, combined with Nosology and Classification of genetic skeletal disorders, we developed the first comprehensive and annotated genetic skeletal disorders database, named 'SkeletonGenetics', which contains information about all GSD-related knowledge including 8225 mutations in 357 genes, with detailed information associated with 481 clinical diseases (2260 clinical phenotype) classified in 42 groups defined by molecular, biochemical and/or radiographic criteria from 1698 publications. Further annotations were performed to each entry including Gene Ontology, pathways analysis, protein-protein interaction, mutation annotations, disease-disease clustering and gene-disease networking. Furthermore, using concise search methods, intuitive graphical displays, convenient browsing functions and constantly updatable features, 'SkeletonGenetics' could serve as a central and integrative database for unveiling the genetic and pathways pre-dispositions of GSD.Database URL: http://101.200.211.232/skeletongenetics/. PMID:27580923

  18. GLM: A relational database system for linkage mapping on PC compatibles

    SciTech Connect

    Lucek, P.; Ott, J.

    1994-09-01

    Collection and management of family data, phenotypes, genotypes and the creation of a catalog of available and potential genetic markers can easily become overwhelming. The General Linkage Mapping (GLM) database and analysis system is designed to be an easy to use program with an intuitive interface for managing the data required for input and the resulting data output from two point linkage mapping analysis programs such as LINKAGE, MLINK, and ILINK. A comprehensive context-sensitive help system in integrated into the program along with data transfer and data backup capabilities. The relational databases managed by the GLM program are structured such that each project/disease can have multiple families, and marker, genotype, and result databases. Family data includes father/mother relationships; twin relationships, sex, age, date of birth/death, availability for typing, laboratory ID, and up to 50 phenotypes or diagnostic criteria, with corresponding liability classes and ages of onset. The liability classes can be entered manually or can be calculated from the individual`s age or age of disease onset. Phenotype data can either be quantitative, binary or of the affection status type. Genotype data, cross-referenced by laboratory ID, can be entered using any unique identification for each allele (e.g. size of dinucleotide repeats). Marker information includes marker name, chromosome, sex-ratio, allele identifications and frequencies. The GLM program creates all of the ASCII output files required by LINKAGE, MLINK and ILINK for input. Multiple or single families can be run. Upon execution of these programs, the GLM program imports the results of the analysis and keeps a database family, marker, date of analysis, and LOD scores. Future versions will include two-point exclusion mapping capabilities and output files for multipoint analysis.

  19. Chapter 6: Children's Environmental Access in Relation to Motor Competence, Physical Activity, and Fitness

    ERIC Educational Resources Information Center

    Erwin, Heather E.; Woods, Amelia Mays; Woods, Martha K.; Castelli, Darla M.

    2007-01-01

    The purpose of this study was to examine levels of physical activity engagement, motor competence, and physical fitness as related to child access to physical activity facilities in the home and school environments. The present investigation attempts to further efforts to examine the relationship between physical activity levels and access.…

  20. Data in support of UbSRD: The Ubiquitin Structural Relational Database

    PubMed Central

    Harrison, Joseph S.; Jacobs, Tim M.; Houlihan, Kevin; Van Doorslaer, Koenraad; Kuhlman, Brian

    2015-01-01

    This article provides information to support the database article titled “UbSRD: The Ubiquitin Structural Relational Database” (Harrison et al., 2015) [1] . The ubiquitin-like homology fold (UBL) represents a large family that encompasses both post-translational modifications, like ubiquitin (UBQ) and SUMO, and functional domains on many biologically important proteins like Parkin, UHRF1 (ubiquitin-like with PDB and RING finger domains-1), and Usp7 (ubiquitin-specific protease-7) (Zhang et al., 2015; Rothbart et al., 2013; Burroughs et al., 2012; Wauer et al., 2015) [2], [3], [4], [5]. The UBL domain can participate in several unique protein–protein interactions (PPI) since protein adducts can be attached to and removed from amino groups of lysine side chains and the N-terminus of proteins. Given the biological significance of UBL domains, many have been characterized with high-resolution techniques, and for UBQ and SUMO, many protein complexes have been characterized. We identified all the UBL domains in the PDB and created a relational database called UbSRD (Ubiquitin Structural Relational Database) by using structural analysis tools in the Rosetta (Leaver et al., 2013; O’Meara et al., 2015; Leaver-fay et al., 2011) [1], [6], [7], [8]. Querying UbSRD permitted us to report many quantitative properties of UBQ and SUMO recognition at different types interfaces (noncovalent: NC, conjugated: CJ, and deubiquitanse: DB). In this data article, we report the average number of non-UBL neighbors, secondary structure of interacting motifs, and the type of inter-molecular hydrogen bonds for each residue of UBQ and SUMO. Additionally, we used PROMALS3D to generate a multiple sequence alignment used to construct a phylogram for the entire set of UBLs (Pei and Grishin, 2014) [9]. The data described here will be generally useful to scientists studying the molecular basis for recognition of UBQ or SUMO. PMID:26958617

  1. Database Marketplace 2002: The Database Universe.

    ERIC Educational Resources Information Center

    Tenopir, Carol; Baker, Gayle; Robinson, William

    2002-01-01

    Reviews the database industry over the past year, including new companies and services, company closures, popular database formats, popular access methods, and changes in existing products and services. Lists 33 firms and their database services; 33 firms and their database products; and 61 company profiles. (LRW)

  2. TR-DB: an open-access database of compounds affecting the ethylene-induced triple response in Arabidopsis.

    PubMed

    Hu, Yuming; Callebert, Pieter; Vandemoortel, Ilse; Nguyen, Long; Audenaert, Dominique; Verschraegen, Luc; Vandenbussche, Filip; Van Der Straeten, Dominique

    2014-02-01

    Small molecules which act as hormone agonists or antagonists represent useful tools in fundamental research and are widely applied in agriculture to control hormone effects. High-throughput screening of large chemical compound libraries has yielded new findings in plant biology, with possible future applications in agriculture and horticulture. To further understand ethylene biosynthesis/signaling and its crosstalk with other hormones, we screened a 12,000 compound chemical library based on an ethylene-related bioassay of dark-grown Arabidopsis thaliana (L.) Heynh. seedlings. From the initial screening, 1313 (∼11%) biologically active small molecules altering the phenotype triggered by the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), were identified. Selection and sorting in classes were based on the angle of curvature of the apical hook, the length and width of the hypocotyl and the root. A MySQL-database was constructed (https://chaos.ugent.be/WE15/) including basic chemical information on the compounds, images illustrating the phenotypes, phenotype descriptions and classification. The research perspectives for different classes of hit compounds will be evaluated, and some general screening tips for customized high-throughput screening and pitfalls will be discussed. PMID:24441765

  3. Usage of the Jess Engine, Rules and Ontology to Query a Relational Database

    NASA Astrophysics Data System (ADS)

    Bak, Jaroslaw; Jedrzejek, Czeslaw; Falkowski, Maciej

    We present a prototypical implementation of a library tool, the Semantic Data Library (SDL), which integrates the Jess (Java Expert System Shell) engine, rules and ontology to query a relational database. The tool extends functionalities of previous OWL2Jess with SWRL implementations and takes full advantage of the Jess engine, by separating forward and backward reasoning. The optimization of integration of all these technologies is an advancement over previous tools. We discuss the complexity of the query algorithm. As a demonstration of capability of the SDL library, we execute queries using crime ontology which is being developed in the Polish PPBW project.

  4. Providing multilingual access to health-related content.

    PubMed

    Plumbaum, Till; Narr, Sascha; Eryilmaz, Elif; Hopfgartner, Frank; Klein-Ellinghaus, Funda; Reese, Anna; Albayrak, Sahin

    2014-01-01

    Finding health-related content is not an easy task. People have to know what to search for, which medical terms to use, and where to find accurate information. This task becomes even harder when people such as immigrants wish to find information in their country of residence and do not speak the national language very well. In this paper, we present a new health information system that allows users to search for health information using natural language queries composed of multiple languages. We present the technical details of the system and outline the results of a preliminary user study to demonstrate the usability of the system. PMID:25160213

  5. GRASP: analysis of genotype–phenotype results from 1390 genome-wide association studies and corresponding open access database

    PubMed Central

    Leslie, Richard; O’Donnell, Christopher J.; Johnson, Andrew D.

    2014-01-01

    Summary: We created a deeply extracted and annotated database of genome-wide association studies (GWAS) results. GRASP v1.0 contains >6.2 million SNP-phenotype association from among 1390 GWAS studies. We re-annotated GWAS results with 16 annotation sources including some rarely compared to GWAS results (e.g. RNAediting sites, lincRNAs, PTMs). Motivation: To create a high-quality resource to facilitate further use and interpretation of human GWAS results in order to address important scientific questions. Results: GWAS have grown exponentially, with increases in sample sizes and markers tested, and continuing bias toward European ancestry samples. GRASP contains >100 000 phenotypes, roughly: eQTLs (71.5%), metabolite QTLs (21.2%), methylation QTLs (4.4%) and diseases, biomarkers and other traits (2.8%). cis-eQTLs, meQTLs, mQTLs and MHC region SNPs are highly enriched among significant results. After removing these categories, GRASP still contains a greater proportion of studies and results than comparable GWAS catalogs. Cardiovascular disease and related risk factors pre-dominate remaining GWAS results, followed by immunological, neurological and cancer traits. Significant results in GWAS display a highly gene-centric tendency. Sex chromosome X (OR = 0.18[0.16-0.20]) and Y (OR = 0.003[0.001-0.01]) genes are depleted for GWAS results. Gene length is correlated with GWAS results at nominal significance (P ≤ 0.05) levels. We show this gene-length correlation decays at increasingly more stringent P-value thresholds. Potential pleotropic genes and SNPs enriched for multi-phenotype association in GWAS are identified. However, we note possible population stratification at some of these loci. Finally, via re-annotation we identify compelling functional hypotheses at GWAS loci, in some cases unrealized in studies to date. Conclusion: Pooling summary-level GWAS results and re-annotating with bioinformatics predictions and molecular features provides a good platform for new

  6. NASA's Global Change Master Directory: Discover and Access Earth Science Data Sets, Related Data Services, and Climate Diagnostics

    NASA Technical Reports Server (NTRS)

    Aleman, Alicia; Olsen, Lola; Ritz, Scott; Morahan, Michael; Cepero, Laurel; Stevens, Tyler

    2011-01-01

    NASA's Global Change Master Directory provides the scientific community with the ability to discover, access, and use Earth science data, data-related services, and climate diagnostics worldwide. The GCMD offers descriptions of Earth science data sets using the Directory Interchange Format (DIF) metadata standard; Earth science related data services are described using the Service Entry Resource Format (SERF); and climate visualizations are described using the Climate Diagnostic (CD) standard. The DIF, SERF and CD standards each capture data attributes used to determine whether a data set, service, or climate visualization is relevant to a user's needs. Metadata fields include: title, summary, science keywords, service keywords, data center, data set citation, personnel, instrument, platform, quality, related URL, temporal and spatial coverage, data resolution and distribution information. In addition, nine valuable sets of controlled vocabularies have been developed to assist users in normalizing the search for data descriptions. An update to the GCMD's search functionality is planned to further capitalize on the controlled vocabularies during database queries. By implementing a dynamic keyword "tree", users will have the ability to search for data sets by combining keywords in new ways. This will allow users to conduct more relevant and efficient database searches to support the free exchange and re-use of Earth science data. http://gcmd.nasa.gov/

  7. A database and model to support proactive management of sediment-related sewer blockages.

    PubMed

    Rodríguez, Juan Pablo; McIntyre, Neil; Díaz-Granados, Mario; Maksimović, Cedo

    2012-10-01

    Due to increasing customer and political pressures, and more stringent environmental regulations, sediment and other blockage issues are now a high priority when assessing sewer system operational performance. Blockages caused by sediment deposits reduce sewer system reliability and demand remedial action at considerable operational cost. Consequently, procedures are required for identifying which parts of the sewer system are in most need of proactive removal of sediments. This paper presents an exceptionally long (7.5 years) and spatially detailed (9658 grid squares--0.03 km² each--covering a population of nearly 7.5 million) data set obtained from a customer complaints database in Bogotá (Colombia). The sediment-related blockage data are modelled using homogeneous and non-homogeneous Poisson process models. In most of the analysed areas the inter-arrival time between blockages can be represented by the homogeneous process, but there are a considerable number of areas (up to 34%) for which there is strong evidence of non-stationarity. In most of these cases, the mean blockage rate increases over time, signifying a continual deterioration of the system despite repairs, this being particularly marked for pipe and gully pot related blockages. The physical properties of the system (mean pipe slope, diameter and pipe length) have a clear but weak influence on observed blockage rates. The Bogotá case study illustrates the potential value of customer complaints databases and formal analysis frameworks for proactive sewerage maintenance scheduling in large cities. PMID:22794800

  8. Access to Cancer Screening in People with Learning Disabilities in the UK: Cohort Study in the Health Improvement Network, a Primary Care Research Database

    PubMed Central

    Osborn, David P. J.; Horsfall, Laura; Hassiotis, Angela; Petersen, Irene; Walters, Kate; Nazareth, Irwin

    2012-01-01

    Objectives To assess whether people with learning disability in the UK have poorer access to cancer screening. Design Four cohort studies comparing people with and without learning disability, within the recommended age ranges for cancer screening in the UK. We used Poisson regression to determine relative incidence rates of cancer screening. Setting The Health Improvement Network, a UK primary care database with over 450 General practices. Participants Individuals with a recorded diagnosis of learning disability including general diagnostic terms, specific syndromes, chromosomal abnormalities and autism in their General Practitioner computerised notes. For each type of cancer screening, a comparison cohort of up to six people without learning disability was selected for each person with a learning disability, using stratified sampling on age within GP practice. Main outcome measures Incidence rate ratios for receiving 1) a cervical smear test, 2) a mammogram, 3) a faecal occult blood test and 4) a prostate specific antigen test. Results Relative rates of screening for all four cancers were significantly lower for people with learning disability. The adjusted incidence rate ratios (95% confidence intervals) were Cervical smears: Number eligible with learning disability = 6,254; IRR = 0.54 (0.52–0.56). Mammograms: Number eligible with learning disability = 2,956; IRR = 0.76 (0.72–0.81); Prostate Specific Antigen: Number eligible = 3,520; IRR = 0.87 (0.80–0.96) and Faecal Occult Blood Number eligible = 6,566; 0.86 (0.78–0.94). Differences in screening rates were less pronounced in more socially deprived areas. Disparities in cervical screening rates narrowed over time, but were 45% lower in 2008/9, those for breast cancer screening appeared to widen and were 35% lower in 2009. Conclusion Despite recent incentives, people with learning disability in the UK are significantly less likely to receive screening tests for cancer that

  9. Data management and language enhancement for generalized set theory computer language for operation of large relational databases

    NASA Technical Reports Server (NTRS)

    Finley, Gail T.

    1988-01-01

    This report covers the study of the relational database implementation in the NASCAD computer program system. The existing system is used primarily for computer aided design. Attention is also directed to a hidden-surface algorithm for final drawing output.

  10. Global coordination and standardisation in marine biodiversity through the World Register of Marine Species (WoRMS) and related databases.

    PubMed

    Costello, Mark J; Bouchet, Philippe; Boxshall, Geoff; Fauchald, Kristian; Gordon, Dennis; Hoeksema, Bert W; Poore, Gary C B; van Soest, Rob W M; Stöhr, Sabine; Walter, T Chad; Vanhoorne, Bart; Decock, Wim; Appeltans, Ward

    2013-01-01

    The World Register of Marine Species is an over 90% complete open-access inventory of all marine species names. Here we illustrate the scale of the problems with species names, synonyms, and their classification, and describe how WoRMS publishes online quality assured information on marine species. Within WoRMS, over 100 global, 12 regional and 4 thematic species databases are integrated with a common taxonomy. Over 240 editors from 133 institutions and 31 countries manage the content. To avoid duplication of effort, content is exchanged with 10 external databases. At present WoRMS contains 460,000 taxonomic names (from Kingdom to subspecies), 368,000 species level combinations of which 215,000 are currently accepted marine species names, and 26,000 related but non-marine species. Associated information includes 150,000 literature sources, 20,000 images, and locations of 44,000 specimens. Usage has grown linearly since its launch in 2007, with about 600,000 unique visitors to the website in 2011, and at least 90 organisations from 12 countries using WoRMS for their data management. By providing easy access to expert-validated content, WoRMS improves quality control in the use of species names, with consequent benefits to taxonomy, ecology, conservation and marine biodiversity research and management. The service manages information on species names that would otherwise be overly costly for individuals, and thus minimises errors in the application of nomenclature standards. WoRMS' content is expanding to include host-parasite relationships, additional literature sources, locations of specimens, images, distribution range, ecological, and biological data. Species are being categorised as introduced (alien, invasive), of conservation importance, and on other attributes. These developments have a multiplier effect on its potential as a resource for biodiversity research and management. As a consequence of WoRMS, we are witnessing improved communication within the

  11. Global Coordination and Standardisation in Marine Biodiversity through the World Register of Marine Species (WoRMS) and Related Databases

    PubMed Central

    Bouchet, Philippe; Boxshall, Geoff; Fauchald, Kristian; Gordon, Dennis; Hoeksema, Bert W.; Poore, Gary C. B.; van Soest, Rob W. M.; Stöhr, Sabine; Walter, T. Chad; Vanhoorne, Bart; Decock, Wim

    2013-01-01

    The World Register of Marine Species is an over 90% complete open-access inventory of all marine species names. Here we illustrate the scale of the problems with species names, synonyms, and their classification, and describe how WoRMS publishes online quality assured information on marine species. Within WoRMS, over 100 global, 12 regional and 4 thematic species databases are integrated with a common taxonomy. Over 240 editors from 133 institutions and 31 countries manage the content. To avoid duplication of effort, content is exchanged with 10 external databases. At present WoRMS contains 460,000 taxonomic names (from Kingdom to subspecies), 368,000 species level combinations of which 215,000 are currently accepted marine species names, and 26,000 related but non-marine species. Associated information includes 150,000 literature sources, 20,000 images, and locations of 44,000 specimens. Usage has grown linearly since its launch in 2007, with about 600,000 unique visitors to the website in 2011, and at least 90 organisations from 12 countries using WoRMS for their data management. By providing easy access to expert-validated content, WoRMS improves quality control in the use of species names, with consequent benefits to taxonomy, ecology, conservation and marine biodiversity research and management. The service manages information on species names that would otherwise be overly costly for individuals, and thus minimises errors in the application of nomenclature standards. WoRMS' content is expanding to include host-parasite relationships, additional literature sources, locations of specimens, images, distribution range, ecological, and biological data. Species are being categorised as introduced (alien, invasive), of conservation importance, and on other attributes. These developments have a multiplier effect on its potential as a resource for biodiversity research and management. As a consequence of WoRMS, we are witnessing improved communication within the

  12. Legal Factors Related to Access to Campuses of Public Colleges and Universities: An Occasional Paper.

    ERIC Educational Resources Information Center

    Lytle, Michael A.

    Legal methods and related case law that can be used by public higher education administrators to deal with intrusions by outsiders onto the campus are examined. The following legal factors related to control of campus access are addressed: risk management, police power, general trespass, school related trespass/loitering statutes, First and…

  13. Achieving a Dream: Meeting Policy Goals Related to Improving Drug Access

    PubMed Central

    Zakus, David; Kohler, Jillian Clare; Zakriova, Venera; Yarmoshuk, Aaron

    2010-01-01

    International experts recognize that significant inequities exist in the accessibility of life-saving medicines among poor and vulnerable populations, especially in developing countries. This article highlights that drug access even for relatively cheap medicines is out of reach for the vast numbers of global poor. This badly affects people living with HIV/AIDS who face serious obstacles in accessing ARVs. The same concerns are attributed to neglected diseases. Despite international meetings, promises from the pharmaceutical industry and a lot of media attention little has changed in the past 20 years. The accessibility gap to life-saving drugs could be reduced by the UNITAID initiative to pool patents for the many different ARVs, but the reality is that UNITAID is still a promise. To surmount this global problem of inequity requires a rethinking of traditional models of drug access and health objectives that should not be compromised by commercial interests. PMID:20148088

  14. Records for Electronic Databases in the Online Catalog at Middle Tennessee State University

    ERIC Educational Resources Information Center

    Geckle, Beverly J.; Pozzebon, Mary Ellen; Williams, Jo

    2008-01-01

    This article recounts a project at the Middle Tennessee State University library to include records for electronic databases in the online catalog. Although electronic databases are accessible via the library's Databases A-Z list and related subject guides, cataloging these resources also provides access via the online catalog, allowing more of…

  15. A Framework for Mapping User-Designed Forms to Relational Databases

    ERIC Educational Resources Information Center

    Khare, Ritu

    2011-01-01

    In the quest for database usability, several applications enable users to design custom forms using a graphical interface, and forward engineer the forms into new databases. The path-breaking aspect of such applications is that users are completely shielded from the technicalities of database creation. Despite this innovation, the process of…

  16. The Neotoma Paleoecology Database

    NASA Astrophysics Data System (ADS)

    Grimm, E. C.; Ashworth, A. C.; Barnosky, A. D.; Betancourt, J. L.; Bills, B.; Booth, R.; Blois, J.; Charles, D. F.; Graham, R. W.; Goring, S. J.; Hausmann, S.; Smith, A. J.; Williams, J. W.; Buckland, P.

    2015-12-01

    The Neotoma Paleoecology Database (www.neotomadb.org) is a multiproxy, open-access, relational database that includes fossil data for the past 5 million years (the late Neogene and Quaternary Periods). Modern distributional data for various organisms are also being made available for calibration and paleoecological analyses. The project is a collaborative effort among individuals from more than 20 institutions worldwide, including domain scientists representing a spectrum of Pliocene-Quaternary fossil data types, as well as experts in information technology. Working groups are active for diatoms, insects, ostracodes, pollen and plant macroscopic remains, testate amoebae, rodent middens, vertebrates, age models, geochemistry and taphonomy. Groups are also active in developing online tools for data analyses and for developing modules for teaching at different levels. A key design concept of NeotomaDB is that stewards for various data types are able to remotely upload and manage data. Cooperatives for different kinds of paleo data, or from different regions, can appoint their own stewards. Over the past year, much progress has been made on development of the steward software-interface that will enable this capability. The steward interface uses web services that provide access to the database. More generally, these web services enable remote programmatic access to the database, which both desktop and web applications can use and which provide real-time access to the most current data. Use of these services can alleviate the need to download the entire database, which can be out-of-date as soon as new data are entered. In general, the Neotoma web services deliver data either from an entire table or from the results of a view. Upon request, new web services can be quickly generated. Future developments will likely expand the spatial and temporal dimensions of the database. NeotomaDB is open to receiving new datasets and stewards from the global Quaternary community

  17. The use of relational database commands in retrieval of pedigree information.

    PubMed

    Yount, E A

    1987-06-01

    Genetic research frequently requires retrieval of information about families afflicted with some genetic disease. These queries may involve simple retrieval of information on individuals with particular attributes or finding data from sibships or families who meet some set of criteria. Although the former case may be handled by almost any file management system, the latter case cannot be easily managed since family relationships are necessary to the query. These family relationships are normally stored by means of a pointer system that links the record of each individual with those of his parents. Given such a pointer system, the standard commands of a relational database system can be used to perform such retrievals, thus diminishing the need for special programs to perform such queries. PMID:2959734

  18. High Availability On-line Relational Databases for Accelerator Control and Operation

    SciTech Connect

    Dohan,D.; Dalesio, L.; Carcassi, G.

    2009-05-04

    The role that relational database (RDB) technology plays in accelerator control and operation continues to grow in such areas as electronic logbooks, machine parameter definitions, and facility infrastructure management. RDBs are increasingly relied upon to provide the official 'master' copy of these data. Whereas the services provided by the RDB have traditionally not been 'mission critical', the availability of modern RDB management systems is now equivalent to that of standard computer file-systems. RDBs can be relied on to supply pseudo real-time response to operator and machine physicist requests. This paper describes recent developments in the IRMIS RDB project. Generic lattice support has been added, serving as the driver for model-based machine control. Abstract physics name service and process variable introspection has been added. Specific emphasis has been placed both on providing fast response time to accelerator operators and modeling code requests, as well as high (24/7) availability of the RDB service.

  19. a Relative Sea Level Database for the Pacific Coast of North America

    NASA Astrophysics Data System (ADS)

    Engelhart, S. E.; Vacchi, M.; Horton, B.; Nelson, A. R.

    2013-12-01

    Reconstruction of relative sea level (RSL) has implications for investigation of crustal movements, calibration of earth rheology models and the reconstruction of ice sheets. Here we present a quality-controlled RSL database compiled using data from the Pacific coast of North America (British Columbia, Canada to California, USA). This dataset includes 446 sea level index points that estimate the position of former RSL in time and space, and 181 limiting dates that constrain whether RSL was above (marine limiting) or below (terrestrial limiting) the sample. This coastal area is characterized by significant tectonic activity due to the Cascadia Subduction Zone in the north from British Columbia to northern California, and the San Andreas Fault in northern and central California. However, the tectonic contribution to RSL change from the Cascadia Subduction Zone and the San Andreas Fault is unknown. Elastic dislocation models of the earthquake deformation cycle have commonly assumed that Glacial Isostatic Adjustment (GIA) in the Cascadia subduction zone is non-existent. However, our data indicate ongoing GIA-related subsidence along the coasts of Washington, Oregon and California of a similar magnitude observed along the Atlantic coast of the USA and other proglacial forebulge regions in Europe. This has implications for GPS observations of vertical land movement from Cascadia that assume all motion is due to subduction zone deformation. Using a late Holocene subset of our database, we estimated the land-level changes associated with the ongoing GIA. Comparing this value with long-term (>50 year) tide gauge records allows us to improve estimates of the ongoing vertical deformation at Cascadia due to the subduction of the Juan de Fuca plate beneath the North American plate.

  20. GDBDICT: A program to extract GDB schema information into a relational database

    SciTech Connect

    Nadkarni, P.M. )

    1994-01-01

    GDBDICT synthesizes the information present in the two schema files and produces three tab-delimited files that can be imported directly into a relational database without further processing. These files are: (i) DIAG, a list of the functional categories into which an individual GDB table may belong; (ii) TABLES, a description of the GDB tables in each category; and (iii) FIELDS, a detailed description of the fields for each GDB table. After import, FIELDS will be related many-to-one to TABLES, which in turn will be related many-to-one to DIAG. This is because GDBDICT creates, for the FIELDS and TABLES files, the appropriate foreign key (i.e., the field linking that table to the table higher in the hierarchy). GDBDICT will report all discrepancies between GDB-DICTIONARY and TABLE-DICTIONARY as it processes them. Running GDBDICT on the current (February 1993) schema files showed 18 discrepancies, none of which, on closer inspection, turned out to be of significant consequence. 2 refs., 1 fig.

  1. Human rights responsibilities of pharmaceutical companies in relation to access to medicines.

    PubMed

    Lee, Joo-Young; Hunt, Paul

    2012-01-01

    Although access to medicines is a vital feature of the right to the highest attainable standard of health ("right to health"), almost two billion people lack access to essential medicines, leading to immense avoidable suffering. While the human rights responsibility to provide access to medicines lies mainly with States, pharmaceutical companies also have human rights responsibilities in relation to access to medicines. This article provides an introduction to these responsibilities. It briefly outlines the new UN Guiding Principles on Business and Human Rights and places the human rights responsibilities of pharmaceutical companies in this context. The authors draw from the work of the first UN Special Rapporteur on the right to the highest attainable standard of health, in particular the Human Rights Guidelines for Pharmaceutical Companies in Relation to Access to Medicines that he presented to the UN General Assembly in 2008, and his UN report on GlaxoSmithKline (GSK). While the Guiding Principles on Business and Human Rights are general human rights standards applicable to all business entities, the Human Rights Guidelines for Pharmaceutical Companies consider the specific human rights responsibilities of one sector (pharmaceutical companies) in relation to one area of activity (access to medicines). The article signals the human rights responsibilities of all pharmaceutical companies, with particular attention to patent-holding pharmaceutical companies. Adopting a right-to-health "lens," the article discusses GSK and accountability. The authors argue that human rights should shape pharmaceutical companies' policies, and provide standards in relation to which pharmaceutical companies could, and should, be held accountable. They conclude that it is now crucial to devise independent, accessible, transparent, and effective mechanisms to monitor pharmaceutical companies and hold them publicly accountable for their human rights responsibilities. PMID:22789042

  2. Physiological Information Database (PID)

    EPA Science Inventory

    EPA has developed a physiological information database (created using Microsoft ACCESS) intended to be used in PBPK modeling. The database contains physiological parameter values for humans from early childhood through senescence as well as similar data for laboratory animal spec...

  3. TRY 3.0 - a substantial upgrade of the global database of plant traits: more data, more species, largely open access

    NASA Astrophysics Data System (ADS)

    Kattge, Jens; Díaz, Sandra; Lavorel, Sandra; Prentice, Ian Colin; Leadley, Paul; Boenisch, Gerhard; Wirth, Christian; TRY Consortium, The

    2015-04-01

    Plant traits determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services, and provide a link from species richness to ecosystem functional diversity. Plant traits thus are a key to understand and predict the adaptation of ecosystems to environmental changes. At the same time ground based measurements of plant trait data are dispersed over a wide range of databases, many of these not publicly available. To overcome this deficiency IGBP and DIVERSITAS have initiated the development of a joint database, called TRY, aiming at constructing a standard resource of ground based plant trait observations for the ecological community and for the development of global vegetation models. The new version of the global database of plant traits - TRY 3.0 - provides substantially improved information on plant traits: 5.6 million trait records for about 100.000 of the worlds 350.000 plant species. More than 50% of the trait records are open access. In combination with recent improvements in gap-filling of sparse trait matrices (e.g., Bayesian Hierarchical Probabilistic Matrix Factrization; see abstract 15696 by Farideh Fazayeli) the new version of TRY provides the opportunity to derive a filled matrix of plant trait estimates for an unprecedented number of traits and species. We expect that this data richness will facilitate qualitatively new analyses and applications of plant traits (e.g., abstract 15724 by Oliver Purschke).

  4. Second primary malignancies among patients with myeloma-related-diseases in the KMF database.

    PubMed

    Kosugi, Satoru; Shibayama, Hirohiko; Nakatani, Eiji; Kida, Toru; Ohta, Kensuke; Kaneko, Hidemi; Yagi, Hideo; Tanaka, Hirokazu; Fuchida, Shin-Ichi; Nakaya, Aya; Kobayashi, Masayuki; Kuroda, Junya; Kamitsuji, Yuri; Uoshima, Nobuhiko; Adachi, Yoko; Tsudo, Mitsuru; Shimazaki, Chihiro; Nomura, Shosaku; Hino, Masayuki; Matsumura, Itaru; Taniwaki, Masashi; Kanakura, Yuzuru; Takaori-Kondo, Akifumi

    2016-07-01

    The incidence of second primary malignancies (SPMs) in Japanese patients with myeloma or myeloma-related diseases was studied by using the Kansai Myeloma Forum (KMF) database registered from November 2012 to March 2015. We studied 1,571 cases. Hematologic malignancies were documented in 10 patients, and solid tumors in 36 during this period. The cumulative 5-year incidence was estimated to be 1.0% for hematological malignancies and 3.7% for solid tumors. In the patients with smoldering myeloma or MGUS without treatment, solid tumors but not hematologic malignancies developed, though the cumulative incidence of each malignancy did not differ significantly from that in patients receiving treatment. Although statistical analysis showed that treatment with melphalan, bortezomib, lenalidomide, or thalidomide had no effect on the occurrence of hematological malignancies, lenalidomide administration was more frequent in the patients with solid tumors. To evaluate the SPMs in myeloma or myeloma-related diseases more accurately, accumulation of a larger number of patients and longer observation are needed. PMID:27498726

  5. Alternatives to relational databases in precision medicine: Comparison of NoSQL approaches for big data storage using supercomputers

    NASA Astrophysics Data System (ADS)

    Velazquez, Enrique Israel

    Improvements in medical and genomic technologies have dramatically increased the production of electronic data over the last decade. As a result, data management is rapidly becoming a major determinant, and urgent challenge, for the development of Precision Medicine. Although successful data management is achievable using Relational Database Management Systems (RDBMS), exponential data growth is a significant contributor to failure scenarios. Growing amounts of data can also be observed in other sectors, such as economics and business, which, together with the previous facts, suggests that alternate database approaches (NoSQL) may soon be required for efficient storage and management of big databases. However, this hypothesis has been difficult to test in the Precision Medicine field since alternate database architectures are complex to assess and means to integrate heterogeneous electronic health records (EHR) with dynamic genomic data are not easily available. In this dissertation, we present a novel set of experiments for identifying NoSQL database approaches that enable effective data storage and management in Precision Medicine using patients' clinical and genomic information from the cancer genome atlas (TCGA). The first experiment draws on performance and scalability from biologically meaningful queries with differing complexity and database sizes. The second experiment measures performance and scalability in database updates without schema changes. The third experiment assesses performance and scalability in database updates with schema modifications due dynamic data. We have identified two NoSQL approach, based on Cassandra and Redis, which seems to be the ideal database management systems for our precision medicine queries in terms of performance and scalability. We present NoSQL approaches and show how they can be used to manage clinical and genomic big data. Our research is relevant to the public health since we are focusing on one of the main

  6. Rdesign: A data dictionary with relational database design capabilities in Ada

    NASA Technical Reports Server (NTRS)

    Lekkos, Anthony A.; Kwok, Teresa Ting-Yin

    1986-01-01

    Data Dictionary is defined to be the set of all data attributes, which describe data objects in terms of their intrinsic attributes, such as name, type, size, format and definition. It is recognized as the data base for the Information Resource Management, to facilitate understanding and communication about the relationship between systems applications and systems data usage and to help assist in achieving data independence by permitting systems applications to access data knowledge of the location or storage characteristics of the data in the system. A research and development effort to use Ada has produced a data dictionary with data base design capabilities. This project supports data specification and analysis and offers a choice of the relational, network, and hierarchical model for logical data based design. It provides a highly integrated set of analysis and design transformation tools which range from templates for data element definition, spreadsheet for defining functional dependencies, normalization, to logical design generator.

  7. AIM: A comprehensive Arabidopsis Interactome Module database and related interologs in plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Systems biology analysis of protein modules is important for understanding the functional relationships between proteins in the interactome. Here, we present a comprehensive database named AIM for Arabidopsis (Arabidopsis thaliana) interactome modules. The database contains almost 250,000 modules th...

  8. Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

    PubMed Central

    2013-01-01

    Background In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. Results We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. Conclusions BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic. PMID:23586394

  9. Access to artemisinin-based anti-malarial treatment and its related factors in rural Tanzania

    PubMed Central

    2013-01-01

    Background Artemisinin-based combination treatment (ACT) has been widely adopted as one of the main malaria control strategies. However, its promise to save thousands of lives in sub-Saharan Africa depends on how effective the use of ACT is within the routine health system. The INESS platform evaluated effective coverage of ACT in several African countries. Timely access within 24 hours to an authorized ACT outlet is one of the determinants of effective coverage and was assessed for artemether-lumefantrine (Alu), in two district health systems in rural Tanzania. Methods From October 2009 to June 2011we conducted continuous rolling household surveys in the Kilombero-Ulanga and the Rufiji Health and Demographic Surveillance Sites (HDSS). Surveys were linked to the routine HDSS update rounds. Members of randomly pre-selected households that had experienced a fever episode in the previous two weeks were eligible for a structured interview. Data on individual treatment seeking, access to treatment, timing, source of treatment and household costs per episode were collected. Data are presented on timely access from a total of 2,112 interviews in relation to demographics, seasonality, and socio economic status. Results In Kilombero-Ulanga, 41.8% (CI: 36.6–45.1) and in Rufiji 36.8% (33.7–40.1) of fever cases had access to an authorized ACT provider within 24 hours of fever onset. In neither of the HDSS site was age, sex, socio-economic status or seasonality of malaria found to be significantly correlated with timely access. Conclusion Timely access to authorized ACT providers is below 50% despite interventions intended to improve access such as social marketing and accreditation of private dispensing outlets. To improve prompt diagnosis and treatment, access remains a major bottle neck and new more innovative interventions are needed to raise effective coverage of malaria treatment in Tanzania. PMID:23651521

  10. Bibliographic database of PACS-related articles from the SPIE literature

    NASA Astrophysics Data System (ADS)

    Shile, Peter E.; Freiermuth, Jennifer

    1996-05-01

    Publications of the International Society of Optical Engineering (SPIE) contain much of the relevant literature on Picture Archiving and Communications Systems (PACS) and related topics. In fact, many PACS-related articles indexed by the National Library of Medicine contain references to articles published by SPIE. Unfortunately, SPIE publications themselves are not indexed by the National Library of Medicine and thus can not be identified through Medline. The lack of a convenient mechanism for searching the SPIE literature is problematic for researchers in medical imaging. With the recent introduction on SPIE's Internet server of their Abstracts Online service and their In-CiteTM title and author searching software, the SPIE literature has become more accessible. However, the searching process is still a cumbersome and time consuming process, and it is not possible to perform key word searches of manuscript abstracts. In this paper we present results of our work on developing a mechanism to more thoroughly search SPIE publications for PACS-related articles.

  11. Web Services-Based Access to Local Clinical Trial Databases: A Standards Initiative of the Association of American Cancer Institutes

    PubMed Central

    Stahl, Douglas C.; Evans, Richard M.; Afrin, Lawrence B.; DeTeresa, Richard M.; Ko, Dave; Mitchell, Kevin

    2003-01-01

    Electronic discovery of the clinical trials being performed at a specific research center is a challenging task, which presently requires manual review of the center’s locally maintained databases or web pages of protocol listings. Near real-time automated discovery of available trials would increase the efficiency and effectiveness of clinical trial searching, and would facilitate the development of new services for information providers and consumers. Automated discovery efforts to date have been hindered by issues such as disparate database schemas, vocabularies, and standards for intersystem exchange of high-level data, but adequate infrastructure now exists that makes possible the development of applications for near real-time automated discovery of trials. This paper describes the current state (design and implementation) of the Web Services Specification for Publication and Discovery of Clinical Trials as developed by the Technology Task Force of the Association of American Cancer Institutes. The paper then briefly discusses a prototype web service-based application that implements the specification. Directions for evolution of this specification are also discussed. PMID:14728248

  12. Hydrologic database user`s manual

    SciTech Connect

    Champman, J.B.; Gray, K.J.; Thompson, C.B.

    1993-09-01

    The Hydrologic Database is an electronic filing cabinet containing water-related data for the Nevada Test Site (NTS). The purpose of the database is to enhance research on hydrologic issues at the NTS by providing efficient access to information gathered by a variety of scientists. Data are often generated for specific projects and are reported to DOE in the context of specific project goals. The originators of the database recognized that much of this information has a general value that transcends project-specific requirements. Allowing researchers access to information generated by a wide variety of projects can prevent needless duplication of data-gathering efforts and can augment new data collection and interpretation. In addition, collecting this information in the database ensures that the results are not lost at the end of discrete projects as long as the database is actively maintained. This document is a guide to using the database.

  13. Internet Information-Seeking and Its Relation to Support for Access to Government Records

    ERIC Educational Resources Information Center

    Cuillier, David; Piotrowski, Suzanne J.

    2009-01-01

    Public access to government records is essential for democratic self-governance, and attitudes toward that right can facilitate or hinder public policy regarding transparency. As more people use the internet for gathering information about their governments and communities, it is unknown whether such online information-seeking is related to…

  14. "On the Sidelines": Access to Autism-Related Services in the West Bank

    ERIC Educational Resources Information Center

    Dababnah, Sarah; Bulson, Kathleen

    2015-01-01

    We examined access to autism-related services among Palestinians (N = 24) raising children with autism spectrum disorder (ASD) in the West Bank. Using qualitative methods, we identified five primary interview themes. Poor screening, diagnostic, and psychoeducational practices were prevalent, as parents reported service providers minimized parental…

  15. Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.

    PubMed

    Xu, Weijia; Ozer, Stuart; Gutell, Robin R

    2009-01-01

    With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure. PMID:20502534

  16. An updated database of Holocene relative sea level changes along the Mediterranean coasts

    NASA Astrophysics Data System (ADS)

    Vacchi, Matteo; Rovere, Alessio

    2014-05-01

    Present-day sea level variations in the Mediterranean depend on various factors, including recent climatic forcing, tectonic activity, anthropogenic effects, and glacio-isostatic adjustment (GIA). Mediterranean coasts offer an exceptional opportunity to investigate the various mechanisms that contribute to sea level variations on different time-scales. In fact, geological, geomorphological and archaeological indicators can be coupled with the available instrumental observations. Several areas of the Mediterranean basin are affected by a significant tectonic activity contributing to a widespread coastal instability. The northern Mediterranean coasts are, potentially, the most affected by the process of isostatic adjustment due to the proximity to the former Alpine and Fennoscandian ice sheets. However, GIA-related deformation of the whole Mediterranean basin is mainly driven by water-loading, which contributes to a significant and widespread subsidence whose extension and strength, in turn, directly depend on ice sheet chronology and Earth viscosity. In the Mediterranean, different kinds of RSL markers have been used to reconstruct RSLs: biological, sedimentary, geomorphological and archaeological. The production of such great amount of literature, which is still rapidly growing in number, has led to the obvious consequence of fragmented information, only occasionally reviewed in some localities, but never collected into an organic database to be analysed at the scale of the Mediterranean basin. We aim to create a database of Holocene (last 10 ka) geological data across the Mediterranean basin. This represents a tool of fundamental importance for understanding and tuning GIA models and to assess sea level rise hazards, which are particularly magnified in low-lying or subsiding coastal areas. Here we present the first results of this study carried out both in tectonically active areas (Aegean Sea, Greece) and stable ones (Southern France and Corsica, NE Spanish coast

  17. The AMMA database

    NASA Astrophysics Data System (ADS)

    Boichard, Jean-Luc; Brissebrat, Guillaume; Cloche, Sophie; Eymard, Laurence; Fleury, Laurence; Mastrorillo, Laurence; Moulaye, Oumarou; Ramage, Karim

    2010-05-01

    concern local, satellite and model data. - Documentation: catalogue of all the available data and their metadata. These tools have been developed using standard and free languages and softwares: - Linux system with an Apache web server and a Tomcat application server; - J2EE tools : JSF and Struts frameworks, hibernate; - relational database management systems: PostgreSQL and MySQL; - OpenLDAP directory. In order to facilitate the access to the data by African scientists, the complete system has been mirrored at AGHRYMET Regional Centre in Niamey and is operational there since January 2009. Users can now access metadata and request data through one or the other of two equivalent portals: http://database.amma-international.org or http://amma.agrhymet.ne/amma-data.

  18. A computerized representation of a medical school curriculum: integration of relational and text management software in database design.

    PubMed Central

    Mattern, W. D.; Wagner, J. A.; Brown, J. S.; Fisher-Neenan, L.

    1991-01-01

    We describe the development of a computer-based representation of the medical school curriculum at the University of North Carolina at Chapel Hill (UNC-CH). Over the past seven years the Medical School's Office of Academic Affairs has employed both relational database and text management software to design an integrated curriculum database system. Depending on the function selected--exploring the curriculum, searching through course outlines, retrieving elective descriptions, identifying teaching faculty, or searching for specific topics--either text management or relational database management routines are activated in a manner transparent to the user. Initial evaluation of the system has been positive but highlights the need for a more robust biomedical language for use as a controlled vocabulary to index content. Efforts are now underway, with support from the Association of American Medical Colleges (AAMC), to engage other interested schools in the U.S. and Canada in collaborating on further development of a system. PMID:1807615

  19. The magnet components database system

    SciTech Connect

    Baggett, M.J. ); Leedy, R.; Saltmarsh, C.; Tompkins, J.C. )

    1990-01-01

    The philosophy, structure, and usage MagCom, the SSC magnet components database, are described. The database has been implemented in Sybase (a powerful relational database management system) on a UNIX-based workstation at the Superconducting Super Collider Laboratory (SSCL); magnet project collaborators can access the database via network connections. The database was designed to contain the specifications and measured values of important properties for major materials, plus configuration information (specifying which individual items were used in each cable, coil, and magnet) and the test results on completed magnets. These data will facilitate the tracking and control of the production process as well as the correlation of magnet performance with the properties of its constituents. 3 refs., 10 figs.

  20. A high performance, ad-hoc, fuzzy query processing system for relational databases

    NASA Technical Reports Server (NTRS)

    Mansfield, William H., Jr.; Fleischman, Robert M.

    1992-01-01

    Database queries involving imprecise or fuzzy predicates are currently an evolving area of academic and industrial research. Such queries place severe stress on the indexing and I/O subsystems of conventional database environments since they involve the search of large numbers of records. The Datacycle architecture and research prototype is a database environment that uses filtering technology to perform an efficient, exhaustive search of an entire database. It has recently been modified to include fuzzy predicates in its query processing. The approach obviates the need for complex index structures, provides unlimited query throughput, permits the use of ad-hoc fuzzy membership functions, and provides a deterministic response time largely independent of query complexity and load. This paper describes the Datacycle prototype implementation of fuzzy queries and some recent performance results.

  1. Transformation of Developmental Neurotoxicity Data into a Structure-Searchable Relational Database

    EPA Science Inventory

    A database of neurotoxicants is critical to support the development and validation of animal alternatives for neurotoxicity. Validation of in vitro test methods can only be done using known animal and human neurotoxicants producing defined responses for neurochemical, neuropatho...

  2. Mouse genome database 2016

    PubMed Central

    Bult, Carol J.; Eppig, Janan T.; Blake, Judith A.; Kadin, James A.; Richardson, Joel E.

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data. PMID:26578600

  3. Mouse genome database 2016.

    PubMed

    Bult, Carol J; Eppig, Janan T; Blake, Judith A; Kadin, James A; Richardson, Joel E

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data. PMID:26578600

  4. Statistical databases

    SciTech Connect

    Kogalovskii, M.R.

    1995-03-01

    This paper presents a review of problems related to statistical database systems, which are wide-spread in various fields of activity. Statistical databases (SDB) are referred to as databases that consist of data and are used for statistical analysis. Topics under consideration are: SDB peculiarities, properties of data models adequate for SDB requirements, metadata functions, null-value problems, SDB compromise protection problems, stored data compression techniques, and statistical data representation means. Also examined is whether the present Database Management Systems (DBMS) satisfy the SDB requirements. Some actual research directions in SDB systems are considered.

  5. Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.

    PubMed

    McIntyre, K M; Setzkorn, C; Wardeh, M; Hepworth, P J; Radford, A D; Baylis, M

    2014-10-01

    What are all the species of pathogen that affect our livestock? As 6 out of every 10 human pathogens came from animals, with a good number from livestock and pets, it seems likely that the majority that emerge in the future, and which could threaten or devastate human health, will come from animals. Only 10 years ago, the first comprehensive pathogen list was compiled for humans; we still have no equivalent for animals. Here we describe the creation of a novel pathogen database, and present outputs from the database that demonstrate its value. The ENHanCEd Infectious Diseases database (EID2) is open-access and evidence-based, and it describes the pathogens of humans and animals, their host and vector species, and also their global occurrence. The EID2 systematically collates information on pathogens into a single resource using evidence from the NCBI Taxonomy database, the NCBI Nucleotide database, the NCBI MeSH (Medical Subject Headings) library and PubMed. Information about pathogens is assigned using data-mining of meta-data and semi-automated literature searches. Here we focus on 47 mammalian and avian hosts, including humans and animals commonly used in Europe as food or kept as pets. Currently, the EID2 evidence suggests that: • Within these host species, 793 (30.5%) pathogens were bacteria species, 395 (15.2%) fungi, 705 (27.1%) helminths, 372 (14.3%) protozoa and 332 (12.8%) viruses. • The odds of pathogens being emerging compared to not emerging differed by taxonomic division, and increased when pathogens had greater numbers of host species associated with them, and were zoonotic rather than non-zoonotic. • The odds of pathogens being zoonotic compared to non-zoonotic differed by taxonomic division and also increased when associated with greater host numbers. • The pathogens affecting the greatest number of hosts included: Escherichia coli, Giardia intestinalis, Toxoplasma gondii, Anaplasma phagocytophilum, Cryptosporidium parvum, Rabies virus

  6. Routine use of ultrasound-guided access reduces access-site related complications after lower extremity percutaneous revascularization

    PubMed Central

    Lo, Ruby C.; Fokkema, Margriet T.M.; Curran, Thomas; Darling, Jeremy; Hamdan, Allen D.; Wyers, Mark; Martin, Michelle; Schermerhorn, Marc L.

    2014-01-01

    Objectives We sought to elucidate the risks for access site-related complications (ASC) following percutaneous lower extremity revascularization and to evaluate benefit of routine ultrasound-guided access (RUS) in decreasing ASC. Methods We reviewed all consecutive percutaneous revascularizations (PTA or stent) performed for lower extremity atherosclerosis at our institution from 2002–2012. RUS began September 2007. Primary outcome was any ASC (bleeding, groin or retroperitoneal [RP] hematoma, vessel rupture, or thrombosis). Multivariable logistic regression was used to determine predictors of ASC. Results A total of 1,371 punctures were performed on 877 patients (43% women, median age 69 [IQR 60–78] yrs for claudication (29%), critical limb ischemia (59%), or bypass graft stenosis (12%) using 4–8Fr sheaths. There were 72 ASCs (5%): 52 instances of bleeding or groin hematoma, 9 pseudoaneurysms, 8 retroperitoneal hematomas, 2 artery lacerations, and 1 thrombosis. ASC were less frequent when RUS was used (4% vs. 7%, P=.02). Multivariable predictors of ASC were age >75 years (OR 2.0, 95% CI 1.1–3.7, P=.03), CHF (OR 1.9, 95% CI 1.1–1.3, P=.02), preoperative warfarin use (OR 2.0, 95% CI 1.1–3.5, P=.02), & RUS (OR 0.4, 95% CI 0.2–0.7, P<.01). Vascular closure devices (VCDs) were not associated with lower rates of ASCs (OR 1.1, 95% CI 0.2–0.7, P<.01). RUS lowered ASCs in those >75 years (5% vs. 12%, P<.01) but not those on warfarin preoperatively (10% vs. 13%, P=.47). RUS did not decrease VCD failure (6% vs. 4%, P=.79). Conclusions We were able to decrease the rate of ASCs during lower extremity revascularization with the implementation of RUS. VCDs did not impact ASCs. Particular care should be taken on patients >75 years old, those with CHF, and those on warfarin. PMID:25240244

  7. Database Manager

    ERIC Educational Resources Information Center

    Martin, Andrew

    2010-01-01

    It is normal practice today for organizations to store large quantities of records of related information as computer-based files or databases. Purposeful information is retrieved by performing queries on the data sets. The purpose of DATABASE MANAGER is to communicate to students the method by which the computer performs these queries. This…

  8. Mining for Murder-Suicide: An Approach to Identifying Cases of Murder-Suicide in the National Violent Death Reporting System Restricted Access Database.

    PubMed

    McNally, Matthew R; Patton, Christina L; Fremouw, William J

    2016-01-01

    The National Violent Death Reporting System (NVDRS) is a United States Centers for Disease Control and Prevention (CDC) database of violent deaths from 2003 to the present. The NVDRS collects information from 32 states on several types of violent deaths, including suicides, homicides, homicides followed by suicides, and deaths resulting from child maltreatment or intimate partner violence, as well as legal intervention and accidental firearm deaths. Despite the availability of data from police narratives, medical examiner reports, and other sources, reliably finding the cases of murder-suicide in the NVDRS has proven problematic due to the lack of a unique code for murder-suicide incidents and outdated descriptions of case-finding procedures from previous researchers. By providing a description of the methods used to access to the NVDRS and coding procedures used to decipher these data, the authors seek to assist future researchers in correctly identifying cases of murder-suicide deaths while avoiding false positives. PMID:26258816

  9. Teradata University Network: A No Cost Web-Portal for Teaching Database, Data Warehousing, and Data-Related Subjects

    ERIC Educational Resources Information Center

    Jukic, Nenad; Gray, Paul

    2008-01-01

    This paper describes the value that information systems faculty and students in classes dealing with database management, data warehousing, decision support systems, and related topics, could derive from the use of the Teradata University Network (TUN), a free comprehensive web-portal. A detailed overview of TUN functionalities and content is…

  10. Using an image-extended relational database to support content-based image retrieval in a PACS.

    PubMed

    Traina, Caetano; Traina, Agma J M; Araújo, Myrian R B; Bueno, Josiane M; Chino, Fabio J T; Razente, Humberto; Azevedo-Marques, Paulo M

    2005-12-01

    This paper presents a new Picture Archiving and Communication System (PACS), called cbPACS, which has content-based image retrieval capabilities. The cbPACS answers range and k-nearest- neighbor similarity queries, employing a relational database manager extended to support images. The images are compared through their features, which are extracted by an image-processing module and stored in the extended relational database. The database extensions were developed aiming at efficiently answering similarity queries by taking advantage of specialized indexing methods. The main concept supporting the extensions is the definition, inside the relational manager, of distance functions based on features extracted from the images. An extension to the SQL language enables the construction of an interpreter that intercepts the extended commands and translates them to standard SQL, allowing any relational database server to be used. By now, the system implemented works on features based on color distribution of the images through normalized histograms as well as metric histograms. Metric histograms are invariant regarding scale, translation and rotation of images and also to brightness transformations. The cbPACS is prepared to integrate new image features, based on texture and shape of the main objects in the image. PMID:16520146

  11. KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome

    PubMed Central

    2013-01-01

    Background Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. Description Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. Conclusions We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of

  12. Object Identification And Measurement From Images With Access To The Database To Select Specific Subpopulations Of Special Interest

    NASA Astrophysics Data System (ADS)

    Rutherford, H. G.; Taub, F. E.; Williams, B.

    1987-06-01

    An automated vision image analysis system to analyze images resulting from nucleic acid hybridizations is presented. Real-time image acquisition from autoradiographs is accomplished with a sensitivity to optical density to the degree that any spot visible by eye can be quantified by digital methods and enhanced by image processing techniques for observation. The system provides a tool for quantification of differences in gene expression, rapid processing of thousands of pairs of genes, storage in a database, search for small differences, large differences, and infrequently occuring genes. Background correction, normalization and pseudocolor "mapping" facilitate comparison and quantification directly from the CRT display. The image pairs, a percent change image and a difference image are presented in a quad display with coordinated spot density and change measurement simultaneously for each of the four images. The system provides a tool for analysis of altered gene expression in response to environmental stress, such as heat-shock and salt water in plant growth; hormone regulation, such as before and after hormone administration in animals; development; and carcinogenesis. The use of this system to study nucleic acid hybridization is contrasted with the study of 2-D protein electrophoresis gels for the determination of changes in gene expression and identification of corresponding proteins of significance.

  13. Development and evaluation of evidence-based nursing (EBN) filters and related databases*

    PubMed Central

    Lavin, Mary A.; Krieger, Mary M.; Meyer, Geralyn A.; Spasser, Mark A.; Cvitan, Tome; Reese, Cordie G.; Carlson, Judith H.; Perry, Anne G.; McNary, Patricia

    2005-01-01

    Objectives: Difficulties encountered in the retrieval of evidence-based nursing (EBN) literature and recognition of terminology, research focus, and design differences between evidence-based medicine and nursing led to the realization that nursing needs its own filter strategies for evidence-based practice. This article describes the development and evaluation of filters that facilitate evidence-based nursing searches. Methods: An inductive, multistep methodology was employed. A sleep search strategy was developed for uniform application to all filters for filter development and evaluation purposes. An EBN matrix was next developed as a framework to illustrate conceptually the placement of nursing-sensitive filters along two axes: horizontally, an adapted nursing process, and vertically, levels of evidence. Nursing diagnosis, patient outcomes, and primary data filters were developed recursively. Through an interface with the PubMed search engine, the EBN matrix filters were inserted into a database that executes filter searches, retrieves citations, and stores and updates retrieved citations sets hourly. For evaluation purposes, the filters were subjected to sensitivity and specificity analyses and retrieval set comparisons. Once the evaluation was complete, hyperlinks providing access to any one or a combination of completed filters to the EBN matrix were created. Subject searches on any topic may be applied to the filters, which interface with PubMed. Results: Sensitivity and specificity for the combined nursing diagnosis and primary data filter were 64% and 99%, respectively; for the patient outcomes filter, the results were 75% and 71%, respectively. Comparisons were made between the EBN matrix filters (nursing diagnosis and primary data) and PubMed's Clinical Queries (diagnosis and sensitivity) filters. Additional comparisons examined publication types and indexing differences. Review articles accounted for the majority of the publication type differences

  14. Solubility Database

    National Institute of Standards and Technology Data Gateway

    SRD 106 IUPAC-NIST Solubility Database (Web, free access)   These solubilities are compiled from 18 volumes (Click here for List) of the International Union for Pure and Applied Chemistry(IUPAC)-NIST Solubility Data Series. The database includes liquid-liquid, solid-liquid, and gas-liquid systems. Typical solvents and solutes include water, seawater, heavy water, inorganic compounds, and a variety of organic compounds such as hydrocarbons, halogenated hydrocarbons, alcohols, acids, esters and nitrogen compounds. There are over 67,500 solubility measurements and over 1800 references.

  15. Human Mitochondrial Protein Database

    National Institute of Standards and Technology Data Gateway

    SRD 131 Human Mitochondrial Protein Database (Web, free access)   The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases.

  16. Exploration of the Chemical Space of Public Genomic Databases

    EPA Science Inventory

    The current project aims to chemically index the content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information.

  17. [Preparation of the database and the homepage on chemical accidents relating to health hazard].

    PubMed

    Yamamoto, M; Morita, M; Kaminuma, T

    1998-01-01

    We collected the data on accidents due to chemicals occurred in Japan, and prepared the database. We also set up the World Wide Web homepage containing the explanation on accidents due to chemicals and the retrieval page for the database. We designed the retrieval page so that users can search the data from keywords such as chemicals (e.g. chlorine gas, hydrogen sulfide, pesticides), places (e.g. home, factory, vehicles, tank), causes (e.g. reaction, leakage, exhaust gas) and others (e.g. cleaning, painting, transportation). PMID:10097523

  18. PhasePlot: A Software Program for Visualizing Phase Relations Computed Using Thermochemical Models and Databases

    NASA Astrophysics Data System (ADS)

    Ghiorso, M. S.

    2011-12-01

    A new software program has been developed for Macintosh computers that permits the visualization of phase relations calculated from thermodynamic data-model collections. The data-model collections of MELTS (Ghiorso and Sack, 1995, CMP 119, 197-212), pMELTS (Ghiorso et al., 2002, G-cubed 3, 10.1029/2001GC000217) and the deep mantle database of Stixrude and Lithgow-Bertelloni (2011, GJI 184, 1180-1213) are currently implemented. The software allows users to enter a system bulk composition and a range of reference conditions and then calculate a grid of phase relations. These relations may be visualized in a variety of ways including phase diagrams, phase proportion plots, and contour diagrams of phase compositions and abundances. Results may be exported into Excel or similar spreadsheet applications. Flexibility in stipulating reference conditions permit the construction of temperature-pressure, temperature-volume, entropy-pressure, or entropy-volume display grids. Calculations on the grid are performed for fixed bulk composition or in open systems governed by user specified constraints on component chemical potentials (e.g., specified oxygen fugacity buffers). The calculation engine for the software is optimized for multi-core compute architectures and is very fast, allowing a typical grid of 64 points to be calculated in under 10 seconds on a dual-core laptop/iMac. The underlying computational thermodynamic algorithms have been optimized for speed and robust behavior. Taken together, both of these advances facilitate in classroom demonstrations and permit novice users to work with the program effectively, focusing on problem specification and interpretation of results rather than on manipulation and mechanics of computation - a key feature of an effective instructional tool. The emphasis in this software package is graphical visualization, which aids in better comprehension of complex phase relations in multicomponent systems. Anecdotal experience in using Phase

  19. Sex-related differences in access to care among patients with premature acute coronary syndrome

    PubMed Central

    Pelletier, Roxanne; Humphries, Karin H.; Shimony, Avi; Bacon, Simon L.; Lavoie, Kim L.; Rabi, Doreen; Karp, Igor; Tsadok, Meytal Avgil; Pilote, Louise

    2014-01-01

    Background: Access to care may be implicated in disparities between men and women in death after acute coronary syndrome, especially among younger adults. We aimed to assess sex-related differences in access to care among patients with premature acute coronary syndrome and to identify clinical and gender-related determinants of access to care. Methods: We studied 1123 patients (18–55 yr) admitted to hospital for acute coronary syndrome and enrolled in the GENESIS-PRAXY cohort study. Outcome measures were door-to-electrocardiography, door-to-needle and door-to-balloon times, as well as proportions of patients undergoing cardiac catheterization, reperfusion or nonprimary percutaneous coronary intervention. We performed univariable and multivariable logistic regression analyses to identify clinical and gender-related determinants of timely procedures and use of invasive procedures. Results: Women were less likely than men to receive care within benchmark times for electrocardiography (≤ 10 min: 29% v. 38%, p = 0.02) or fibrinolysis (≤ 30 min: 32% v. 57%, p = 0.01). Women with ST-segment elevation myocardial infarction (MI) were less likely than men to undergo reperfusion therapy (primary percutaneous coronary intervention or fibrinolysis) (83% v. 91%, p = 0.01), and women with non–ST-segment elevation MI or unstable angina were less likely to undergo nonprimary percutaneous coronary intervention (48% v. 66%, p < 0.001). Clinical determinants of poorer access to care included anxiety, increased number of risk factors and absence of chest pain. Gender-related determinants included feminine traits of personality and responsibility for housework. Interpretation: Among younger adults with acute coronary syndrome, women and men had different access to care. Moreover, fewer than half of men and women with ST-segment elevation MI received timely primary coronary intervention. Our results also highlight that men and women with no chest pain and those with anxiety

  20. Atomic Spectra Database (ASD)

    National Institute of Standards and Technology Data Gateway

    SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

  1. Ionic Liquids Database- (ILThermo)

    National Institute of Standards and Technology Data Gateway

    SRD 147 Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

  2. Village poultry consumption and marketing in relation to gender, religious festivals and market access.

    PubMed

    Aklilu, H A; Almekinders, C J M; Udo, H M J; Van der Zijpp, A J

    2007-04-01

    This study aimed to examine village poultry consumption and marketing in Ethiopia in relation to gender, socio-cultural events and market access. The main objects of the research were producers, poultry markets, producer-sellers, and intermediary sellers in three locations representing different levels of market access in Tigray. About 3000 farm records were collected over a period of 12 months from 131 producers to obtain quantitative data on sales and consumption. Ninety-three semi-structured interviews with 58 producer-sellers and 35 intermediaries and 12 group discussions with these market actors were conducted to explore organization, price dynamics and socio-cultural aspects of poultry marketing. In total, 928 producer-sellers and 225 intermediaries were monitored monthly to examine participation by gender in poultry marketing. Better market access was associated with a shorter market chain and higher prices for the producers. Female-headed households had smaller poultry sales and consumption per household but sale and consumption per family member were 25% and 66% higher, respectively, than in male-headed households. While women dominated in the producer-sellers group, intermediaries were mainly men. Religious festivals periodically shifted local demand and prices of poultry. To improve the benefit of poultry keeping, poverty-stricken households may profit from better market access through better market information, infrastructure, market group formation and careful planning to match the dynamics in demand. PMID:17691541

  3. Opening CEM vendor databases

    SciTech Connect

    Long, A.; Patel, D.

    1995-12-31

    CEM database performance requirements (i.e., voluminous data storage, rapid response times) often conflict with the concept of an open, accessible database. Utilities would like to use their CEM data for more purposes than simply submitting environmental reports. But in most cases, other uses are inhibited because today`s sophisticated CEM systems incorporate databases that have forsaken openness and accessibility in favor of performance. Several options are available for CEM vendors wishing to move in the direction of open, accessible CEM databases.

  4. Using homology relations within a database markedly boosts protein sequence similarity search.

    PubMed

    Tong, Jing; Sadreyev, Ruslan I; Pei, Jimin; Kinch, Lisa N; Grishin, Nick V

    2015-06-01

    Inference of homology from protein sequences provides an essential tool for analyzing protein structure, function, and evolution. Current sequence-based homology search methods are still unable to detect many similarities evident from protein spatial structures. In computer science a search engine can be improved by considering networks of known relationships within the search database. Here, we apply this idea to protein-sequence-based homology search and show that it dramatically enhances the search accuracy. Our new method, COMPADRE (COmparison of Multiple Protein sequence Alignments using Database RElationships) assesses the relationship between the query sequence and a hit in the database by considering the similarity between the query and hit's known homologs. This approach increases detection quality, boosting the precision rate from 18% to 83% at half-coverage of all database homologs. The increased precision rate allows detection of a large fraction of protein structural relationships, thus providing structure and function predictions for previously uncharacterized proteins. Our results suggest that this general approach is applicable to a wide variety of methods for detection of biological similarities. The web server is available at prodata.swmed.edu/compadre. PMID:26038555

  5. Using homology relations within a database markedly boosts protein sequence similarity search

    PubMed Central

    Tong, Jing; Sadreyev, Ruslan I.; Pei, Jimin; Kinch, Lisa N.; Grishin, Nick V.

    2015-01-01

    Inference of homology from protein sequences provides an essential tool for analyzing protein structure, function, and evolution. Current sequence-based homology search methods are still unable to detect many similarities evident from protein spatial structures. In computer science a search engine can be improved by considering networks of known relationships within the search database. Here, we apply this idea to protein-sequence–based homology search and show that it dramatically enhances the search accuracy. Our new method, COMPADRE (COmparison of Multiple Protein sequence Alignments using Database RElationships) assesses the relationship between the query sequence and a hit in the database by considering the similarity between the query and hit’s known homologs. This approach increases detection quality, boosting the precision rate from 18% to 83% at half-coverage of all database homologs. The increased precision rate allows detection of a large fraction of protein structural relationships, thus providing structure and function predictions for previously uncharacterized proteins. Our results suggest that this general approach is applicable to a wide variety of methods for detection of biological similarities. The web server is available at prodata.swmed.edu/compadre. PMID:26038555

  6. Literature Review and Database of Relations Between Salinity and Aquatic Biota: Applications to Bowdoin National Wildlife Refuge, Montana

    USGS Publications Warehouse

    Gleason, Robert A.; Tangen, Brian A.; Laubhan, Murray K.; Finocchiaro, Raymond G.; Stamm, John F.

    2009-01-01

    Long-term accumulation of salts in wetlands at Bowdoin National Wildlife Refuge (NWR), Mont., has raised concern among wetland managers that increasing salinity may threaten plant and invertebrate communities that provide important habitat and food resources for migratory waterfowl. Currently, the U.S. Fish and Wildlife Service (USFWS) is evaluating various water management strategies to help maintain suitable ranges of salinity to sustain plant and invertebrate resources of importance to wildlife. To support this evaluation, the USFWS requested that the U.S. Geological Survey (USGS) provide information on salinity ranges of water and soil for common plants and invertebrates on Bowdoin NWR lands. To address this need, we conducted a search of the literature on occurrences of plants and invertebrates in relation to salinity and pH of the water and soil. The compiled literature was used to (1) provide a general overview of salinity concepts, (2) document published tolerances and adaptations of biota to salinity, (3) develop databases that the USFWS can use to summarize the range of reported salinity values associated with plant and invertebrate taxa, and (4) perform database summaries that describe reported salinity ranges associated with plants and invertebrates at Bowdoin NWR. The purpose of this report is to synthesize information to facilitate a better understanding of the ecological relations between salinity and flora and fauna when developing wetland management strategies. A primary focus of this report is to provide information to help evaluate and address salinity issues at Bowdoin NWR; however, the accompanying databases, as well as concepts and information discussed, are applicable to other areas or refuges. The accompanying databases include salinity values reported for 411 plant taxa and 330 invertebrate taxa. The databases are available in Microsoft Excel version 2007 (http://pubs.usgs.gov/sir/2009/5098/downloads/databases_21april2009.xls) and contain

  7. A Holocene Database of Relative Sea Levels for North America and the Caribbean: Implications for Geophysical Models

    NASA Astrophysics Data System (ADS)

    Engelhart, S. E.; Peltier, W. R.; Horton, B. P.; Khan, N. S.; Liu, S.; Vacchi, M.

    2011-12-01

    We have expanded the previously available quality-controlled database of relative sea-level (RSL) observations for the U.S. Atlantic coast with data from the Atlantic coast of Canada, the Pacific coast of North America and the Caribbean. The Holocene sea-level database for the U.S. Atlantic coast consisted of 836 sea-level indicators. The database documented a decreasing rate of relative sea-level (RSL) rise through time with no evidence of sea level being above present in the middle to late Holocene. The highest rates of rise were found in the mid-Atlantic region. We employed the database to constrain an ensemble of glacial isostatic adjustment (GIA) models using two ice (ICE-5G and ICE-6G) and two mantle viscosity variation (VM5a and VM5b). We identified significant misfits between observations and predictions using ICE-5G with the VM5a viscosity profile. ICE-6G provides some improvement for the northern Atlantic region, but misfits remain elsewhere. Decreasing the upper mantle and transition zone viscosity from 0.5*1021 Pa s (VM5a) to 0.25*1021 Pa s (VM5b) removed significant discrepancies between observations and predictions along the mid-Atlantic coastline, although misfits remained in the southern Atlantic region. The addition of new data from areas more proximal and distal to Laurentide ice loading has allowed us to further investigate the VM5b mantle viscosity profile.

  8. Database for the geologic map of upper Eocene to Holocene volcanic and related rocks in the Cascade Range, Washington

    USGS Publications Warehouse

    Barron, Andrew D.; Ramsey, David W.; Smith, James G.

    2014-01-01

    This digital database contains information used to produce the geologic map published as Sheet 1 in U.S. Geological Survey Miscellaneous Investigations Series Map I-2005. (Sheet 2 of Map I-2005 shows sources of geologic data used in the compilation and is available separately). Sheet 1 of Map I-2005 shows the distribution and relations of volcanic and related rock units in the Cascade Range of Washington at a scale of 1:500,000. This digital release is produced from stable materials originally compiled at 1:250,000 scale that were used to publish Sheet 1. The database therefore contains more detailed geologic information than is portrayed on Sheet 1. This is most noticeable in the database as expanded polygons of surficial units and the presence of additional strands of concealed faults. No stable compilation materials exist for Sheet 1 at 1:500,000 scale. The main component of this digital release is a spatial database prepared using geographic information systems (GIS) applications. This release also contains links to files to view or print the map sheet, main report text, and accompanying mapping reference sheet from Map I-2005. For more information on volcanoes in the Cascade Range in Washington, Oregon, or California, please refer to the U.S. Geological Survey Volcano Hazards Program website.

  9. An open-access database of grape harvest dates for climate research: data description and quality assessment

    NASA Astrophysics Data System (ADS)

    Daux, V.; Garcia de Cortazar-Atauri, I.; Yiou, P.; Chuine, I.; Garnier, E.; Ladurie, E. Le Roy; Mestre, O.; Tardaguila, J.

    2012-09-01

    We present an open-access dataset of grape harvest dates (GHD) series that has been compiled from international, French and Spanish literature and from unpublished documentary sources from public organizations and from wine-growers. As of June 2011, this GHD dataset comprises 380 series mainly from France (93% of the data) as well as series from Switzerland, Italy, Spain and Luxemburg. The series have variable length (from 1 to 479 data, mean length of 45 data) and contain gaps of variable sizes (mean ratio of observations/series length of 0.74). The longest and most complete ones are from Burgundy, Switzerland, Southern Rhône valley, Jura and Ile-de-France. The most ancient harvest date of the dataset is in 1354 in Burgundy. The GHD series were grouped into 27 regions according to their location, to geomorphological and geological criteria, and to past and present grape varieties. The GHD regional composite series (GHD-RCS) were calculated and compared pairwise to assess their reliability assuming that series close to one another are highly correlated. Most of the pairwise correlations are significant (p-value < 0.001) and strong (mean pairwise correlation coefficient of 0.58). As expected, the correlations tend to be higher when the vineyards are closer. The highest correlation (R = 0.91) is obtained between the High Loire Valley and the Ile-de-France GHD-RCS. The strong dependence of the vine cycle on temperature and, therefore, the strong link between the harvest dates and the temperature of the growing season was also used to test the quality of the GHD series. The strongest correlations are obtained between the GHD-RCS and the temperature series of the nearest weather stations. Moreover, the GHD-RCS/temperature correlation maps show spatial patterns similar to temperature correlation maps. The stability of the correlations over time is explored. The most striking feature is their generalised deterioration at the late 19th-early 20th century. The possible

  10. IPD—the Immuno Polymorphism Database

    PubMed Central

    Robinson, James; Mistry, Kavita; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G. E.

    2010-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; IPD-human platelet antigens, alloantigens expressed only on platelets and IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines. The data is currently available online from the website and ftp directory. PMID:19875415

  11. IPD--the Immuno Polymorphism Database.

    PubMed

    Robinson, James; Mistry, Kavita; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G E

    2010-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; IPD-human platelet antigens, alloantigens expressed only on platelets and IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines. The data is currently available online from the website and ftp directory. PMID:19875415

  12. Electronic Access to Literature in Mathematics Education.

    ERIC Educational Resources Information Center

    Konig, Gerhard; Ruffer, Beate

    Fast and comfortable access to literature in teaching mathematics at all levels is discussed. For this purpose the most important bibliographic database for theory and practice in mathematics education, the database MATHDI, is presented in more detail. The literature search in MATHDI is exemplified by identifying literature relating to the topic…

  13. The effects of drug-prevention messages on the accessibility of identity-related constructs.

    PubMed

    Comello, Maria Leonora G; Slater, Michael D

    2011-05-01

    Recent theoretical work has posited that the self-system guides behavior via currently activated self-concepts. The authors adopted this framework to the study of drug-prevention messages by examining the extent to which messages can alter the accessibility of views of self and of drugs that would support nonuse. Participants were exposed to 1 of 3 print-ad conditions: autonomy-themed prevention messages (treatment), health-information themed prevention messages (comparison), and informational consumer ads (control). Outcomes were reaction times to make dichotomous judgments. Relative to comparison and control ads, treatment ads were more successful at activating a self-view as a nonuser, a view that marijuana use is inconsistent with autonomy, and unwillingness to use marijuana. Post-hoc analysis revealed that the effect of ad condition on unwillingness was partially mediated by the accessibility of self-view as a nonuser. PMID:21271426

  14. "On the Sidelines": Access to Autism-Related Services in the West Bank.

    PubMed

    Dababnah, Sarah; Bulson, Kathleen

    2015-12-01

    We examined access to autism-related services among Palestinians (N = 24) raising children with autism spectrum disorder (ASD) in the West Bank. Using qualitative methods, we identified five primary interview themes. Poor screening, diagnostic, and psychoeducational practices were prevalent, as parents reported service providers minimized parental concerns and communicated ineffectively with the caregivers regarding treatment options. Geographic barriers and financial burdens prevented many families from seeking or maintaining services. Limited service availability was a dominant barrier: parents reported limited or denied access to education, community-based services, and ASD-specific interventions. Consequently, several families noted their children did not receive any services whatsoever. Research, practices and policies to address the shortage of services for children with ASD are urgently needed in the West Bank. PMID:26219419

  15. The Effects of Drug-Prevention Messages on the Accessibility of Identity-Related Constructs

    PubMed Central

    COMELLO, MARIA LEONORA G.; SLATER, MICHAEL D.

    2011-01-01

    Recent theoretical work has posited that the self-system guides behavior via currently activated self-concepts. We adopt this framework to the study of drug-prevention messages by examining the extent to which messages can alter the accessibility of views of self and of drugs that would support non-use. Participants were exposed to one of three print-ad conditions: autonomy-themed prevention messages (treatment), health-information themed prevention messages (comparison), and informational consumer ads (control). Outcomes were reaction times to make dichotomous judgments. Relative to comparison and control ads, treatment ads were more successful at activating a self-view as a nonuser, a view that marijuana use is inconsistent with autonomy, and unwillingness to use marijuana. Post-hoc analysis revealed that the effect of ad condition on unwillingness was partially mediated by the accessibility of self-view as a nonuser. PMID:21271426

  16. BDNF DNA methylation changes as a biomarker of psychiatric disorders: literature review and open access database analysis.

    PubMed

    Zheleznyakova, Galina Y; Cao, Hao; Schiöth, Helgi B

    2016-01-01

    Brain-derived neurotrophic factor (BDNF) plays an important role in nervous system development and function and it is well established that BDNF is involved in the pathogenesis of a wide range of psychiatric disorders. Recently, numerous studies have associated the DNA methylation level of BDNF promoters with certain psychiatric phenotypes. In this review, we summarize data from current literature as well as from our own analysis with respect to the correlation of BDNF methylation changes with psychiatric disorders and address questions about whether DNA methylation related to the BDNF can be useful as biomarker for specific neuropsychiatric disorders. PMID:27267954

  17. Performance of popular open source databases for HEP related computing problems

    NASA Astrophysics Data System (ADS)

    Kovalskyi, D.; Sfiligoi, I.; Wuerthwein, F.; Yagil, A.

    2014-06-01

    Databases are used in many software components of HEP computing, from monitoring and job scheduling to data storage and processing. It is not always clear at the beginning of a project if a problem can be handled by a single server, or if one needs to plan for a multi-server solution. Before a scalable solution is adopted, it helps to know how well it performs in a single server case to avoid situations when a multi-server solution is adopted mostly due to sub-optimal performance per node. This paper presents comparison benchmarks of popular open source database management systems. As a test application we use a user job monitoring system based on the Glidein workflow management system used in the CMS Collaboration.

  18. Use of a Drosophila Genome-Wide Conserved Sequence Database to Identify Functionally Related cis-Regulatory Enhancers

    PubMed Central

    Brody, Thomas; Yavatkar, Amarendra S; Kuzin, Alexander; Kundu, Mukta; Tyson, Leonard J; Ross, Jermaine; Lin, Tzu-Yang; Lee, Chi-Hon; Awasaki, Takeshi; Lee, Tzumin; Odenwald, Ward F

    2012-01-01

    Background: Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs. Results: We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis-regulatory function. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. Conclusions: cis-Decoder reveals that co-regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process. Developmental Dynamics 241:169–189, 2012. © 2011 Wiley Periodicals, Inc. Key findings A genome-wide catalog of Drosophila conserved DNA sequence clusters. cis-Decoder discovers functionally related enhancers. Functionally related enhancers share balanced sequence element copy numbers. Many enhancers function during multiple phases of development. PMID:22174086

  19. Aviation Safety Issues Database

    NASA Technical Reports Server (NTRS)

    Morello, Samuel A.; Ricks, Wendell R.

    2009-01-01

    The aviation safety issues database was instrumental in the refinement and substantiation of the National Aviation Safety Strategic Plan (NASSP). The issues database is a comprehensive set of issues from an extremely broad base of aviation functions, personnel, and vehicle categories, both nationally and internationally. Several aviation safety stakeholders such as the Commercial Aviation Safety Team (CAST) have already used the database. This broader interest was the genesis to making the database publically accessible and writing this report.

  20. US Department of Energy Chernobyl Database

    SciTech Connect

    Kennedy, R.A.; Mahaffey, J.A.; Smith, S.K.; Carr, F. Jr.

    1992-05-01

    The Chernobyl Database project is developing and maintaining an information to provide researchers with data and resource materials relating to the Chernobyl nuclear accident of April 1986. The system is the official United States repository for Chernobyl data. The system includes a collection of Chernobyl-related documents, a database of bibliographic references, and a collection of radiological measurements records. In addition, projects have been developed to make the resources more accessible and easy to use. These products include a personal-computer-based bibliographic search system (ChernoLit{trademark}), two printed bibliographies, and a personal- computer-based radiological measurements database system (ChernoDat).

  1. Item response theory analysis of the Amyotrophic Lateral Sclerosis Functional Rating Scale-Revised in the Pooled Resource Open-Access ALS Clinical Trials Database.

    PubMed

    Bacci, Elizabeth D; Staniewska, Dorota; Coyne, Karin S; Boyer, Stacey; White, Leigh Ann; Zach, Neta; Cedarbaum, Jesse M

    2016-01-01

    Our objective was to examine dimensionality and item-level performance of the Amyotrophic Lateral Sclerosis Functional Rating Scale-Revised (ALSFRS-R) across time using classical and modern test theory approaches. Confirmatory factor analysis (CFA) and Item Response Theory (IRT) analyses were conducted using data from patients with amyotrophic lateral sclerosis (ALS) Pooled Resources Open-Access ALS Clinical Trials (PRO-ACT) database with complete ALSFRS-R data (n = 888) at three time-points (Time 0, Time 1 (6-months), Time 2 (1-year)). Results demonstrated that in this population of 888 patients, mean age was 54.6 years, 64.4% were male, and 93.7% were Caucasian. The CFA supported a 4* individual-domain structure (bulbar, gross motor, fine motor, and respiratory domains). IRT analysis within each domain revealed misfitting items and overlapping item response category thresholds at all time-points, particularly in the gross motor and respiratory domain items. Results indicate that many of the items of the ALSFRS-R may sub-optimally distinguish among varying levels of disability assessed by each domain, particularly in patients with less severe disability. Measure performance improved across time as patient disability severity increased. In conclusion, modifications to select ALSFRS-R items may improve the instrument's specificity to disability level and sensitivity to treatment effects. PMID:26473473

  2. A survey of commercial object-oriented database management systems

    NASA Technical Reports Server (NTRS)

    Atkins, John

    1992-01-01

    The object-oriented data model is the culmination of over thirty years of database research. Initially, database research focused on the need to provide information in a consistent and efficient manner to the business community. Early data models such as the hierarchical model and the network model met the goal of consistent and efficient access to data and were substantial improvements over simple file mechanisms for storing and accessing data. However, these models required highly skilled programmers to provide access to the data. Consequently, in the early 70's E.F. Codd, an IBM research computer scientists, proposed a new data model based on the simple mathematical notion of the relation. This model is known as the Relational Model. In the relational model, data is represented in flat tables (or relations) which have no physical or internal links between them. The simplicity of this model fostered the development of powerful but relatively simple query languages that now made data directly accessible to the general database user. Except for large, multi-user database systems, a database professional was in general no longer necessary. Database professionals found that traditional data in the form of character data, dates, and numeric data were easily represented and managed via the relational model. Commercial relational database management systems proliferated and performance of relational databases improved dramatically. However, there was a growing community of potential database users whose needs were not met by the relational model. These users needed to store data with data types not available in the relational model and who required a far richer modelling environment than that provided by the relational model. Indeed, the complexity of the objects to be represented in the model mandated a new approach to database technology. The Object-Oriented Model was the result.

  3. Heterogeneous distributed databases: A case study

    NASA Technical Reports Server (NTRS)

    Stewart, Tracy R.; Mukkamala, Ravi

    1991-01-01

    Alternatives are reviewed for accessing distributed heterogeneous databases and a recommended solution is proposed. The current study is limited to the Automated Information Systems Center at the Naval Sea Combat Systems Engineering Station at Norfolk, VA. This center maintains two databases located on Digital Equipment Corporation's VAX computers running under the VMS operating system. The first data base, ICMS, resides on a VAX11/780 and has been implemented using VAX DBMS, a CODASYL based system. The second database, CSA, resides on a VAX 6460 and has been implemented using the ORACLE relational database management system (RDBMS). Both databases are used for configuration management within the U.S. Navy. Different customer bases are supported by each database. ICMS tracks U.S. Navy ships and major systems (anti-sub, sonar, etc.). Even though the major systems on ships and submarines have totally different functions, some of the equipment within the major systems are common to both ships and submarines.

  4. Analysis of TRMM-LIS Lightning and Related Microphysics Using a Cell-Scale Database

    NASA Technical Reports Server (NTRS)

    Leroy, Anita; Petersen, Walter A.

    2010-01-01

    Previous studies of tropical lightning activity using Tropical Rainfall Measurement Mission (TRMM) Lightning Imaging Sensor (LIS) data performed analyses of lightning behavior over mesoscale "feature" scales or over uniform grids. In order to study lightning and the governing ice microphysics intrinsic to thunderstorms at a more process-specific scale (i.e., the scale over which electrification processes and lightning occur in a "unit" thunderstorm), a new convective cell-scale database was developed by analyzing and refining the University of Utah's Precipitation Features database and retaining precipitation data parameters computed from the TRMM precipitation radar (PR), microwave imager (TMI) and LIS instruments. The resulting data base was to conduct a limited four-year study of tropical continental convection occurring over the Amazon Basin, Congo, Maritime Continent and the western Pacific Ocean. The analysis reveals expected strong correlations between lightning flash counts per cell and ice proxies, such as ice water path, minimum and average 85GHz brightness temperatures, and 18dBz echo top heights above the freezing level in all regimes, as well as regime-specific relationships between lighting flash counts and PR-derived surface rainfall rates. Additionally, radar CFADs were used to partition the 3D structure of cells in each regime at different flash counts. The resulting cell-scale analyses are compared to previous mesoscale feature and gridded studies wherever possible.

  5. The role of databases in areawide pest management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A database is a comprehensive collection of related data organized for convenient access, generally in a computer. The evolution of computer software and the need to distinguish the specialized computer systems for storing and manipulating data, stimulated development of database management systems...

  6. GrainGenes: Changing Times, Changing Databases, Digital Evolution.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The GrainGenes database is one of few agricultural databases that had an early start on the Internet and that has changed with the times. Initial goals were to collect a wide range of data relating to the developing maps and attributes of small grains crops, and to make them easily accessible. The ...

  7. MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins

    PubMed Central

    Pesole, Graziano; Gissi, Carmela; Catalano, Domenico; Grillo, Giorgio; Licciulli, Flavio; Liuni, Sabino; Attimonelli, Marcella; Saccone, Cecilia

    2000-01-01

    Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many degenerative diseases. All functions of mitochondria depend on the interaction of nuclear and organellar genomes. Mitochondrial genomes have been extensively sequenced and analysed and the data collected in several specialised databases. In order to collect information on nuclear coded mitochondrial proteins we developed MitoNuc and MitoAln, two related databases containing, respectively, detailed information on sequenced nuclear genes coding for mitochondrial proteins in Metazoa and yeast, and the multiple alignments of the relevant homologous protein coding regions. MitoNuc and MitoAln retrieval through SRS at http://bio-www.ba.cnr.it:8000/srs6/ can easily allow the extraction of sequence data, subsequences defined by specific features and nucleotide or amino acid multiple alignments. PMID:10592211

  8. Detection of Anomalous Insiders in Collaborative Environments via Relational Analysis of Access Logs

    PubMed Central

    Chen, You; Malin, Bradley

    2014-01-01

    Collaborative information systems (CIS) are deployed within a diverse array of environments, ranging from the Internet to intelligence agencies to healthcare. It is increasingly the case that such systems are applied to manage sensitive information, making them targets for malicious insiders. While sophisticated security mechanisms have been developed to detect insider threats in various file systems, they are neither designed to model nor to monitor collaborative environments in which users function in dynamic teams with complex behavior. In this paper, we introduce a community-based anomaly detection system (CADS), an unsupervised learning framework to detect insider threats based on information recorded in the access logs of collaborative environments. CADS is based on the observation that typical users tend to form community structures, such that users with low a nity to such communities are indicative of anomalous and potentially illicit behavior. The model consists of two primary components: relational pattern extraction and anomaly detection. For relational pattern extraction, CADS infers community structures from CIS access logs, and subsequently derives communities, which serve as the CADS pattern core. CADS then uses a formal statistical model to measure the deviation of users from the inferred communities to predict which users are anomalies. To empirically evaluate the threat detection model, we perform an analysis with six months of access logs from a real electronic health record system in a large medical center, as well as a publicly-available dataset for replication purposes. The results illustrate that CADS can distinguish simulated anomalous users in the context of real user behavior with a high degree of certainty and with significant performance gains in comparison to several competing anomaly detection models. PMID:25485309

  9. Improving the analysis, storage and sharing of neuroimaging data using relational databases and distributed computing.

    PubMed

    Hasson, Uri; Skipper, Jeremy I; Wilde, Michael J; Nusbaum, Howard C; Small, Steven L

    2008-01-15

    The increasingly complex research questions addressed by neuroimaging research impose substantial demands on computational infrastructures. These infrastructures need to support management of massive amounts of data in a way that affords rapid and precise data analysis, to allow collaborative research, and to achieve these aims securely and with minimum management overhead. Here we present an approach that overcomes many current limitations in data analysis and data sharing. This approach is based on open source database management systems that support complex data queries as an integral part of data analysis, flexible data sharing, and parallel and distributed data processing using cluster computing and Grid computing resources. We assess the strengths of these approaches as compared to current frameworks based on storage of binary or text files. We then describe in detail the implementation of such a system and provide a concrete description of how it was used to enable a complex analysis of fMRI time series data. PMID:17964812

  10. Improving the Analysis, Storage and Sharing of Neuroimaging Data using Relational Databases and Distributed Computing

    PubMed Central

    Hasson, Uri; Skipper, Jeremy I.; Wilde, Michael J.; Nusbaum, Howard C.; Small, Steven L.

    2007-01-01

    The increasingly complex research questions addressed by neuroimaging research impose substantial demands on computational infrastructures. These infrastructures need to support management of massive amounts of data in a way that affords rapid and precise data analysis, to allow collaborative research, and to achieve these aims securely and with minimum management overhead. Here we present an approach that overcomes many current limitations in data analysis and data sharing. This approach is based on open source database management systems that support complex data queries as an integral part of data analysis, flexible data sharing, and parallel and distributed data processing using cluster computing and Grid computing resources. We assess the strengths of these approaches as compared to current frameworks based on storage of binary or text files. We then describe in detail the implementation of such a system and provide a concrete description of how it was used to enable a complex analysis of fMRI time series data. PMID:17964812

  11. WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions

    PubMed Central

    Karr, Jonathan R.; Phillips, Nolan C.; Covert, Markus W.

    2014-01-01

    Mechanistic ‘whole-cell’ models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations. We developed WholeCellSimDB, a database for organizing whole-cell simulations. WholeCellSimDB was designed to enable researchers to search simulation metadata to identify simulations for further analysis, and quickly slice and aggregate simulation results data. In addition, WholeCellSimDB enables users to share simulations with the broader research community. The database uses a hybrid relational/hierarchical data format architecture to efficiently store and retrieve both simulation setup metadata and results data. WholeCellSimDB provides a graphical Web-based interface to search, browse, plot and export simulations; a JavaScript Object Notation (JSON) Web service to retrieve data for Web-based visualizations; a command-line interface to deposit simulations; and a Python API to retrieve data for advanced analysis. Overall, we believe WholeCellSimDB will help researchers use whole-cell models to advance basic biological science and bioengineering. Database URL: http://www.wholecellsimdb.org Source code repository URL: http://github.com/CovertLab/WholeCellSimDB PMID:25231498

  12. Programming database tools for the casual user

    SciTech Connect

    Katz, R.A; Griffiths, C.

    1990-01-01

    The AGS Distributed Control System (AGSDCS) uses a relational database management system (INTERBASE) for the storage of all data associated with the control of the particle accelerator complex. This includes the static data which describes the component devices of the complex, as well as data for application program startup and data records that are used in analysis. Due to licensing restraints, it was necessary to develop tools to allow programs requiring access to a database to be unconcerned whether or not they were running on a licensed node. An in-house database server program was written, using Apollo mailbox communication protocols, allowing application programs via calls to this server to access the interbase database. Initially, the tools used by the server to actually access the database were written using the GDML C host language interface. Through the evolutionary learning process these tools have been converted to Dynamic SQL. Additionally, these tools have been extracted from the exclusive province of the database server and placed in their own library. This enables application programs to use these same tools on a licensed node without using the database server and without having to modify the application code. The syntax of the C calls remain the same.

  13. Values, inter-attitudinal structure, and attitude change: value accessibility can increase a related attitude's resistance to change.

    PubMed

    Blankenship, Kevin L; Wegener, Duane T; Murray, Renee A

    2015-12-01

    Accessibility is one of the most basic structural properties of an attitude and an important factor to consider in attitude strength. Despite its importance, relatively little work has examined the role of attitude accessibility in an inter-attitudinal context, particularly as it relates to the strength of related attitudes in the network. The present research examines accessibility as a property of one attitude (toward an abstract goal or end-state, that is, a value) that might influence the strength of a different but related attitude (toward a social policy conceptually related to the value). In Study 1, a highly accessible evaluative component of a value increased resistance to change of attitudes and behavioral intentions toward a social policy related to that value. Similarly, a manipulation of value accessibility (Studies 2 and 3) led to increased resistance of attitudes and behavioral intentions toward a social policy related to that value. Implications for the role of accessibility in inter-attitudinal strength are discussed. PMID:26542639

  14. 'It cuts both ways': a relational approach to access and accommodation for autism.

    PubMed

    Davidson, Joyce

    2010-01-01

    Drawing on a qualitative study of 45 autobiographical texts by authors with autism spectrum disorders (ASDs), this paper examines and attempts to aggregate recommendations for challenging barriers to socio-spatial inclusion. The autobiographies were selected by means of purposive sampling and subjected to a sequential process of detailed annotation, manual coding for emergent themes, and ongoing critical discourse analysis until data-saturation occurred. Resulting findings reveal that the extraordinarily heightened senses typically associated with ASDs mean that those on the spectrum often struggle to process environmental stimuli in a way that makes sense. Negotiating the sensory geographies of daily life requires considerable work, and while the access afforded by such cognitive and emotional labour may be rewarding, ASD authors reveal that their efforts are rarely understood - or assisted - by non-autistic others. Many proposed accommodations could, however, be made with relative ease, and ASD texts provide good reasons and recommendations for toning down 'toxic' stimuli - such as fluorescent lights - and for redesigning or reorganizing the shared sensory 'furniture' of social space. The paper thus suggests that by attending closely to voices from the spectrum, the non-autistic majority might ensure responsibilities to open access are taken seriously, and do indeed 'cut both ways'. PMID:19883964

  15. NEUSE RIVER WATER QUALITY DATABASE

    EPA Science Inventory

    The Neuse River water quality database is a Microsoft Access application that includes multiple data tables and some associated queries. The database was developed by Prof. Jim Bowen's research group.

  16. High Temperature Superconducting Materials Database

    National Institute of Standards and Technology Data Gateway

    SRD 149 NIST High Temperature Superconducting Materials Database (Web, free access)   The NIST High Temperature Superconducting Materials Database (WebHTS) provides evaluated thermal, mechanical, and superconducting property data for oxides and other nonconventional superconductors.

  17. Evidence generation from healthcare databases: recommendations for managing change.

    PubMed

    Bourke, Alison; Bate, Andrew; Sauer, Brian C; Brown, Jeffrey S; Hall, Gillian C

    2016-07-01

    There is an increasing reliance on databases of healthcare records for pharmacoepidemiology and other medical research, and such resources are often accessed over a long period of time so it is vital to consider the impact of changes in data, access methodology and the environment. The authors discuss change in communication and management, and provide a checklist of issues to consider for both database providers and users. The scope of the paper is database research, and changes are considered in relation to the three main components of database research: the data content itself, how it is accessed, and the support and tools needed to use the database. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27183900

  18. Laser Safety Audit and Inventory System Database

    SciTech Connect

    AUGUSTONI, ARNOLD L.

    2003-05-01

    A laser safety auditing and inventory system has been in use at Sandia National Laboratories--Albuquerque for the past five years and has recently been considered for adoption by Sandia National Laboratories--Livermore. The system utilizes the ''Microsoft Access'' database application, part of the Office 2000 software package. Audit and inventory data is available on-line for ready access by laser users. Data is updated weekly to provide users with current information relating to laser facility audits and laser inventories.

  19. Food Composition Database Format and Structure: A User Focused Approach

    PubMed Central

    Clancy, Annabel K.; Woods, Kaitlyn; McMahon, Anne; Probst, Yasmine

    2015-01-01

    This study aimed to investigate the needs of Australian food composition database user’s regarding database format and relate this to the format of databases available globally. Three semi structured synchronous online focus groups (M = 3, F = 11) and n = 6 female key informant interviews were recorded. Beliefs surrounding the use, training, understanding, benefits and limitations of food composition data and databases were explored. Verbatim transcriptions underwent preliminary coding followed by thematic analysis with NVivo qualitative analysis software to extract the final themes. Schematic analysis was applied to the final themes related to database format. Desktop analysis also examined the format of six key globally available databases. 24 dominant themes were established, of which five related to format; database use, food classification, framework, accessibility and availability, and data derivation. Desktop analysis revealed that food classification systems varied considerably between databases. Microsoft Excel was a common file format used in all databases, and available software varied between countries. User’s also recognised that food composition databases format should ideally be designed specifically for the intended use, have a user-friendly food classification system, incorporate accurate data with clear explanation of data derivation and feature user input. However, such databases are limited by data availability and resources. Further exploration of data sharing options should be considered. Furthermore, user’s understanding of food composition data and databases limitations is inherent to the correct application of non-specific databases. Therefore, further exploration of user FCDB training should also be considered. PMID:26554836

  20. [Genetic demography of populations of three megalopolises in relation to the problem of creating genetic databases].

    PubMed

    Kurbatova, O L; Pobedonostseva, E Iu; Veremeĭchik, V M; Prudnikova, A S; Atramentova, L A; Tsybovskiĭ, I S; Udina, I G

    2013-04-01

    Based on data collected from urban residents by questionnaire, the basic parameters of the genetic-demographic structure of populations of the three megalopolises, i.e., Moscow, Kharkov, and Minsk, have been calculated, including the migration coefficients and their dynamics in generations, the radius of the cities migration attraction, the parameters of marriage structure (the proportion ofinterethnic marriages, the level of intraethnic assortative mating, the marital distances), and the gene flow between the ethnic groups. It is shown that the representatives of the most numerous ethnic groups in each megalopolis have considerable amount of admixture. For Russians of Moscow, Ukrainians of Kharkov, and Belarusians of Minsk, the proportion of individuals whose ancestors were all born in the given city for at least three generations and belonged to the same nationality turned out to be very low (4.75% in Moscow, 1.83% in Kharkov, and 3.13% in Minsk). This finding questions the formation of a reference population in the megalopolis as a sampling of aboriginals of certain ethnic origins. In the paper, we justify principles of creating genetic databases for the population of the megalopolis taking into account the complexity and dynamism of its population structure. PMID:23866628

  1. Prediction Enhancement of Residue Real-Value Relative Accessible Surface Area in Transmembrane Helical Proteins by Solving the Output Preference Problem of Machine Learning-Based Predictors.

    PubMed

    Xiao, Feng; Shen, Hong-Bin

    2015-11-23

    The α-helical transmembrane proteins constitute 25% of the entire human proteome space and are difficult targets in high-resolution wet-lab structural studies, calling for accurate computational predictors. We present a novel sequence-based method called MemBrain-Rasa to predict relative solvent accessibility surface area (rASA) from primary sequences. MemBrain-Rasa features by an ensemble prediction protocol composed of a statistical machine-learning engine, which is trained in the sequential feature space, and a segment template similarity-based engine, which is constructed with solved structures and sequence alignment. We locally constructed a comprehensive database of residue relative solvent accessibility surface area from the solved protein 3D structures in the PDB database. It is searched against for segment templates that are expected to be structurally similar to the query sequence's segments. The segment template-based prediction is then fused with the support vector regression outputs using knowledge rules. Our experiments show that pure machine learning output cannot cover the entire rASA solution space and will have a serious prediction preference problem due to the relatively small size of membrane protein structures that can be used as the training samples. The template-based engine solves this problem very well, resulting in significant improvement of the prediction performance. MemBrain-Rasa achieves a Pearson correlation coefficient of 0.733 and mean absolute error of 13.593 on the benchmark dataset, which are 26.4% and 26.1% better than existing predictors. MemBrain-Rasa represents a new progress in structure modeling of α-helical transmembrane proteins. MemBrain-Rasa is available at www.csbio.sjtu.edu.cn/bioinf/MemBrain/. PMID:26455366

  2. The relationship between relative solvent accessibility and evolutionary rate in protein evolution.

    PubMed

    Ramsey, Duncan C; Scherrer, Michael P; Zhou, Tong; Wilke, Claus O

    2011-06-01

    Recent work with Saccharomyces cerevisiae shows a linear relationship between the evolutionary rate of sites and the relative solvent accessibility (RSA) of the corresponding residues in the folded protein. Here, we aim to develop a mathematical model that can reproduce this linear relationship. We first demonstrate that two models that both seem reasonable choices (a simple model in which selection strength correlates with RSA and a more complex model based on RSA-dependent amino acid distributions) fail to reproduce the observed relationship. We then develop a model on the basis of observed site-specific amino acid distributions and show that this model behaves appropriately. We conclude that evolutionary rates are directly linked to the distribution of amino acids at individual sites. Because of this link, any future insight into the biophysical mechanisms that determine amino acid distributions will improve our understanding of evolutionary rates. PMID:21467571

  3. The International Database of HOme blood pressure in relation to Cardiovascular Outcome (IDHOCO): moving from baseline characteristics to research perspectives

    PubMed Central

    Niiranen, Teemu J; Thijs, Lutgarde; Asayama, Kei; Johansson, Jouni K; Ohkubo, Takayoshi; Kikuya, Masahiro; Boggia, José; Hozawa, Atsushi; Sandoya, Edgardo; Stergiou, George S; Tsuji, Ichiro; Jula, Antti M; Imai, Yutaka; Staessen, Jan A

    2013-01-01

    The objective of this study is to construct an International Database of HOme blood pressure in relation to Cardiovascular Outcome (IDHOCO). The main goal of this database is to determine outcome-based diagnostic thresholds for the self-measured home blood pressure (BP). Secondary objectives include investigating the predictive value of white-coat and masked hypertension, morning and evening BP, BP and heart rate variability, and the home arterial stiffness index. We also aim to determine an optimal schedule for home BP measurements that provides the most accurate risk stratification. Eligible studies are population-based, have fatal as well as nonfatal outcomes available for analysis, comply with ethical standards, and have been previously published in peer-reviewed journals. In a meta-analysis based on individual subject data, composite and cause-specific cardiovascular events will be related to various indexes derived by home BP measurement. The analyses will be stratified by a cohort and adjusted for the clinic BP and established cardiovascular risk factors. The database includes 6753 subjects from five cohorts recruited in Ohasama, Japan (n = 2777); Finland (n = 2075); Tsurugaya, Japan (n = 836); Didima, Greece (n = 665); and Montevideo, Uruguay (n = 400). In these five cohorts, during a total of 62 106 person-years of follow-up (mean 9.2 years), 852 subjects died and 740 participants experienced a fatal or nonfatal cardiovascular event. IDHOCO provides a unique opportunity to investigate several hypotheses that could not reliably be studied in individual studies. The results of these analyses should be of help to clinicians involved in the management of patients with suspected or established hypertension. PMID:22763485

  4. Database constraints applied to metabolic pathway reconstruction tools.

    PubMed

    Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

    2014-01-01

    Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes. PMID:25202745

  5. Database Constraints Applied to Metabolic Pathway Reconstruction Tools

    PubMed Central

    Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

    2014-01-01

    Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes. PMID:25202745

  6. ARTI Refrigerant Database

    SciTech Connect

    Calm, J.M.

    1994-05-27

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  7. ARTI Refrigerant Database

    SciTech Connect

    Calm, J.M.

    1995-06-01

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  8. ARTI Refrigerant Database

    SciTech Connect

    Calm, J.M.

    1995-02-01

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase-out of chemical compounds of environmental concern.

  9. Identification of Anhydrobiosis-related Genes from an Expressed Sequence Tag Database in the Cryptobiotic Midge Polypedilum vanderplanki (Diptera; Chironomidae)*

    PubMed Central

    Cornette, Richard; Kanamori, Yasushi; Watanabe, Masahiko; Nakahara, Yuichi; Gusev, Oleg; Mitsumasu, Kanako; Kadono-Okuda, Keiko; Shimomura, Michihiko; Mita, Kazuei; Kikawada, Takahiro; Okuda, Takashi

    2010-01-01

    Some organisms are able to survive the loss of almost all their body water content, entering a latent state known as anhydrobiosis. The sleeping chironomid (Polypedilum vanderplanki) lives in the semi-arid regions of Africa, and its larvae can survive desiccation in an anhydrobiotic form during the dry season. To unveil the molecular mechanisms of this resistance to desiccation, an anhydrobiosis-related Expressed Sequence Tag (EST) database was obtained from the sequences of three cDNA libraries constructed from P. vanderplanki larvae after 0, 12, and 36 h of desiccation. The database contained 15,056 ESTs distributed into 4,807 UniGene clusters. ESTs were classified according to gene ontology categories, and putative expression patterns were deduced for all clusters on the basis of the number of clones in each library; expression patterns were confirmed by real-time PCR for selected genes. Among up-regulated genes, antioxidants, late embryogenesis abundant (LEA) proteins, and heat shock proteins (Hsps) were identified as important groups for anhydrobiosis. Genes related to trehalose metabolism and various transporters were also strongly induced by desiccation. Those results suggest that the oxidative stress response plays a central role in successful anhydrobiosis. Similarly, protein denaturation and aggregation may be prevented by marked up-regulation of Hsps and the anhydrobiosis-specific LEA proteins. A third major feature is the predicted increase in trehalose synthesis and in the expression of various transporter proteins allowing the distribution of trehalose and other solutes to all tissues. PMID:20833722

  10. The Thiamine diphosphate dependent Enzyme Engineering Database: A tool for the systematic analysis of sequence and structure relations

    PubMed Central

    2010-01-01

    Background Thiamine diphosphate (ThDP)-dependent enzymes form a vast and diverse class of proteins, catalyzing a wide variety of enzymatic reactions including the formation or cleavage of carbon-sulfur, carbon-oxygen, carbon-nitrogen, and especially carbon-carbon bonds. Although very diverse in sequence and domain organisation, they share two common protein domains, the pyrophosphate (PP) and the pyrimidine (PYR) domain. For the comprehensive and systematic comparison of protein sequences and structures the Thiamine diphosphate (ThDP)-dependent Enzyme Engineering Database (TEED) was established. Description The TEED http://www.teed.uni-stuttgart.de contains 12048 sequence entries which were assigned to 9443 different proteins and 379 structure entries. Proteins were assigned to 8 different superfamilies and 63 homologous protein families. For each family, the TEED offers multisequence alignments, phylogenetic trees, and family-specific HMM profiles. The conserved pyrophosphate (PP) and pyrimidine (PYR) domains have been annotated, which allows the analysis of sequence similarities for a broad variety of proteins. Human ThDP-dependent enzymes are known to be involved in many diseases. 20 different proteins and over 40 single nucleotide polymorphisms (SNPs) of human ThDP-dependent enzymes were identified in the TEED. Conclusions The online accessible version of the TEED has been designed to serve as a navigation and analysis tool for the large and diverse family of ThDP-dependent enzymes. PMID:20122171

  11. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation

    PubMed Central

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as ‘CHEMICAL-1 compared to CHEMICAL-2.’ With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical–disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked

  12. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.

    PubMed

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as 'CHEMICAL-1 compared to CHEMICAL-2' With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical-disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked order

  13. Database Searching by Managers.

    ERIC Educational Resources Information Center

    Arnold, Stephen E.

    Managers and executives need the easy and quick access to business and management information that online databases can provide, but many have difficulty articulating their search needs to an intermediary. One possible solution would be to encourage managers and their immediate support staff members to search textual databases directly as they now…

  14. HIV Structural Database

    National Institute of Standards and Technology Data Gateway

    SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

  15. Biological Macromolecule Crystallization Database

    National Institute of Standards and Technology Data Gateway

    SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

  16. Database in Artificial Intelligence.

    ERIC Educational Resources Information Center

    Wilkinson, Julia

    1986-01-01

    Describes a specialist bibliographic database of literature in the field of artificial intelligence created by the Turing Institute (Glasgow, Scotland) using the BRS/Search information retrieval software. The subscription method for end-users--i.e., annual fee entitles user to unlimited access to database, document provision, and printed awareness…

  17. Structural Ceramics Database

    National Institute of Standards and Technology Data Gateway

    SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

  18. National Vulnerability Database (NVD)

    National Institute of Standards and Technology Data Gateway

    National Vulnerability Database (NVD) (Web, free access)   NVD is a comprehensive cyber security vulnerability database that integrates all publicly available U.S. Government vulnerability resources and provides references to industry resources. It is based on and synchronized with the CVE vulnerability naming standard.

  19. Using the Structure-Function Linkage Database to Characterize Functional Domains in Enzymes

    PubMed Central

    Brown, Shoshana; Babbitt, Patricia

    2015-01-01

    The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a web-accessible database designed to link enzyme sequence, structure and functional information. This unit describes the protocol by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. It is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases. PMID:25501940

  20. Access to Money and Relation to Women's Use of Family Planning Methods Among Young Married Women in Rural India.

    PubMed

    Reed, Elizabeth; Donta, Balaiah; Dasgupta, Anindita; Ghule, Mohan; Battala, Madhusudana; Nair, Saritha; Silverman, Jay; Jadhav, Arun; Palaye, Prajakta; Saggurti, Niranjan; Raj, Anita

    2016-06-01

    Objectives The social positioning (i.e. social status and autonomy) of women in the household facilitates women's access to and decision-making power related to family planning (FP). Women's access to spending money, which may be an indicator of greater social positioning in the household, may also be greater among women who engage in income generating activities for their families, regardless of women's status in the household. However, in both scenarios, access to money may independently afford greater opportunity to obtain family planning services among women. This study seeks to assess whether access to money is associated with FP outcomes independently of women's social positioning in their households. Methods Using survey data from married couples in rural Maharashtra, India (n = 855), crude and adjusted regression was used to assess women's access to their own spending money in relation to past 3 month use of condoms and other forms of contraceptives (pills, injectables, intrauterine device). Results Access to money (59 %) was associated with condom and other contraceptive use (AORs ranged 1.5-1.8). These findings remained significant after adjusting for women's FP decision-making power in the household and mobility to seek FP services. Conclusion While preliminary, findings suggest that access to money may increase women's ability to obtain FP methods, even in contexts where social norms to support women's power in FP decision-making may not be readily adopted. PMID:26971270

  1. ITS-90 Thermocouple Database

    National Institute of Standards and Technology Data Gateway

    SRD 60 NIST ITS-90 Thermocouple Database (Web, free access)   Web version of Standard Reference Database 60 and NIST Monograph 175. The database gives temperature -- electromotive force (emf) reference functions and tables for the letter-designated thermocouple types B, E, J, K, N, R, S and T. These reference functions have been adopted as standards by the American Society for Testing and Materials (ASTM) and the International Electrotechnical Commission (IEC).

  2. Availability of genotypic data for USDA-ARS National Plant Germplasm System accessions using the Genetic Resources Information Network (GRIN) database

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The National Plant Germplasm System (NPGS) provides critical genetic resources to researchers and breeders world wide. Users of the NPGS materials need access to both genotypic and phenotypic data for accessions. Descriptor records at the accession level within the Germplasm Resources Information ...

  3. REDIdb: the RNA editing database

    PubMed Central

    Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

    2007-01-01

    The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at . PMID:17175530

  4. The Genopolis Microarray Database

    PubMed Central

    Splendiani, Andrea; Brandizi, Marco; Even, Gael; Beretta, Ottavio; Pavelka, Norman; Pelizzola, Mattia; Mayhaus, Manuel; Foti, Maria; Mauri, Giancarlo; Ricciardi-Castagnoli, Paola

    2007-01-01

    Background Gene expression databases are key resources for microarray data management and analysis and the importance of a proper annotation of their content is well understood. Public repositories as well as microarray database systems that can be implemented by single laboratories exist. However, there is not yet a tool that can easily support a collaborative environment where different users with different rights of access to data can interact to define a common highly coherent content. The scope of the Genopolis database is to provide a resource that allows different groups performing microarray experiments related to a common subject to create a common coherent knowledge base and to analyse it. The Genopolis database has been implemented as a dedicated system for the scientific community studying dendritic and macrophage cells functions and host-parasite interactions. Results The Genopolis Database system allows the community to build an object based MIAME compliant annotation of their experiments and to store images, raw and processed data from the Affymetrix GeneChip® platform. It supports dynamical definition of controlled vocabularies and provides automated and supervised steps to control the coherence of data and annotations. It allows a precise control of the visibility of the database content to different sub groups in the community and facilitates exports of its content to public repositories. It provides an interactive users interface for data analysis: this allows users to visualize data matrices based on functional lists and sample characterization, and to navigate to other data matrices defined by similarity of expression values as well as functional characterizations of genes involved. A collaborative environment is also provided for the definition and sharing of functional annotation by users. Conclusion The Genopolis Database supports a community in building a common coherent knowledge base and analyse it. This fills a gap between a local

  5. Animacy-Based Accessibility and Competition in Relative Clause Production in Hindi and Malayalam.

    PubMed

    Perera, C K; Srivastava, A K

    2016-08-01

    Two studies investigated interaction of animacy-based accessibility and competition processes with language specific constraints in shaping production preferences. Relative clause elicitation tasks (Gennari et al. in Cogn Psychol 65:141-176, 2012) were performed by two groups with 40 participants in each. Significantly more passives were produced with animate question/focus and assigned subject function to them in Malayalam, while the difference was insignificant in Hindi with animacy not equating with grammatical function assignment. Both languages produced active objects with OSV order significantly more with animate question/focus. This indicates animacy effect on word order. Animacy also influenced the expression of the agent phase in both languages as a tendency was found to omit the agent by-phase or to delay its appearance, when the two animate nouns entering into the structure are highly similar. The results point to language specific constraints in relative clause production and variability in the role of animacy-based retrieval order across languages. PMID:26108301

  6. EMU Lessons Learned Database

    NASA Technical Reports Server (NTRS)

    Matthews, Kevin M., Jr.; Crocker, Lori; Cupples, J. Scott

    2011-01-01

    As manned space exploration takes on the task of traveling beyond low Earth orbit, many problems arise that must be solved in order to make the journey possible. One major task is protecting humans from the harsh space environment. The current method of protecting astronauts during Extravehicular Activity (EVA) is through use of the specially designed Extravehicular Mobility Unit (EMU). As more rigorous EVA conditions need to be endured at new destinations, the suit will need to be tailored and improved in order to accommodate the astronaut. The Objective behind the EMU Lessons Learned Database(LLD) is to be able to create a tool which will assist in the development of next-generation EMUs, along with maintenance and improvement of the current EMU, by compiling data from Failure Investigation and Analysis Reports (FIARs) which have information on past suit failures. FIARs use a system of codes that give more information on the aspects of the failure, but if one is unfamiliar with the EMU they will be unable to decipher the information. A goal of the EMU LLD is to not only compile the information, but to present it in a user-friendly, organized, searchable database accessible to all familiarity levels with the EMU; both newcomers and veterans alike. The EMU LLD originally started as an Excel database, which allowed easy navigation and analysis of the data through pivot charts. Creating an entry requires access to the Problem Reporting And Corrective Action database (PRACA), which contains the original FIAR data for all hardware. FIAR data are then transferred to, defined, and formatted in the LLD. Work is being done to create a web-based version of the LLD in order to increase accessibility to all of Johnson Space Center (JSC), which includes converting entries from Excel to the HTML format. FIARs related to the EMU have been completed in the Excel version, and now focus has shifted to expanding FIAR data in the LLD to include EVA tools and support hardware such as

  7. 77 FR 22312 - Access by EPA Contractors to Confidential Business Information Related to the Greenhouse Gas...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-13

    ...EPA's Office of Atmospheric Programs plans to authorize the contractors named in this notice to access information submitted to EPA under the Greenhouse Gas Reporting Program that may be designated or claimed as confidential business information. Contractor access to this information will begin no sooner than April 19,...

  8. 76 FR 52659 - Access by EPA Contractors to Confidential Business Information (CBI) Related to the Greenhouse...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-23

    ...EPA's Office of Atmospheric Programs plans to authorize the contractors named in this notice to access information that will be submitted to EPA under the Greenhouse Gas Reporting Program that may be designated or claimed as confidential business information. Contractor access to this information will begin on August 29,...

  9. Where Are the Women? A Report into Issues Related to Women's Access to Workplace Literacy Programs.

    ERIC Educational Resources Information Center

    Milton, Marion

    A study investigated provision of workplace literacy courses available for women in female-dominated industries and women's access to and participation in those courses. A literature review revealed very little research on the required increased literacy skills in Australia and no previous studies on women's access to workplace literacy courses in…

  10. International Comparisions Database

    National Institute of Standards and Technology Data Gateway

    International Comparisions Database (Web, free access)   The International Comparisons Database (ICDB) serves the U.S. and the Inter-American System of Metrology (SIM) with information based on Appendices B (International Comparisons), C (Calibration and Measurement Capabilities) and D (List of Participating Countries) of the Comit� International des Poids et Mesures (CIPM) Mutual Recognition Arrangement (MRA). The official source of the data is The BIPM key comparison database. The ICDB provides access to results of comparisons of measurements and standards organized by the consultative committees of the CIPM and the Regional Metrology Organizations.

  11. Differences in Hispanic Access and Success Rates for Health-Related Studies in Texas Health-Related Institutions: A Multiyear, Statewide Investigation

    ERIC Educational Resources Information Center

    Cox, Shelley M.

    2013-01-01

    Purpose: The purpose of this study was to examine Hispanic student access and success in health-related degrees by examining enrollment and graduation rates over a period of 13 years. Archival data were obtained from the THECB consisting of the number of Hispanic students enrolled and number of degrees awarded in the health-related degrees at…

  12. Access and management of HIV-related diseases in resource-constrained settings: a workshop report.

    PubMed

    Dimba, Eao; Yengopal, V; Joshua, E; Thavarajah, R; Balasundaram, S

    2016-04-01

    With advancement of medical interventions, the lifespan of people living with HIV has increased globally. However, low- and middle-income countries (LMICs) which bear the greatest burden of the HIV pandemic face a constant challenge in addressing the treatment needs of immune-suppressed patients. An analysis of the current management protocols and access to medication in resource-poor settings was conducted at this workshop, with emphasis on the situation in resource-poor settings. The participants developed a consensus document based on the need to respond to the constantly changing HIV pandemic. Provision of oral health care must be guided by interconnecting principles based on population based strategies that address upstream determinants of health. Basic oral health coverage in developing countries can only be realized with a strong foundation at the primary health level. Early diagnosis of HIV-related comorbidities including the adverse effects of ARVs is essential for the improvement of treatment outcomes. Standardization of oral health care delivery mechanisms will facilitate evaluation at national and regional levels. Oral health care workers have a moral obligation to participate in sustained campaigns to reduce the social stigma associated with HIV/AIDS in their work places at every stage of the referral chain. Future research also needs to realign itself towards prevention using the common risk factor approach, which has a broader impact on non-communicable diseases, which are increasingly affecting patients with HIV/AIDS as their life expectancies increase. PMID:27109288

  13. Co-design of application software and NAND flash memory in solid-state drive for relational database storage system

    NASA Astrophysics Data System (ADS)

    Miyaji, Kousuke; Sun, Chao; Soga, Ayumi; Takeuchi, Ken

    2014-01-01

    A relational database management system (RDBMS) is designed based on NAND flash solid-state drive (SSD) for storage. By vertically integrating the storage engine (SE) and the flash translation layer (FTL), system performance is maximized and the internal SSD overhead is minimized. The proposed RDBMS SE utilizes physical information about the NAND flash memory which is supplied from the FTL. The query operation is also optimized for SSD. By these treatments, page-copy-less garbage collection is achieved and data fragmentation in the NAND flash memory is suppressed. As a result, RDBMS performance increases by 3.8 times, power consumption of SSD decreases by 46% and SSD life time is increased by 61%. The effectiveness of the proposed scheme increases with larger erase block sizes, which matches the future scaling trend of three-dimensional (3D-) NAND flash memories. The preferable row data size of the proposed scheme is below 500 byte for 16 kbyte page size.

  14. Curcumin Resource Database

    PubMed Central

    Kumar, Anil; Chetia, Hasnahana; Sharma, Swagata; Kabiraj, Debajyoti; Talukdar, Narayan Chandra; Bora, Utpal

    2015-01-01

    Curcumin is one of the most intensively studied diarylheptanoid, Curcuma longa being its principal producer. This apart, a class of promising curcumin analogs has been generated in laboratories, aptly named as Curcuminoids which are showing huge potential in the fields of medicine, food technology, etc. The lack of a universal source of data on curcumin as well as curcuminoids has been felt by the curcumin research community for long. Hence, in an attempt to address this stumbling block, we have developed Curcumin Resource Database (CRDB) that aims to perform as a gateway-cum-repository to access all relevant data and related information on curcumin and its analogs. Currently, this database encompasses 1186 curcumin analogs, 195 molecular targets, 9075 peer reviewed publications, 489 patents and 176 varieties of C. longa obtained by extensive data mining and careful curation from numerous sources. Each data entry is identified by a unique CRDB ID (identifier). Furnished with a user-friendly web interface and in-built search engine, CRDB provides well-curated and cross-referenced information that are hyperlinked with external sources. CRDB is expected to be highly useful to the researchers working on structure as well as ligand-based molecular design of curcumin analogs. Database URL: http://www.crdb.in PMID:26220923

  15. Human cancer databases (review).

    PubMed

    Pavlopoulou, Athanasia; Spandidos, Demetrios A; Michalopoulos, Ioannis

    2015-01-01

    Cancer is one of the four major non‑communicable diseases (NCD), responsible for ~14.6% of all human deaths. Currently, there are >100 different known types of cancer and >500 genes involved in cancer. Ongoing research efforts have been focused on cancer etiology and therapy. As a result, there is an exponential growth of cancer‑associated data from diverse resources, such as scientific publications, genome‑wide association studies, gene expression experiments, gene‑gene or protein‑protein interaction data, enzymatic assays, epigenomics, immunomics and cytogenetics, stored in relevant repositories. These data are complex and heterogeneous, ranging from unprocessed, unstructured data in the form of raw sequences and polymorphisms to well‑annotated, structured data. Consequently, the storage, mining, retrieval and analysis of these data in an efficient and meaningful manner pose a major challenge to biomedical investigators. In the current review, we present the central, publicly accessible databases that contain data pertinent to cancer, the resources available for delivering and analyzing information from these databases, as well as databases dedicated to specific types of cancer. Examples for this wealth of cancer‑related information and bioinformatic tools have also been provided. PMID:25369839

  16. Potash: a global overview of evaporate-related potash resources, including spatial databases of deposits, occurrences, and permissive tracts: Chapter S in Global mineral resource assessment

    USGS Publications Warehouse

    Orris, Greta J.; Cocker, Mark D.; Dunlap, Pamela; Wynn, Jeff C.; Spanski, Gregory T.; Briggs, Deborah A.; Gass, Leila; Bliss, James D.; Bolm, Karen S.; Yang, Chao; Lipin, Bruce R.; Ludington, Stephen; Miller, Robert J.; Slowakiewicz, Miroslaw

    2014-01-01

    This report describes a global, evaporite-related potash deposits and occurrences database and a potash tracts database. Chapter 1 summarizes potash resource history and use. Chapter 2 describes a global potash deposits and occurrences database, which contains more than 900 site records. Chapter 3 describes a potash tracts database, which contains 84 tracts with geology permissive for the presence of evaporite-hosted potash resources, including areas with active evaporite-related potash production, areas with known mineralization that has not been quantified or exploited, and areas with potential for undiscovered potash resources. Chapter 4 describes geographic information system (GIS) data files that include (1) potash deposits and occurrences data, (2) potash tract data, (3) reference databases for potash deposit and tract data, and (4) representative graphics of geologic features related to potash tracts and deposits. Summary descriptive models for stratabound potash-bearing salt and halokinetic potash-bearing salt are included in appendixes A and B, respectively. A glossary of salt- and potash-related terms is contained in appendix C and a list of database abbreviations is given in appendix D. Appendix E describes GIS data files, and appendix F is a guide to using the geodatabase.

  17. Consummatory, anxiety-related and metabolic adaptations in female rats with alternating access to preferred food.

    PubMed

    Cottone, Pietro; Sabino, Valentina; Steardo, Luca; Zorrilla, Eric P

    2009-01-01

    Avoidance of and relapse to palatable foods is a qualitative aspect of dieting, a putative risk factor for eating disorders or obesity. The present studies tested the hypotheses that rats with alternating access to highly preferred foods would show: (1) hypophagia, a function of the relative hedonic value of the underaccepted diet, (2) increased anxiety-like behavior and psychomotor arousal when preferred diet was unavailable, (3) obesity-like changes, and (4) stable individual differences in diet-switch-induced hypophagia. Preferences among three high-carbohydrate diets were determined in female Wistar rats (n=16). Adolescent rats (n=162) received the following weekly diet schedules: (1) continuous regular chow (7 days/week), (2) chow (5 days/week) followed by a more preferred diet (2 days/week), or (3) chow (5 days/week) followed by a less preferred chow (2 days/week). Some animals were yoke-restricted (75% calories) when provided chow to increase its rewarding properties. Diurnal locomotor activity was measured in a familiar environment, and anxiety-like behavior was assessed in the elevated plus-maze and defensive withdrawal tests. Rats withdrawn from the preferred diet showed hypophagia, anxiogenic-like behavior, increased locomotion, and weight loss. Chow hypophagia was progressive, individual-specific in magnitude, (partly) non-homeostatic in nature, and blunted by previous chow restriction. Despite eating less, rats cycled with the preferred diet became heavier, fatter, and diurnally less active, with greater feed efficiency and proinflammatory adipokine levels than chow controls. The present diet cycling procedure may model consummatory, anxiety-related, and metabolic effects of qualitative dieting in humans. PMID:18842344

  18. IPD—the Immuno Polymorphism Database

    PubMed Central

    Robinson, James; Waller, Matthew J.; Stoehr, Peter; Marsh, Steven G. E.

    2005-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute. PMID:15608253

  19. IPD--the Immuno Polymorphism Database.

    PubMed

    Robinson, James; Waller, Matthew J; Stoehr, Peter; Marsh, Steven G E

    2005-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute. PMID:15608253

  20. Vascular access-related infections in HIV patients undergoing hemodialysis: case description and literature review.

    PubMed

    Castro, Carlos E Figueroa; Madariaga, Miguel G

    2008-12-01

    Poor immune status, the use of a vascular access different from an AV fistula, and intravenous drug use (IDU) may favor increased rates of vascular access infections among HIV infected patients on hemodialysis. Staphylococcus spp. and Streptococcus spp. are the main cause of these infections, but Gram-negative rods and fungi have been found as well. Using an AV fistula when possible, and eliciting a history of IVDU on every visit may prevent this type of infection. When infections are present, coverage for both Gram-positive and negative organisms is recommended. Additional studies specifically addressing the issue of vascular access infection in HIV infected patients are required. PMID:19287844

  1. DIP: The Database of Interacting Proteins

    DOE Data Explorer

    The DIP Database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. By interaction, the DIP Database creators mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organisation and complexity of the protein interaction network at the cellular level. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. It is a relational database that can be searched by protein, sequence, motif, article information, and pathBLAST. The website also serves as an access point to a number of projects related to DIP, such as LiveDIP, The Database of Ligand-Receptor Partners (DLRP) and JDIP. Users have free and open access to DIP after login. [Taken from the DIP Guide and the DIP website] (Specialized Interface) (Registration Required)

  2. A database of macromolecular motions.

    PubMed Central

    Gerstein, M; Krebs, W

    1998-01-01

    We describe a database of macromolecular motions meant to be of general use to the structural community. The database, which is accessible on the World Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB , attempts to systematize all instances of protein and nucleic acid movement for which there is at least some structural information. At present it contains >120 motions, most of which are of proteins. Protein motions are further classified hierarchically into a limited number of categories, first on the basis of size (distinguishing between fragment, domain and subunit motions) and then on the basis of packing. Our packing classification divides motions into various categories (shear, hinge, other) depending on whether or not they involve sliding over a continuously maintained and tightly packed interface. In addition, the database provides some indication about the evidence behind each motion (i.e. the type of experimental information or whether the motion is inferred based on structural similarity) and attempts to describe many aspects of a motion in terms of a standardized nomenclature (e.g. the maximum rotation, the residue selection of a fixed core, etc.). Currently, we use a standard relational design to implement the database. However, the complexity and heterogeneity of the information kept in the database makes it an ideal application for an object-relational approach, and we are moving it in this direction. Specifically, in terms of storing complex information, the database contains plausible representations for motion pathways, derived from restrained 3D interpolation between known endpoint conformations. These pathways can be viewed in a variety of movie formats, and the database is associated with a server that can automatically generate these movies from submitted coordinates. PMID:9722650

  3. Multiple-Site Hemodynamic Analysis of Doppler Ultrasound with an Adaptive Color Relation Classifier for Arteriovenous Access Occlusion Evaluation

    PubMed Central

    Wu, Jian-Xing; Du, Yi-Chun; Wu, Ming-Jui; Li, Chien-Ming; Lin, Chia-Hung; Chen, Tainsong

    2014-01-01

    This study proposes multiple-site hemodynamic analysis of Doppler ultrasound with an adaptive color relation classifier for arteriovenous access occlusion evaluation in routine examinations. The hemodynamic analysis is used to express the properties of blood flow through a vital access or a tube, using dimensionless numbers. An acoustic measurement is carried out to detect the peak-systolic and peak-diastolic velocities of blood flow from the arterial anastomosis sites (A) to the venous anastomosis sites (V). The ratio of the supracritical Reynolds (Resupra) number and the resistive (Res) index quantitates the degrees of stenosis (DOS) at multiple measurement sites. Then, an adaptive color relation classifier is designed as a nonlinear estimate model to survey the occlusion level in monthly examinations. For 30 long-term follow-up patients, the experimental results show the proposed screening model efficiently evaluates access occlusion. PMID:24892039

  4. Analysis of anesthesia-related medical disputes in the 2009-2014 period using the Korean Society of Anesthesiologists database.

    PubMed

    Roh, Woon-Seok; Kim, Duk-Kyung; Jeon, Young-Hun; Kim, Seong-Hyop; Lee, Seung-Cheol; Ko, Young-Kwon; Lee, Yong-Cheol; Lee, Gyu-Hong

    2015-02-01

    Using the Korean Society of Anesthesiologists database of anesthesia-related medical disputes (July 2009-June 2014), causative mechanisms and injury patterns were analyzed. In total, 105 cases were analyzed. Most patients were aged < 60 yr (82.9%) and were classified as American Society of Anesthesiologists physical status ≤ II (90.5%). In 42.9% of all cases, the injuries were determined to be 'avoidable' if the appropriate standard of care had been applied. Sedation was the sec most common type of anesthesia (37.1% of all cases), following by general anesthesia. Most sedation cases (27/39, 69.2%) showed a common lack of vigilance: no pre-procedural testing (82.1%), absence of anesthesia record (89.7%), and non-use of intra-procedural monitoring (15.4%). Most sedation (92.3%) was provided simultaneously by the non-anesthesiologists who performed the procedures. After the resulting injuries were grouped into four categories (temporary, permanent/minor, permanent/major, and death), their causative mechanisms were analyzed in cases with permanent injuries (n=20) and death (n=82). A 'respiratory events' was the leading causative mechanism (56/102, 54.9%). Of these, the most common specific mechanism was hypoxia secondary to airway obstruction or respiratory depression (n=31). The sec most common damaging event was a 'cardiovascular events' (26/102, 25.5%), in which myocardial infarction was the most common specific mechanism (n=12). Our database analysis demonstrated several typical injury profiles (a lack of vigilance in seemingly safe procedures or sedation, non-compliance with the airway management guidelines, and the prevalence of myocardial infarction) and can be helpful to improve patient safety. PMID:25653494

  5. Analysis of Diagnoses Associated with Multiple Sclerosis–Related In-Hospital Mortality Using the Premier Hospital Database

    PubMed Central

    Pocoski, Jennifer; Cutter, Gary; Kaufman, David W.; Pleimes, Dirk

    2016-01-01

    Background: We sought to compare mortality rates and related diagnoses in hospitalized patients with multiple sclerosis (MS), those with diabetes mellitus (DM), and the general hospitalized population (GHP). Methods: Patients who died between 2007 and 2011 were identified in the US hospital–based Premier Healthcare Database. Demographic information was collected, mortality rates calculated, and principal diagnoses categorized. Results: Of 55,152 unique patients with MS identified, 1518 died. Mean age at death was 10 years younger for the MS group (63.4 years) than for the DM (73.3 years) and GHP (73.1 years) groups. Age-adjusted mortality rates, based on the 2000 US Standard Million Population, were 1077, 1248, and 1133 per 100,000, respectively. Infection was the most common principal diagnosis at the hospital stay during which the patient died in the MS cohort (43.1% vs. 26.3% and 24.0% in the DM and GHP groups, respectively). Other common principal diagnoses in the MS group included pulmonary (17.5%) and cardiovascular (12.1%) disease. Septicemia/sepsis/septic shock was a secondary diagnosis for 50.7% of patients with MS versus 36.0% and 31.0% of patients in the DM and GHP cohorts, respectively. Conclusions: Patients with MS had a shorter life span than patients with DM or the GHP and were more likely to have a principal diagnosis of infection at their final hospital stay. However, the database was limited to codes recorded in the hospital; diagnoses received outside the hospital were not captured. PMID:27252603

  6. The IPD and IMGT/HLA database: allele variant databases

    PubMed Central

    Robinson, James; Halliwell, Jason A.; Hayhurst, James D.; Flicek, Paul; Parham, Peter; Marsh, Steven G. E.

    2015-01-01

    The Immuno Polymorphism Database (IPD) was developed to provide a centralized system for the study of polymorphism in genes of the immune system. Through the IPD project we have established a central platform for the curation and publication of locus-specific databases involved either directly or related to the function of the Major Histocompatibility Complex in a number of different species. We have collaborated with specialist groups or nomenclature committees that curate the individual sections before they are submitted to IPD for online publication. IPD consists of five core databases, with the IMGT/HLA Database as the primary database. Through the work of the various nomenclature committees, the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/. The IPD project continues to develop with new tools being added to address scientific developments, such as Next Generation Sequencing, and to address user feedback and requests. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities. PMID:25414341

  7. ACCESS PENNSYLVANIA Curriculum Guide.

    ERIC Educational Resources Information Center

    Pennsylvania State Library, Harrisburg.

    This curriculum guide was prepared as a tool for teaching students the purpose and function of the ACCESS PENNSYLVANIA database in the total concept of information literacy. The database on compact laser disc contains information about the holdings of hundreds of school, public, academic, and special use libraries. The database can be searched at…

  8. Creation of geographic information database of subsatellite calibration test site

    NASA Astrophysics Data System (ADS)

    Zyelyk, Ya. I.; Semeniv, O. V.

    2014-12-01

    The prototype of geographic information database (DB) of the sub-satellite calibration test site has been created, to which user can be accessed from the free open-source geographic information system Quantum GIS (QGIS) environment. QGIS is used as an integrator of all data and applications and visualizer of the satellite imagery and vector layers of test sites in the cartographic interface. Conversion of the database from the local representation in the MS Access to the server representation in the PostgreSQL environment has been performed. Dynamic application to QGIS for user interaction from QGIS environment with the object-relational database and to display information from the database has been created. Functional-algorithmic part of these application and the interface for user interaction with the database has been developed.

  9. Does the Noun Phrase Accessibility Hierarchy Predict the Difficulty Order in the Acquisition of Japanese Relative Clauses?

    ERIC Educational Resources Information Center

    Ozeki, Hiromi; Shirai, Yasuhiro

    2007-01-01

    Although Keenan and Comrie's (1977) noun phrase accessibility hierarchy (NPAH) has been shown to predict the difficulty order of relative clauses (RCs) in SLA, most studies of the NPAH have been on European languages. This paper tests the prediction for Japanese. Study 1 analyzes RCs in an oral interview corpus from 90 learners of Japanese at four…

  10. Risk Factors for Asthma-Related Healthcare Use: Longitudinal Analysis Using the NHI Claims Database in a Korean Asthma Cohort

    PubMed Central

    Kim, Kyoungjoo; Park, Yunjin; Kim, Yuri; Lee, Yoon Su; Kwon, Hyouk-Soo; Kim, Sae-Hoon; Chang, Yoon-Seok; Cho, You Sook; Jang, An-Soo; Park, Jung-Won; Nahm, Dong-Ho; Yoon, Ho-Joo; Cho, Sang-Heon; Cho, Young-Joo; Choi, Byoung Whui; Moon, Hee-Bom; Kim, Tae-Bum

    2014-01-01

    Background Though insurance claims data are useful for researching asthma, they have important limitations, such as a diagnostic inaccuracy and a lack of clinical information. To overcome these drawbacks, we used the novel method by merging the clinical data from our asthma cohort with the National Health Insurance (NHI) claims data. Methods and Results Longitudinal analysis of asthma-related healthcare use from the NHI claims database, merged with data of 736 patients registered in a Korean asthma cohort, was conducted for three consecutive years from registration of the cohort. Asthma-related asthma healthcare referred to outpatient and emergency department visits, hospitalizations, and the use of systemic corticosteroids. Univariate and multivariate logistic regression analysis was used to evaluate risk factors for asthma-related healthcare. Over three years after enrollment, many patients changed from tertiary to primary/secondary hospitals with a lack of maintenance of inhaled corticosteroid-based controllers. An independent risk factor for emergency visits was a previous history of asthma exacerbation. In hospitalizations, old age and Asthma Control Test (ACT) score variability were independent risk factors. An independent risk factor for per person cumulative duration of systemic corticosteroids was the FEV1 (Forced expiratory volume in one second)%. The use of systemic corticosteroids was independently associated with being female, the FEV1%, and ACT score variability. Conclusion We found that old age, being female, long-standing asthma, a low FEV1%, asthma brittleness, asthma drug compliance, and a history of asthma exacerbation were independent risk factors for increased asthma-related healthcare use in Korea. PMID:25397972

  11. Vaccine-preventable disease-related hospitalization among immigrants and refugees to Canada: Study of linked population-based databases.

    PubMed

    Ng, Edward; Sanmartin, Claudia; Elien-Massenat, Dominique; Manuel, Douglas G

    2016-08-17

    While immigrants tend to be healthier especially when they first arrived, this healthy immigrant effect may not apply to vaccine-preventable diseases (VPD) especially among immigrants from countries without vaccination programs. There is therefore an important information gap regarding differential health outcome and hospitalization usage by immigrant status, landing cohort, world region and immigrant category. This study focused on acute-care hospitalization, and used two recently linked population-based databases in Canada, namely, the 2006 Census linked to the Hospital Discharge Abstract (DAD), and the Immigrant Landing File linked to the DAD (ILF-DAD) to estimate crude and age-standardized VPD-related hospitalization rates (ASHR) by the above-mentioned immigrant characteristics to be compared with that for overall Canadian-born reference population. Based on the 2006 Census-DAD linked database, VPD-specific ASHR for overall immigrants was significantly higher than that for the Canadian-born population (1.6, 95% CI, 1.5, 1.6 vs 1.2, 95% CI, 1.1, 1.2, respectively). VPD-specific ASHRs by landing cohorts also increased with years in Canada (e.g. 1.4, 95% CI, 1.3, 1.5 for the 1990-2006 cohort, and 1.6, 95% CI, 1.5, 1.7 for the pre-1980 cohort). Based on the 1980-2006 ILF-DAD, the VPD-specific ASHRs were highest among Southeast and East Asians (e.g. 2.1, 95% CI, 1.9, 2.3 for East Asia). Compared with the Canadian-born, economic class immigrants overall had significantly lower ASHR (1.4, 95% CI 1.2, 1.6), but the low rate was mainly due to the dependants (spouse or children) within this class (0.8, 95% CI 0.6, 1.1). Both family and refugee categories had significantly higher ASHRs (1.3, 95% CI, 1.2, 1.5 and 1.7, 95% CI, 1.4, 2.1, respectively), especially among those refugees assisted by government (2.0, 95% CI, 1.4, 2.6). With increasing immigration, changing source countries and emerging needs for refugee settlements in Canada, these newly linked datasets help to

  12. Performance Issues Related to Web Service Usage for Remote Data Access

    SciTech Connect

    Pais, V. F.; Stancalie, V.; Mihailescu, F. A.; Totolici, M. C.

    2008-04-07

    Web services are starting to be widely used in applications for remotely accessing data. This is of special interest for research based on small and medium scale fusion devices, since scientists participating remotely to experiments are accessing large amounts of data over the Internet. Recent tests were conducted to see how the new network traffic, generated by the use of web services, can be integrated in the existing infrastructure and what would be the impact over existing applications, especially those used in a remote participation scenario.

  13. Age-related patterns of vigorous-intensity physical activity in youth: The International Children's Accelerometry Database.

    PubMed

    Corder, Kirsten; Sharp, Stephen J; Atkin, Andrew J; Andersen, Lars B; Cardon, Greet; Page, Angie; Davey, Rachel; Grøntved, Anders; Hallal, Pedro C; Janz, Kathleen F; Kordas, Katarzyna; Kriemler, Susi; Puder, Jardena J; Sardinha, Luis B; Ekelund, Ulf; van Sluijs, Esther M F

    2016-12-01

    Physical activity declines during youth but most evidence reports on combined moderate and vigorous-intensity physical activity. We investigated how vigorous-intensity activity varies with age. Cross-sectional data from 24,025 participants (5.0-18.0 y; from 20 studies in 10 countries obtained 2008-2010) providing ≥ 1 day accelerometer data (International Children's Accelerometry Database (ICAD)). Linear regression was used to investigate age-related patterns in vigorous-intensity activity; models included age (exposure), adjustments for monitor wear-time and study. Moderate-intensity activity was examined for comparison. Interactions were used to investigate whether the age/vigorous-activity association differed by sex, weight status, ethnicity, maternal education and region. A 6.9% (95% CI 6.2, 7.5) relative reduction in mean vigorous-intensity activity with every year of age was observed; for moderate activity the relative reduction was 6.0% (5.6%, 6.4%). The age-related decrease in vigorous-intensity activity remained after adjustment for moderate activity. A larger age-related decrease in vigorous activity was observed for girls (- 10.7%) versus boys (- 2.9%), non-white (- 12.9% to - 9.4%) versus white individuals (- 6.1%), lowest maternal education (high school (- 2.0%)) versus college/university (ns) and for overweight/obese (- 6.1%) versus healthy-weight participants (- 8.1%). In addition to larger annual decreases in vigorous-intensity activity, overweight/obese individuals, girls and North Americans had comparatively lower average vigorous-intensity activity at 5.0-5.9 y. Age-related declines in vigorous-intensity activity during youth appear relatively greater than those of moderate activity. However, due to a higher baseline, absolute moderate-intensity activity decreases more than vigorous. Overweight/obese individuals, girls, and North Americans appear especially in need of vigorous-intensity activity promotion due to low levels at 5

  14. The MenUSE System for Multilingual Assisted Access to Online Databases, in the Context of Current EC-Funded Projects.

    ERIC Educational Resources Information Center

    Blake, Paul

    1992-01-01

    Describes the MenUSE (Menu-based User Search Engine) retrieval system for multilingual database searching and reviews the status of other similar projects funded by the European Communities Commission. A Japanese-English version of MenUSE is explained, including its use of HyperCard software. (LRW)

  15. GPO Access: Scaled Down Version of WINDO/GATEWAY Legislation.

    ERIC Educational Resources Information Center

    Machovec, George S.

    1993-01-01

    Addresses issues relating to federal legislation that provides electronic access to federal databases and information through the Government Printing Office (GPO). Highlights include the role of depository libraries; public access; funding; publishing restrictions; national standards; and political issues, including opposition from the National…

  16. Major-Effect Alleles at Relatively Few Loci Underlie Distinct Vernalization and Flowering Variation in Arabidopsis Accessions

    PubMed Central

    Lister, Clare; Anderson, Jillian; Warthmann, Norman; Shindo, Chikako; Irwin, Judith; Nordborg, Magnus; Dean, Caroline

    2011-01-01

    We have explored the genetic basis of variation in vernalization requirement and response in Arabidopsis accessions, selected on the basis of their phenotypic distinctiveness. Phenotyping of F2 populations in different environments, plus fine mapping, indicated possible causative genes. Our data support the identification of FRI and FLC as candidates for the major-effect QTL underlying variation in vernalization response, and identify a weak FLC allele, caused by a Mutator-like transposon, contributing to flowering time variation in two N. American accessions. They also reveal a number of additional QTL that contribute to flowering time variation after saturating vernalization. One of these was the result of expression variation at the FT locus. Overall, our data suggest that distinct phenotypic variation in the vernalization and flowering response of Arabidopsis accessions is accounted for by variation that has arisen independently at relatively few major-effect loci. PMID:21625501

  17. Mining Roles and Access Control for Relational Data under Privacy and Accuracy Constraints

    ERIC Educational Resources Information Center

    Pervaiz, Zahid

    2013-01-01

    Access control mechanisms protect sensitive information from unauthorized users. However, when sensitive information is shared and a Privacy Protection Mechanism (PPM) is not in place, an authorized insider can still compromise the privacy of a person leading to identity disclosure. A PPM can use suppression and generalization to anonymize and…

  18. 76 FR 11667 - Procedures Relating to Awards Under the Equal Access to Justice Act

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-03

    ... proposed rule (75 FR 44928, July 30, 2010) to amend its regulations implementing the Equal Access to... 7 CFR part 1, subpart J, an EAJA award will be made. The mere status of the entity as an... a material way. Furthermore, it does not raise a novel legal or policy issue arising out of...

  19. Socializing in an Open Drug Scene: The relationship Between Access to Private Space and Drug-Related Street Disorder

    PubMed Central

    DeBeck, Kora; Wood, Evan; Qi, Jiezhi; Fu, Eric; McArthur, Doug; Montaner, Julio; Kerr, Thomas

    2011-01-01

    Background Limited attention has been given to the potential role that the structure of housing available to people who are entrenched in street-based drug scenes may play in influencing the amount of time injection drug users (IDU) spend on public streets. We sought to examine the relationship between time spent socializing in Vancouver's drug scene and access to private space. Methods Using multivariate logistic regression we evaluated factors associated with socializing (three+ hours each day) in Vancouver's open drug scene among a prospective cohort of IDU. We also assessed attitudes towards relocating socializing activities if greater access to private indoor space was provided. Results Among our sample of 1114 IDU, 43% fit our criteria for socializing in the open drug scene. In multivariate analysis, having limited access to private space was independently associated with socializing (adjusted odds ratio: 1.80, 95% confidence interval: 1.28 – 2.55). In further analysis, 65% of ‘socializers’ reported positive attitudes towards relocating socializing if they had greater access to private space. Conclusion These findings suggest that providing IDU with greater access to private indoor space may reduce one component of drug-related street disorder. Low-threshold supportive housing based on the ‘housing first’ model that include safeguards to manage behaviors associated with illicit drug use appear to offer important opportunities to create the types of private spaces that could support a reduction in street disorder. PMID:21764528

  20. CEMTDD: The database for elucidating the relationships among herbs, compounds, targets and related diseases for Chinese ethnic minority traditional drugs

    PubMed Central

    Xie, Tao; Yao, Hong; Pang, Xiaobo; Sun, Fuzhou; Ouyang, Liang; Wang, Jinhui

    2015-01-01

    China has different ethnic minorities that establish their own medical systems and practice experience for thousand years, thereafter named Chinese Ethnic Minority Traditional Drugs (CEMTDs) (http://www.cemtdd.com/index.html). Since many compounds from CEMTDs have been reported to perturb human's dysfunction network and restore human normal physiological conditions, the relationships amongst a series of compounds from specific herbs, their targets and relevant diseases have become our main focus in CEMTD modernization. Herein, we have constructed the first Chinese Ethnic Minority Traditional Drug Database (CEMTDD) mainly from Xinjiang Uygur Autonomous Region (XUAR), retrieving CEMTD-related information from different resources. CEMTDD contains about 621 herbs, 4, 060 compounds, 2, 163 targets and 210 diseases, among which most of herbs can be applied into gerontology therapy including inflammation, cardiovascular disease and neurodegenerative disease. Gerontology is highly occurred in XUAR, and has abundant experience in treating such diseases, which may benefit for developing a new gerontology therapeutic strategy. CEMTDD displays networks for intricate relationships between CEMTDs and treated diseases, as well as the interrelations between active compounds and action targets, which may shed new light on the combination therapy of CEMTDs and further understanding of their herb molecular mechanisms for better modernized utilizations of CEMTDs, especially in gerontology. PMID:25970778

  1. Annual Review of Database Developments 1991.

    ERIC Educational Resources Information Center

    Basch, Reva

    1991-01-01

    Review of developments in databases highlights a new emphasis on accessibility. Topics discussed include the internationalization of databases; databases that deal with finance, drugs, and toxic waste; access to public records, both personal and corporate; media online; reducing large files of data to smaller, more manageable files; and…

  2. Querying genomic databases

    SciTech Connect

    Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

    1991-09-01

    A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

  3. The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency

    PubMed Central

    Rubinstein, Wendy S.; Maglott, Donna R.; Lee, Jennifer M.; Kattman, Brandi L.; Malheiro, Adriana J.; Ovetsky, Michael; Hem, Vichet; Gorelenkov, Viatcheslav; Song, Guangfeng; Wallin, Craig; Husain, Nora; Chitipiralla, Shanmuga; Katz, Kenneth S.; Hoffman, Douglas; Jang, Wonhee; Johnson, Mark; Karmanov, Fedor; Ukrainchik, Alexander; Denisenko, Mikhail; Fomous, Cathy; Hudson, Kathy; Ostell, James M.

    2013-01-01

    The National Institutes of Health Genetic Testing Registry (GTR; available online at http://www.ncbi.nlm.nih.gov/gtr/) maintains comprehensive information about testing offered worldwide for disorders with a genetic basis. Information is voluntarily submitted by test providers. The database provides details of each test (e.g. its purpose, target populations, methods, what it measures, analytical validity, clinical validity, clinical utility, ordering information) and laboratory (e.g. location, contact information, certifications and licenses). Each test is assigned a stable identifier of the format GTR000000000, which is versioned when the submitter updates information. Data submitted by test providers are integrated with basic information maintained in National Center for Biotechnology Information’s databases and presented on the web and through FTP (ftp.ncbi.nih.gov/pub/GTR/_README.html). PMID:23193275

  4. MalAvi: a public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochrome b lineages.

    PubMed

    Bensch, Staffan; Hellgren, Olof; Pérez-Tris, Javier

    2009-09-01

    Research in avian blood parasites has seen a remarkable increase since the introduction of polymerase chain reaction-based methods for parasite identification. New data are revealing complex multihost-multiparasite systems which are difficult to understand without good knowledge of the host range and geographical distribution of the parasite lineages. However, such information is currently difficult to obtain from the literature, or from general repositories such as GenBank, mainly because (i) different research groups use different parasite lineage names, (ii) GenBank entries frequently refer only to the first host and locality at which each parasite was sampled, and (iii) different researchers use different gene fragments to identify parasite lineages. We propose a unified database of avian blood parasites of the genera Plasmodium, Haemoproteus and Leucocytozoon identified by a partial region of their cytochrome b sequences. The database uses a standardized nomenclature to remove synonymy, and concentrates all available information about each parasite in a public reference site, thereby facilitating access to all researchers. Initial data include a list of host species and localities, as well as genetic markers that can be used for phylogenetical analyses. The database is free to download and will be regularly updated by the authors. Prior to publication of new lineages, we encourage researchers to assign names to match the existing database. We anticipate that the value of the database as a source for determining host range and geographical distribution of the parasites will grow with its size and substantially enhance the understanding of this remarkably diverse group of parasites. PMID:21564906

  5. CottonGen: a genomics, genetics and breeding database for cotton research

    Technology Transfer Automated Retrieval System (TEKTRAN)

    CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, vis...

  6. Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues.

    PubMed

    Topham, Christopher M; Smith, Jeremy C

    2015-02-01

    Relative amino acid residue solvent accessibility values allow the quantitative comparison of atomic solvent-accessible surface areas in different residue types and physical environments in proteins and in protein structural alignments. Geometry-optimised tri-peptide structures in extended solvent-exposed reference conformations have been obtained for 43 amino acid residue types at a high level of quantum chemical theory. Significant increases in side-chain solvent accessibility, offset by reductions in main-chain atom solvent exposure, were observed for standard residue types in partially geometry-optimised structures when compared to non-minimised models built from identical sets of proper dihedral angles abstracted from the literature. Optimisation of proper dihedral angles led most notably to marked increases of up to 54% in proline main-chain atom solvent accessibility compared to literature values. Similar effects were observed for fully-optimised tri-peptides in implicit solvent. The relief of internal strain energy was associated with systematic variation in N, C(α) and C(β) atom solvent accessibility across all standard residue types. The results underline the importance of optimisation of 'hard' degrees of freedom (bond lengths and valence bond angles) and improper dihedral angle values from force field or other context-independent reference values, and impact on the use of standardised fixed internal co-ordinate geometry in sampling approaches to the determination of absolute values of protein amino acid residue solvent accessibility. Quantum chemical methods provide a useful and accurate alternative to molecular mechanics methods to perform energy minimisation of peptides containing non-standard (chemically modified) amino acid residues frequently present in experimental protein structure data sets, for which force field parameters may not be available. Reference tri-peptide atomic co-ordinate sets including hydrogen atoms are made freely available

  7. Interconnecting heterogeneous database management systems

    NASA Technical Reports Server (NTRS)

    Gligor, V. D.; Luckenbaugh, G. L.

    1984-01-01

    It is pointed out that there is still a great need for the development of improved communication between remote, heterogeneous database management systems (DBMS). Problems regarding the effective communication between distributed DBMSs are primarily related to significant differences between local data managers, local data models and representations, and local transaction managers. A system of interconnected DBMSs which exhibit such differences is called a network of distributed, heterogeneous DBMSs. In order to achieve effective interconnection of remote, heterogeneous DBMSs, the users must have uniform, integrated access to the different DBMs. The present investigation is mainly concerned with an analysis of the existing approaches to interconnecting heterogeneous DBMSs, taking into account four experimental DBMS projects.

  8. Curcumin Resource Database.

    PubMed

    Kumar, Anil; Chetia, Hasnahana; Sharma, Swagata; Kabiraj, Debajyoti; Talukdar, Narayan Chandra; Bora, Utpal

    2015-01-01

    Curcumin is one of the most intensively studied diarylheptanoid, Curcuma longa being its principal producer. This apart, a class of promising curcumin analogs has been generated in laboratories, aptly named as Curcuminoids which are showing huge potential in the fields of medicine, food technology, etc. The lack of a universal source of data on curcumin as well as curcuminoids has been felt by the curcumin research community for long. Hence, in an attempt to address this stumbling block, we have developed Curcumin Resource Database (CRDB) that aims to perform as a gateway-cum-repository to access all relevant data and related information on curcumin and its analogs. Currently, this database encompasses 1186 curcumin analogs, 195 molecular targets, 9075 peer reviewed publications, 489 patents and 176 varieties of C. longa obtained by extensive data mining and careful curation from numerous sources. Each data entry is identified by a unique CRDB ID (identifier). Furnished with a user-friendly web interface and in-built search engine, CRDB provides well-curated and cross-referenced information that are hyperlinked with external sources. CRDB is expected to be highly useful to the researchers working on structure as well as ligand-based molecular design of curcumin analogs. PMID:26220923

  9. Higher relative risk for multiple sclerosis in a pediatric and adolescent diabetic population: analysis from DPV database.

    PubMed

    Bechtold, Susanne; Blaschek, Astrid; Raile, Klemens; Dost, Axel; Freiberg, Clemens; Askenas, Meik; Fröhlich-Reiterer, Elke; Molz, Esther; Holl, Reinhard W

    2014-01-01

    OBJECTIVE Type 1 diabetes and multiple sclerosis (MS) are typical autoimmune diseases in children and young adults. We assessed the co-occurrence of type 1 diabetes and MS by estimating the relative risk (RR) for MS in a pediatric and adolescent diabetic population and looked for possible influencing factors. RESEARCH DESIGN AND METHODS Within the Diabetes Patienten Verlaufsdokumentation (DPV)-Wiss Project, from January 1995 to October 2012, data from 56,653 patients with type 1 diabetes were collected in 248 centers in Germany and Austria. Published data on German and Mid-European MS prevalence were taken for comparison. Multivariable regression analysis was used to identify confounders for co-occurrence of type 1 diabetes and MS. RESULTS The RR for MS in patients with type 1 diabetes was estimated at 3.35-4.79 (95% CI 1.56-7.21 and 2.01-11.39, respectively). Immigration status in all patients (P < 0.05) and the presence of thyroid antibodies in male patients only (P = 0.05) were identified as influencing factors on MS incidence within the DPV database. The month-of-birth pattern revealed that risk was higher during the spring and summer months in the population with type 1 diabetes and MS in comparison with the population with type 1 diabetes. CONCLUSIONS The present cohort study demonstrates a higher risk of co-occurrence of MS in a pediatric and adolescent diabetic population. Immigration status and thyroid antibodies in male patients were independent risk indicators for the incidental rate of MS. Diabetic patients born during spring and summer had a higher risk for the development of MS. We suggest that environmental factors modulate the individual's risk for the co-occurrence of both diseases. PMID:23990514

  10. Patient-Safety-Related Hospital Deaths in England: Thematic Analysis of Incidents Reported to a National Database, 2010–2012

    PubMed Central

    Donaldson, Liam J.; Panesar, Sukhmeet S.; Darzi, Ara

    2014-01-01

    Background Hospital mortality is increasingly being regarded as a key indicator of patient safety, yet methodologies for assessing mortality are frequently contested and seldom point directly to areas of risk and solutions. The aim of our study was to classify reports of deaths due to unsafe care into broad areas of systemic failure capable of being addressed by stronger policies, procedures, and practices. The deaths were reported to a patient safety incident reporting system after mandatory reporting of such incidents was introduced. Methods and Findings The UK National Health Service database was searched for incidents resulting in a reported death of an adult over the period of the study. The study population comprised 2,010 incidents involving patients aged 16 y and over in acute hospital settings. Each incident report was reviewed by two of the authors, and, by scrutinising the structured information together with the free text, a main reason for the harm was identified and recorded as one of 18 incident types. These incident types were then aggregated into six areas of apparent systemic failure: mismanagement of deterioration (35%), failure of prevention (26%), deficient checking and oversight (11%), dysfunctional patient flow (10%), equipment-related errors (6%), and other (12%). The most common incident types were failure to act on or recognise deterioration (23%), inpatient falls (10%), healthcare-associated infections (10%), unexpected per-operative death (6%), and poor or inadequate handover (5%). Analysis of these 2,010 fatal incidents reveals patterns of issues that point to actionable areas for improvement. Conclusions Our approach demonstrates the potential utility of patient safety incident reports in identifying areas of service failure and highlights opportunities for corrective action to save lives. Please see later in the article for the Editors' Summary PMID:24959751

  11. The Role of Inhibition in Age-related Off-Topic Verbosity: Not Access but Deletion and Restraint Functions.

    PubMed

    Yin, Shufei; Peng, Huamao

    2016-01-01

    The speech of older adults is commonly described as verbose and off-topic, which is thought to influence their social communication. This study investigated the role of inhibition in age-related off-topic verbosity (OTV). Inhibition consists of three functions: access, deletion, and restraint. The access function is responsible for preventing irrelevant information from accessing the attention center (pre-mechanism of inhibition); The deletion function is responsible for deleting previously relevant but currently irrelevant information from working memory, and the restraint function is responsible for restraining strong but inappropriate responses (post-mechanisms of inhibition). A referential communication task was used to determine whether OTV was influenced by the pre-mechanism of inhibition. A self-involved event interview task was used to investigate the effect of the post-mechanisms of inhibition on OTV. Results showed that the OTV of the elderly participants was associated with an age-related decline in the post-mechanisms of inhibition, while the OTV exhibited by young adults was most likely due to deficits in the pre-mechanism function of inhibition. This research contributed to fill gaps in the existing knowledge about the potential relationship between specific functions of inhibition and age-related OTV. PMID:27199793

  12. The Role of Inhibition in Age-related Off-Topic Verbosity: Not Access but Deletion and Restraint Functions

    PubMed Central

    Yin, Shufei; Peng, Huamao

    2016-01-01

    The speech of older adults is commonly described as verbose and off-topic, which is thought to influence their social communication. This study investigated the role of inhibition in age-related off-topic verbosity (OTV). Inhibition consists of three functions: access, deletion, and restraint. The access function is responsible for preventing irrelevant information from accessing the attention center (pre-mechanism of inhibition); The deletion function is responsible for deleting previously relevant but currently irrelevant information from working memory, and the restraint function is responsible for restraining strong but inappropriate responses (post-mechanisms of inhibition). A referential communication task was used to determine whether OTV was influenced by the pre-mechanism of inhibition. A self-involved event interview task was used to investigate the effect of the post-mechanisms of inhibition on OTV. Results showed that the OTV of the elderly participants was associated with an age-related decline in the post-mechanisms of inhibition, while the OTV exhibited by young adults was most likely due to deficits in the pre-mechanism function of inhibition. This research contributed to fill gaps in the existing knowledge about the potential relationship between specific functions of inhibition and age-related OTV. PMID:27199793

  13. Access and Quality of HIV-Related Point-of-Care Diagnostic Testing in Global Health Programs.

    PubMed

    Fonjungo, Peter N; Boeras, Debrah I; Zeh, Clement; Alexander, Heather; Parekh, Bharat S; Nkengasong, John N

    2016-02-01

    Access to point-of-care testing (POCT) improves patient care, especially in resource-limited settings where laboratory infrastructure is poor and the bulk of the population lives in rural settings. However, because of challenges in rolling out the technology and weak quality assurance measures, the promise of human immunodeficiency virus (HIV)-related POCT in resource-limited settings has not been fully exploited to improve patient care and impact public health. Because of these challenges, the Joint United Nations Programme on HIV/AIDS (UNAIDS), in partnership with other organizations, recently launched the Diagnostics Access Initiative. Expanding HIV programs, including the "test and treat" strategies and the newly established UNAIDS 90-90-90 targets, will require increased access to reliable and accurate POCT results. In this review, we examine various components that could improve access and uptake of quality-assured POC tests to ensure coverage and public health impact. These components include evaluation, policy, regulation, and innovative approaches to strengthen the quality of POCT. PMID:26423384

  14. Analogical Reasoning in 2-Year-Olds: The Development of Access and Relational Inference

    ERIC Educational Resources Information Center

    Singer-Freeman, K.E.

    2005-01-01

    Eighty-four 24- and 30-month-old children were tested with two analogy tasks: formal and problem solving. Experiment 1 included three Groups: relations specified, relations unspecified, and associative control (no exposure to base relations). In Experiment 2 the relation that linked that a- and b-terms in formal problems was explicitly shown in…

  15. The IMGT/HLA and IPD databases.

    PubMed

    Robinson, James; Waller, Matthew J; Fail, Sylvie C; Marsh, Steven G E

    2006-12-01

    The IMGT/HLA database (www.ebi.ac.uk/imgt/hla) has provided a centralized repository for the sequences of the alleles named by the WHO Nomenclature Committee for Factors of the HLA System since 1998. Since its initial release, the database has rapidly grown in size and is recognized as the primary source of information for the study of sequences of the human major histocompatibility complex. The Immuno Polymorphism Database (IPD; www.ebi.ac.uk/ipd) is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD currently consists of four databases: IPD-KIR contains the allelic sequences of killer-cell immunoglobulin-like receptors; IPD-MHC is a database of sequences of the major histocompatibility complex of different species; IPD-HPA contains alloantigens expressed only on platelets (human platelet antigens or HPA); and IPD-ESTDAB provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. PMID:16944494

  16. The Amma-Sat Database

    NASA Astrophysics Data System (ADS)

    Ramage, K.; Desbois, M.; Eymard, L.

    2004-12-01

    The African Monsoon Multidisciplinary Analysis project is a French initiative, which aims at identifying and analysing in details the multidisciplinary and multi-scales processes that lead to a better understanding of the physical mechanisms linked to the African Monsoon. The main components of the African Monsoon are: Atmospheric Dynamics, the Continental Water Cycle, Atmospheric Chemistry, Oceanic and Continental Surface Conditions. Satellites contribute to various objectives of the project both for process analysis and for large scale-long term studies: some series of satellites (METEOSAT, NOAA,.) have been flown for more than 20 years, ensuring a good quality monitoring of some of the West African atmosphere and surface characteristics. Moreover, several recent missions, and several projects will strongly improve and complement this survey. The AMMA project offers an opportunity to develop the exploitation of satellite data and to make collaboration between specialist and non-specialist users. In this purpose databases are being developed to collect all past and future satellite data related to the African Monsoon. It will then be possible to compare different types of data from different resolution, to validate satellite data with in situ measurements or numerical simulations. AMMA-SAT database main goal is to offer an easy access to satellite data to the AMMA scientific community. The database contains geophysical products estimated from operational or research algorithms and covering the different components of the AMMA project. Nevertheless, the choice has been made to group data within pertinent scales rather than within their thematic. In this purpose, five regions of interest where defined to extract the data: An area covering Tropical Atlantic and Africa for large scale studies, an area covering West Africa for mesoscale studies and three local areas surrounding sites of in situ observations. Within each of these regions satellite data are projected on

  17. PLANT-PIs: a database for plant protease inhibitors and their genes

    PubMed Central

    De Leo, F.; Volpicella, M.; Licciulli, F.; Liuni, S.; Gallerani, R.; Ceci, L. R.

    2002-01-01

    PLANT-PIs is a database developed to facilitate retrieval of information on plant protease inhibitors (PIs) and related genes. For each PI, links to sequence databases are reported together with a summary of the functional properties of the molecule (and its mutants) as deduced from literature. PLANT-PIs contains information for 351 plant PIs, plus several isoinhibitors. The database is accessible at http://bighost.area.ba.cnr.it/PLANT-PIs. PMID:11752333

  18. European Community Databases: Online to Europe.

    ERIC Educational Resources Information Center

    Hensley, Colin

    1989-01-01

    Describes three groups of databases sponsored by the European Communities Commission: Eurobases, a textual database of the contents of the "Official Journal" of the European Community; the European Community Host Organization (ECHO) databases, which offer multilingual information about Europe; and statistical databases. Information on access and…

  19. WMC Database Evaluation. Case Study Report

    SciTech Connect

    Palounek, Andrea P. T

    2015-10-29

    The WMC Database is ultimately envisioned to hold a collection of experimental data, design information, and information from computational models. This project was a first attempt at using the Database to access experimental data and extract information from it. This evaluation shows that the Database concept is sound and robust, and that the Database, once fully populated, should remain eminently usable for future researchers.

  20. Income Related Inequality of Health Care Access in Japan: A Retrospective Cohort Study

    PubMed Central

    Fujita, Misuzu; Hata, Akira

    2016-01-01

    The purpose of this retrospective cohort study was to analyze the association between income level and health care access in Japan. Data from a total of 222,259 subjects (age range, 0–74 years) who submitted National Health Insurance claims in Chiba City from April 2012 to March 2014 and who declared income for the tax period from January 1 to December 31, 2012 were integrated and analyzed. The generalized estimating equation, in which household was defined as a cluster, was used to evaluate the association between equivalent income and utilization and duration of hospitalization and outpatient care services. A significant positive linear association was observed between income level and outpatient visit rates among all age groups of both sexes; however, a significantly higher rate and longer period of hospitalization, and longer outpatient care, were observed among certain lower income subgroups. To control for decreased income due to hospitalization, subjects hospitalized during the previous year were excluded, and the data was then reanalyzed. Significant inverse associations remained in the hospitalization rate among 40–59-year-old men and 60–69-year-old women, and in duration of hospitalization among 40–59 and 60–69-year-olds of both sexes and 70–74-year-old women. These results suggest that low-income individuals in Japan have poorer access to outpatient care and more serious health conditions than their higher income counterparts. PMID:26978270

  1. 2DBase: 2D-PAGE database of Escherichia coli.

    PubMed

    Vijayendran, Chandran; Burgemeister, Sebastian; Friehs, Karl; Niehaus, Karsten; Flaschel, Erwin

    2007-11-23

    We present a web-based integrated proteome database, termed 2DBase of Escherichia coli which was designed to store, compare, analyse, and retrieve various information obtained by 2D polyacrylamide gel electrophoresis and mass spectrometry. The main objectives of this database are (1) to provide the features for query and data-mining applications to access the stored proteomics data (2) to efficiently compare the specific protein spots present in the comparable proteome maps and (3) to analyse the data with the integrated classification for cellular functions of gene products of E. coli. This database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins were identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analyzed, and compared in a tabular format based on various functional categories enabling quick and subsequent analyses. Our database satisfies the requirement to be a federated 2-DE database by accomplishing various tasks through a web interface providing access to a relational database system. The 2DBase of E. coli database can be accessed at http://2dbase.techfak.uni-bielefeld.de/. PMID:17904107

  2. National Geochronological Database

    USGS Publications Warehouse

    Revised by Sloan, Jan; Henry, Christopher D.; Hopkins, Melanie; Ludington, Steve; Original database by Zartman, Robert E.; Bush, Charles A.; Abston, Carl

    2003-01-01

    The National Geochronological Data Base (NGDB) was established by the United States Geological Survey (USGS) to collect and organize published isotopic (also known as radiometric) ages of rocks in the United States. The NGDB (originally known as the Radioactive Age Data Base, RADB) was started in 1974. A committee appointed by the Director of the USGS was given the mission to investigate the feasibility of compiling the published radiometric ages for the United States into a computerized data bank for ready access by the user community. A successful pilot program, which was conducted in 1975 and 1976 for the State of Wyoming, led to a decision to proceed with the compilation of the entire United States. For each dated rock sample reported in published literature, a record containing information on sample location, rock description, analytical data, age, interpretation, and literature citation was constructed and included in the NGDB. The NGDB was originally constructed and maintained on a mainframe computer, and later converted to a Helix Express relational database maintained on an Apple Macintosh desktop computer. The NGDB and a program to search the data files were published and distributed on Compact Disc-Read Only Memory (CD-ROM) in standard ISO 9660 format as USGS Digital Data Series DDS-14 (Zartman and others, 1995). As of May 1994, the NGDB consisted of more than 18,000 records containing over 30,000 individual ages, which is believed to represent approximately one-half the number of ages published for the United States through 1991. Because the organizational unit responsible for maintaining the database was abolished in 1996, and because we wanted to provide the data in more usable formats, we have reformatted the data, checked and edited the information in some records, and provided this online version of the NGDB. This report describes the changes made to the data and formats, and provides instructions for the use of the database in geographic

  3. Quantum search of a real unstructured database

    NASA Astrophysics Data System (ADS)

    Broda, Bogusław

    2016-02-01

    A simple circuit implementation of the oracle for Grover's quantum search of a real unstructured classical database is proposed. The oracle contains a kind of quantumly accessible classical memory, which stores the database.

  4. Effect of Relation Availability on the Interpretation and Access of Familiar Noun-Noun Compounds

    ERIC Educational Resources Information Center

    Gagne, Christina L.; Spalding, Thomas L.

    2004-01-01

    Two experiments investigate whether relations that link the constituents of compounds during compound formation (e.g., "teapot" is formed by combining "tea" and "pot" using the relation "head noun FOR modifier") also influence the processing of familiar compounds. Although there is evidence for the use of such relations in forming compounds,…

  5. BioImaging Database

    2006-10-25

    The Biolmaging Database (BID) is a relational database developed to store the data and meta-data for the 3D gene expression in early Drosophila embryo development on a cellular level. The schema was written to be used with the MySQL DBMS but with minor modifications can be used on any SQL compliant relational DBMS.

  6. Karst database development in Minnesota: Design and data assembly

    USGS Publications Warehouse

    Gao, Y.; Alexander, E.C., Jr.; Tipping, R.G.

    2005-01-01

    The Karst Feature Database (KFD) of Minnesota is a relational GIS-based Database Management System (DBMS). Previous karst feature datasets used inconsistent attributes to describe karst features in different areas of Minnesota. Existing metadata were modified and standardized to represent a comprehensive metadata for all the karst features in Minnesota. Microsoft Access 2000 and ArcView 3.2 were used to develop this working database. Existing county and sub-county karst feature datasets have been assembled into the KFD, which is capable of visualizing and analyzing the entire data set. By November 17 2002, 11,682 karst features were stored in the KFD of Minnesota. Data tables are stored in a Microsoft Access 2000 DBMS and linked to corresponding ArcView applications. The current KFD of Minnesota has been moved from a Windows NT server to a Windows 2000 Citrix server accessible to researchers and planners through networked interfaces. ?? Springer-Verlag 2005.

  7. An integrated database to support research on Escherichia coli

    SciTech Connect

    Baehr, A.; Dunham, G.; Matsuda, Hideo; Michaels, G.; Taylor, R.; Overbeek, R.; Rudd, K.E. ); Ginsburg, A.; Joerg, D.; Kazic, T. . Dept. of Genetics); Hagstrom, R.; Zawada, D. ); Smith, C.; Yoshida, Kaoru )

    1992-01-01

    We have used logic programming to design and implement a prototype database of genomic information for the model bacterial organism Escherichia coli. This report presents the fundamental database primitives that can be used to access and manipulate data relating to the E. coli genome. The present system, combined with a tutorial manual, provides immediate access to the integrated knowledge base for E. coli chromosome data. It also serves as the foundation for development of more user-friendly interfaces that have the same retrieval power and high-level tools to analyze complex chromosome organization.

  8. Scale out databases for CERN use cases

    NASA Astrophysics Data System (ADS)

    Baranowski, Zbigniew; Grzybek, Maciej; Canali, Luca; Lanza Garcia, Daniel; Surdy, Kacper

    2015-12-01

    Data generation rates are expected to grow very fast for some database workloads going into LHC run 2 and beyond. In particular this is expected for data coming from controls, logging and monitoring systems. Storing, administering and accessing big data sets in a relational database system can quickly become a very hard technical challenge, as the size of the active data set and the number of concurrent users increase. Scale-out database technologies are a rapidly developing set of solutions for deploying and managing very large data warehouses on commodity hardware and with open source software. In this paper we will describe the architecture and tests on database systems based on Hadoop and the Cloudera Impala engine. We will discuss the results of our tests, including tests of data loading and integration with existing data sources and in particular with relational databases. We will report on query performance tests done with various data sets of interest at CERN, notably data from the accelerator log database.

  9. IPD—the Immuno Polymorphism Database

    PubMed Central

    Robinson, James; Halliwell, Jason A.; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G. E.

    2013-01-01

    The Immuno Polymorphism Database (IPD), http://www.ebi.ac.uk/ipd/ is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project. PMID:23180793

  10. IPD--the Immuno Polymorphism Database.

    PubMed

    Robinson, James; Halliwell, Jason A; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G E

    2013-01-01

    The Immuno Polymorphism Database (IPD), http://www.ebi.ac.uk/ipd/ is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project. PMID:23180793

  11. Automated storage of gas chromatography-mass spectrometry data in a relational database to facilitate compound screening and identification.

    PubMed

    Staeb, J A; Epema, O J; van Duijn, P; Steevens, J; Klap, V A; Freriks, I L

    2002-10-18

    This paper describes a database containing massspectra from gas chromatography-mass spectrometry(GC-MS) measurements as a tool for easy screening for multiple compounds. In this way additional compounds can be reported from the same run together with routine pesticide monitoring with little effort. The relevant analytical data from the GC-MS measurements are transferred automatically to a database. Search algorithms in the database, containing the US EPA and Dutch NEN GC-MS identification criteria as standard settings, are used to identify compounds in the data. Screening of samples analysed in our laboratory show the ubiquitous presence of--up until now in monitoring largely overlooked--compounds in surface waters in The Netherlands. Most frequently found compounds include TAED (complexing agent), 2-methyl quinoline (industrial solvent), atrazin and desethylatrazin (pesticide and degradation product), caffeine (human consumption), surfinol-104 (anti foaming agent), HHCB (Galaxolide) and AHTN (Tonalide; fragrances). The database can also be used to quickly search a large number of datafiles for rare contaminants. This way, some interesting compounds such as pentoxifilin (a pharmaceutical) and Irgarol 1051 (an antifouling compound) were found. PMID:12458939

  12. CONSTRUCTION OF A REGIONAL RELATIONAL/GIS DATABASE IN SUPPORT OF OCEAN DISPOSAL ISSUES IN MASSACHUSETTS BAY

    EPA Science Inventory

    All geographic information system (GIS) databases rely on locational information and derive much of their power and utility from their ability to efficiently manipulate and place complex data in space and time. undamental constraint on these systems is the accuracy of the locatio...

  13. Non-Agricultural Databases and Thesauri: Retrieval of Subject Headings and Non-Controlled Terms in Relation to Agriculture

    ERIC Educational Resources Information Center

    Bartol, Tomaz

    2012-01-01

    Purpose: The paper aims to assess the utility of non-agriculture-specific information systems, databases, and respective controlled vocabularies (thesauri) in organising and retrieving agricultural information. The purpose is to identify thesaurus-linked tree structures, controlled subject headings/terms (heading words, descriptors), and principal…

  14. Triatomic Spectral Database

    National Institute of Standards and Technology Data Gateway

    SRD 117 Triatomic Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 55 triatomic molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty and reference are given for each transition reported.

  15. Hydrocarbon Spectral Database

    National Institute of Standards and Technology Data Gateway

    SRD 115 Hydrocarbon Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 91 hydrocarbon molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty and reference are given for each transition reported.

  16. Diatomic Spectral Database

    National Institute of Standards and Technology Data Gateway

    SRD 114 Diatomic Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 121 diatomic molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty, and reference are given for each transition reported.

  17. WETLANDS TREATMENT DATABASE

    EPA Science Inventory

    The U.S. EPA sponsored a project to collect and catalog information from wastewater treatment wetlands into a computer database. PA has also written a user friendly, stand-alone, menu-driven computer program to allow anyone with DOS 3.3 or higher to access the information in the ...

  18. The Gaia Parameter Database

    NASA Astrophysics Data System (ADS)

    de Bruijne, J. H. J.; Lammers, U.; Perryman, M. A. C.

    2005-01-01

    The parallel development of many aspects of a complex mission like Gaia, which includes numerous participants in ESA, industrial companies, and a large and active scientific collaboration throughout Europe, makes keeping track of the many design changes, instrument and operational complexities, and numerical values for the data analysis a very challenging problem. A comprehensive, easily-accessible, up-to-date, and definitive compilation of a large range of numerical quantities is required, and the Gaia parameter database has been established to satisfy these needs. The database is a centralised repository containing, besides mathematical, physical, and astronomical constants, many satellite and subsystem design parameters. At the end of 2004, more than 1600 parameters had been included. Version control has been implemented, providing, next to a `live' version with the most recent parameters, well-defined reference versions of the full database contents. The database can be queried or browsed using a regular Web browser (http://www.rssd.esa.int/Gaia/paramdb). Query results are formated by default in HTML. Data can also be retrieved as Fortran-77, Fortran-90, Java, ANSIC, C++, or XML structures for direct inclusion into software codes in these languages. The idea is that all collaborating scientists can use the database parameters and values, once retrieved, directly linked to computational routines. An off-line access mode is also available, enabling users to automatically download the contents of the database. The database will be maintained actively, and significant extensions of the contents are planned. Consistent use in the future of the database by the Gaia community at large, including all industrial teams, will ensure correct numerical values throughout the complex software systems being built up as details of the Gaia design develop. The database is already being used for the telemetry simulation chain in ESTEC, and in the data simulations for GDAAS2.

  19. National Ambient Radiation Database

    SciTech Connect

    Dziuban, J.; Sears, R.

    2003-02-25

    The U.S. Environmental Protection Agency (EPA) recently developed a searchable database and website for the Environmental Radiation Ambient Monitoring System (ERAMS) data. This site contains nationwide radiation monitoring data for air particulates, precipitation, drinking water, surface water and pasteurized milk. This site provides location-specific as well as national information on environmental radioactivity across several media. It provides high quality data for assessing public exposure and environmental impacts resulting from nuclear emergencies and provides baseline data during routine conditions. The database and website are accessible at www.epa.gov/enviro/. This site contains (1) a query for the general public which is easy to use--limits the amount of information provided, but includes the ability to graph the data with risk benchmarks and (2) a query for a more technical user which allows access to all of the data in the database, (3) background information on ER AMS.

  20. Crude Oil Analysis Database

    DOE Data Explorer

    Shay, Johanna Y.

    The composition and physical properties of crude oil vary widely from one reservoir to another within an oil field, as well as from one field or region to another. Although all oils consist of hydrocarbons and their derivatives, the proportions of various types of compounds differ greatly. This makes some oils more suitable than others for specific refining processes and uses. To take advantage of this diversity, one needs access to information in a large database of crude oil analyses. The Crude Oil Analysis Database (COADB) currently satisfies this need by offering 9,056 crude oil analyses. Of these, 8,500 are United States domestic oils. The database contains results of analysis of the general properties and chemical composition, as well as the field, formation, and geographic location of the crude oil sample. [Taken from the Introduction to COAMDATA_DESC.pdf, part of the zipped software and database file at http://www.netl.doe.gov/technologies/oil-gas/Software/database.html] Save the zipped file to your PC. When opened, it will contain PDF documents and a large Excel spreadsheet. It will also contain the database in Microsoft Access 2002.

  1. A Scalable Database Infrastructure

    NASA Astrophysics Data System (ADS)

    Arko, R. A.; Chayes, D. N.

    2001-12-01

    The rapidly increasing volume and complexity of MG&G data, and the growing demand from funding agencies and the user community that it be easily accessible, demand that we improve our approach to data management in order to reach a broader user-base and operate more efficient and effectively. We have chosen an approach based on industry-standard relational database management systems (RDBMS) that use community-wide data specifications, where there is a clear and well-documented external interface that allows use of general purpose as well as customized clients. Rapid prototypes assembled with this approach show significant advantages over the traditional, custom-built data management systems that often use "in-house" legacy file formats, data specifications, and access tools. We have developed an effective database prototype based a public domain RDBMS (PostgreSQL) and metadata standard (FGDC), and used it as a template for several ongoing MG&G database management projects - including ADGRAV (Antarctic Digital Gravity Synthesis), MARGINS, the Community Review system of the Digital Library for Earth Science Education, multibeam swath bathymetry metadata, and the R/V Maurice Ewing onboard acquisition system. By using standard formats and specifications, and working from a common prototype, we are able to reuse code and deploy rapidly. Rather than spend time on low-level details such as storage and indexing (which are built into the RDBMS), we can focus on high-level details such as documentation and quality control. In addition, because many commercial off-the-shelf (COTS) and public domain data browsers and visualization tools have built-in RDBMS support, we can focus on backend development and leave the choice of a frontend client(s) up to the end user. While our prototype is running under an open source RDBMS on a single processor host, the choice of standard components allows this implementation to scale to commercial RDBMS products and multiprocessor servers as

  2. The summary database system for the RFX reversed field pinch experiment

    SciTech Connect

    Innocente, P. ); Klare, K. )

    1995-01-01

    The RFX Summary Database System contains the most important experimental data, and provides tools to collect and insert the data and to interactively study their dependence. It was developed to allow a fast search for shots with given characteristics for follow-up, detailed shot analysis, and study of the scaling laws of the RFX plasmas. The database uses the Rdb/VMS relational database and is accessed using Structured Query Language syntax. A program automatically inserts the most important data for each shot while the users can access the database with their own programs using high-level routines. An Interactive Data Language interface to the database allows the users to interactively insert and extract data from the database, combine, or modify the data as they want, plot and fit the extracted or computed data, and perform general multiple regression analysis.

  3. Database Administrator

    ERIC Educational Resources Information Center

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  4. THE NATIONAL EXPOSURE RESEARCH LABORATORY'S CONSOLIDATED HUMAN ACTIVITY DATABASE

    EPA Science Inventory

    EPA's National Exposure Research Laboratory (NERL) has combined data from 12 U.S. studies related to human activities into one comprehensive data system that can be accessed via the Internet. The data system is called the Consolidated Human Activity Database (CHAD), and it is ...

  5. THE NATIONAL EXPOSURE RESEARCH LABORATORY'S COMPREHENSIVE HUMAN ACTIVITY DATABASE

    EPA Science Inventory

    EPA's National Exposure Research Laboratory (NERL) has combined data from nine U.S. studies related to human activities into one comprehensive data system that can be accessed via the world-wide web. The data system is called CHAD-Consolidated Human Activity Database-and it is ...

  6. The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content.

    PubMed

    Bakker, Rembrandt; Tiesinga, Paul; Kötter, Rolf

    2015-07-01

    The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of brain atlas templates for different species. Its main component is an atlas viewer that displays brain atlas data as a stack of slices in which stereotaxic coordinates and brain regions can be selected. These are subsequently used to launch web queries to resources that require coordinates or region names as input. It supports plugins which run inside the viewer and respond when a new slice, coordinate or region is selected. It contains 20 atlas templates in six species, and plugins to compute coordinate transformations, display anatomical connectivity and fiducial points, and retrieve properties, descriptions, definitions and 3d reconstructions of brain regions. The ambition of SBA is to provide a unified representation of all publicly available brain atlases directly in the web browser, while remaining a responsive and light weight resource that specializes in atlas comparisons, searches, coordinate transformations and interactive displays. PMID:25682754

  7. Discourse accessibility constraints in children’s processing of object relative clauses

    PubMed Central

    Haendler, Yair; Kliegl, Reinhold; Adani, Flavia

    2015-01-01

    Children’s poor performance on object relative clauses has been explained in terms of intervention locality. This approach predicts that object relatives with a full DP head and an embedded pronominal subject are easier than object relatives in which both the head noun and the embedded subject are full DPs. This prediction is shared by other accounts formulated to explain processing mechanisms. We conducted a visual-world study designed to test the off-line comprehension and on-line processing of object relatives in German-speaking 5-year-olds. Children were tested on three types of object relatives, all having a full DP head noun and differing with respect to the type of nominal phrase that appeared in the embedded subject position: another full DP, a 1st- or a 3rd-person pronoun. Grammatical skills and memory capacity were also assessed in order to see whether and how they affect children’s performance. Most accurately processed were object relatives with 1st-person pronoun, independently of children’s language and memory skills. Performance on object relatives with two full DPs was overall more accurate than on object relatives with 3rd-person pronoun. In the former condition, children with stronger grammatical skills accurately processed the structure and their memory abilities determined how fast they were; in the latter condition, children only processed accurately the structure if they were strong both in their grammatical skills and in their memory capacity. The results are discussed in the light of accounts that predict different pronoun effects like the ones we find, which depend on the referential properties of the pronouns. We then discuss which role language and memory abilities might have in processing object relatives with various embedded nominal phrases. PMID:26157410

  8. Title: An Overview of NOAA's Climate Database Modernization Program (CDMP) whose goal is to make major climate and environmental databases available via the Internet thus increasing the access and utilization of this national resource

    NASA Astrophysics Data System (ADS)

    Ross, T. F.

    2004-12-01

    Instead of being kept in a dusty warehouse, NOAA records are becoming more available to researchers and the public for use in various studies and projects. Modernization efforts involve keying of observations; imaging of original records on paper, microform, or photographs; vectorizing of shoreline charts; converting analog records to a digital format and web hosting data on the WSSRD (Web, Search, Store, Retrieve, Display) system. The number of images on-line via the WSSRD system has grown from just one-half million in 2000 to currently over forty-three million. CDMP has over 40 separate NOAA tasks underway, in an effort to provide increased access to its vast archive of climate and environmental data. The scope and variety of these data recovery projects range from producing digital files of Franklin and Thomas Jefferson's weather and climate diaries, keying early 20th century ionospheric data, building climatologies of the near-earth space environment using satellite data, to digitizing Mechanical Bathythermograph Data measurements of water temperatures at various ocean depths. Many of the records being converted from an analog to digital format are the original records housed in various NOAA Offices and storage facilities. These and many other NOAA records are available only in their original manuscript form and have deteriorated over time. The CDMP program allows these records to be saved for current and future scientists and historians by imaging and keying the data. The images are indexed so they can be more easily located via the Internet. The CDMP program is an example of a successful government project working hand- in-hand with the private sector to recover valuable climate and environmental data. For more information, see the latest annual report at: ncdc.noaa.gov/ oa/climate/cdmp/files/annualreport2003.pdf

  9. Predicting fluctuations in widespread interest: memory decay and goal-related memory accessibility in internet search trends.

    PubMed

    Masicampo, E J; Ambady, Nalini

    2014-02-01

    Memory and interest respond in similar ways to people's shifting needs and motivations. We therefore tested whether memory and interest might produce similar, observable patterns in people's responses over time. Specifically, the present studies examined whether fluctuations in widespread interest (as measured by Internet search trends) resemble two well-established memory patterns: memory decay and goal-related memory accessibility. We examined national and international events (e.g., Nobel Prize selections, holidays) that produced spikes in widespread interest in certain people and foods. When the events that triggered widespread interest were incidental (e.g., the death of a celebrity), widespread interest conformed to memory decay patterns: It rose quickly, fell slowly according to a power function, and was higher after the event than before it. When the events that triggered widespread interest were goal related (e.g., political elections), widespread interest conformed to patterns of goal-related memory accessibility: It rose slowly, fell quickly according to a sigmoid function, and was lower after the event than before it. Fluctuations in widespread interest over time are thus similar to standard memory patterns observed at the individual level due perhaps to common mechanisms and functions. PMID:23127417

  10. PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes.

    PubMed

    R Lorenzetti, Alan P; A de Antonio, Gabriel Y; Paschoal, Alexandre R; Domingues, Douglas S

    2016-05-01

    Transposable elements (TEs) comprise a major fraction of many plant genomes and are known to drive their organization and evolution. Several studies show that these repetitive elements have a prominent role in shaping noncoding regions of the genome such as microRNA (miRNA) loci, which are components of post-transcriptional regulation mechanisms. Although some studies have reported initial formation of miRNA loci from TE sequences, especially in model plants, the approaches that were used did not employ systems that would allow results to be delivered by a user-friendly database. In this study, we identified 152 precursor miRNAs overlapping TEs in 10 plant species. PlanTE-MIR DB was designed to assemble this data and deliver it to the scientific community interested in miRNA origin, evolution, and regulation pathways. Users can browse the database through a web interface and search for entries using various parameters. This resource is cross-referenced with repetitive element (Repbase Update) and miRNA (miRBase) repositories, where sequences can be checked for further analysis. All data in PlanTE-MIR DB are publicly available for download in several file formats to facilitate their understanding and use. The database is hosted at http://bioinfo-tool.cp.utfpr.edu.br/plantemirdb/ . PMID:26887375

  11. View discovery in OLAP databases through statistical combinatorial optimization

    SciTech Connect

    Hengartner, Nick W; Burke, John; Critchlow, Terence; Joslyn, Cliff; Hogan, Emilie

    2009-01-01

    OnLine Analytical Processing (OLAP) is a relational database technology providing users with rapid access to summary, aggregated views of a single large database, and is widely recognized for knowledge representation and discovery in high-dimensional relational databases. OLAP technologies provide intuitive and graphical access to the massively complex set of possible summary views available in large relational (SQL) structured data repositories. The capability of OLAP database software systems to handle data complexity comes at a high price for analysts, presenting them a combinatorially vast space of views of a relational database. We respond to the need to deploy technologies sufficient to allow users to guide themselves to areas of local structure by casting the space of 'views' of an OLAP database as a combinatorial object of all projections and subsets, and 'view discovery' as an search process over that lattice. We equip the view lattice with statistical information theoretical measures sufficient to support a combinatorial optimization process. We outline 'hop-chaining' as a particular view discovery algorithm over this object, wherein users are guided across a permutation of the dimensions by searching for successive two-dimensional views, pushing seen dimensions into an increasingly large background filter in a 'spiraling' search process. We illustrate this work in the context of data cubes recording summary statistics for radiation portal monitors at US ports.

  12. XCOM: Photon Cross Sections Database

    National Institute of Standards and Technology Data Gateway

    SRD 8 XCOM: Photon Cross Sections Database (Web, free access)   A web database is provided which can be used to calculate photon cross sections for scattering, photoelectric absorption and pair production, as well as total attenuation coefficients, for any element, compound or mixture (Z <= 100) at energies from 1 keV to 100 GeV.

  13. Chemists, Access, Statistics

    NASA Astrophysics Data System (ADS)

    Holmes, Jon L.

    2000-06-01

    IP-number access. Current subscriptions can be upgraded to IP-number access at little additional cost. We are pleased to be able to offer to institutions and libraries this convenient mode of access to subscriber only resources at JCE Online. JCE Online Usage Statistics We are continually amazed by the activity at JCE Online. So far, the year 2000 has shown a marked increase. Given the phenomenal overall growth of the Internet, perhaps our surprise is not warranted. However, during the months of January and February 2000, over 38,000 visitors requested over 275,000 pages. This is a monthly increase of over 33% from the October-December 1999 levels. It is good to know that people are visiting, but we would very much like to know what you would most like to see at JCE Online. Please send your suggestions to JCEOnline@chem.wisc.edu. For those who are interested, JCE Online year-to-date statistics are available. Biographical Snapshots of Famous Chemists: Mission Statement Feature Editor: Barbara Burke Chemistry Department, California State Polytechnic University-Pomona, Pomona, CA 91768 phone: 909/869-3664 fax: 909/869-4616 email: baburke@csupomona.edu The primary goal of this JCE Internet column is to provide information about chemists who have made important contributions to chemistry. For each chemist, there is a short biographical "snapshot" that provides basic information about the person's chemical work, gender, ethnicity, and cultural background. Each snapshot includes links to related websites and to a biobibliographic database. The database provides references for the individual and can be searched through key words listed at the end of each snapshot. All students, not just science majors, need to understand science as it really is: an exciting, challenging, human, and creative way of learning about our natural world. Investigating the life experiences of chemists can provide a means for students to gain a more realistic view of chemistry. In addition students

  14. Chemical Kinetics Database

    National Institute of Standards and Technology Data Gateway

    SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.

  15. Nuclear Science References Database

    SciTech Connect

    Pritychenko, B.; Běták, E.; Singh, B.; Totans, J.

    2014-06-15

    The Nuclear Science References (NSR) database together with its associated Web interface, is the world's only comprehensive source of easily accessible low- and intermediate-energy nuclear physics bibliographic information for more than 210,000 articles since the beginning of nuclear science. The weekly-updated NSR database provides essential support for nuclear data evaluation, compilation and research activities. The principles of the database and Web application development and maintenance are described. Examples of nuclear structure, reaction and decay applications are specifically included. The complete NSR database is freely available at the websites of the National Nuclear Data Center (http://www.nndc.bnl.gov/nsr) and the International Atomic Energy Agency (http://www-nds.iaea.org/nsr)

  16. Database machines for large statistical databases. Final report, January 16, 1983-January 15, 1986

    SciTech Connect

    DeWitt, D.J.

    1986-01-01

    Research activities have been directed towards the design and implementation of a high performance database machine for accessing, manipulating, and analyzing very large statistical data sets. Topics of discussion include statistical databases, parallel algorithms and secondary storage methods, methodology for database system performance evaluation, implementation techniques for main memory database systems, intelligent buffer management systems, Gamma-a high performance dataflow database machine, and extensible database management systems. 1 fig. (DWL)

  17. The ChArMEx database

    NASA Astrophysics Data System (ADS)

    Ferré, Hélène; Belmahfoud, Nizar; Boichard, Jean-Luc; Brissebrat, Guillaume; Cloché, Sophie; Descloitres, Jacques; Fleury, Laurence; Focsa, Loredana; Henriot, Nicolas; Mière, Arnaud; Ramage, Karim; Vermeulen, Anne; Boulanger, Damien

    2015-04-01

    have been inserted in a relational database, in order to enable more accurate selection and download of different datasets in a shared format. Many dedicated satellite products (SEVIRI, TRIMM, PARASOL...) are processed and will soon be accessible through the database website. In order to meet the operational needs of the airborne and ground based observational teams during the ChArMEx campaigns, a day-to-day chart display website has been developed and operated: http://choc.sedoo.org. It offers a convenient way to browse weather conditions and chemical composition during the campaign periods. Every scientist is invited to visit the ChArMEx websites, to register and to request data. Feel free to contact charmex-database@sedoo.fr for any question.

  18. Space Station Freedom environmental database system (FEDS) for MSFC testing

    NASA Technical Reports Server (NTRS)

    Story, Gail S.; Williams, Wendy; Chiu, Charles

    1991-01-01

    The Water Recovery Test (WRT) at Marshall Space Flight Center (MSFC) is the first demonstration of integrated water recovery systems for potable and hygiene water reuse as envisioned for Space Station Freedom (SSF). In order to satisfy the safety and health requirements placed on the SSF program and facilitate test data assessment, an extensive laboratory analysis database was established to provide a central archive and data retrieval function. The database is required to store analysis results for physical, chemical, and microbial parameters measured from water, air and surface samples collected at various locations throughout the test facility. The Oracle Relational Database Management System (RDBMS) was utilized to implement a secured on-line information system with the ECLSS WRT program as the foundation for this system. The database is supported on a VAX/VMS 8810 series mainframe and is accessible from the Marshall Information Network System (MINS). This paper summarizes the database requirements, system design, interfaces, and future enhancements.

  19. Network Configuration of Oracle and Database Programming Using SQL

    NASA Technical Reports Server (NTRS)

    Davis, Melton; Abdurrashid, Jibril; Diaz, Philip; Harris, W. C.

    2000-01-01

    A database can be defined as a collection of information organized in such a way that it can be retrieved and used. A database management system (DBMS) can further be defined as the tool that enables us to manage and interact with the database. The Oracle 8 Server is a state-of-the-art information management environment. It is a repository for very large amounts of data, and gives users rapid access to that data. The Oracle 8 Server allows for sharing of data between applications; the information is stored in one place and used by many systems. My research will focus primarily on SQL (Structured Query Language) programming. SQL is the way you define and manipulate data in Oracle's relational database. SQL is the industry standard adopted by all database vendors. When programming with SQL, you work on sets of data (i.e., information is not processed one record at a time).

  20. Dynameomics: A comprehensive database of protein dynamics

    PubMed Central

    van der Kamp, Marc W.; Schaeffer, Richard D.; Jonsson, Amanda L.; Scouras, Alexander D.; Simms, Andrew; Toofanny, Rudesh D.; Benson, Noah C.; Anderson, Peter C.; Merkley, Eric D.; Rysavy, Steve; Bromley, Denny; Beck, David A. C.; Daggett, Valerie

    2010-01-01

    Summary The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 1000 proteins, representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through www.dynameomics.org. PMID:20399180