WorldWideScience

Sample records for integrate existing databases

  1. Extending Database Integration Technology

    National Research Council Canada - National Science Library

    Buneman, Peter

    1999-01-01

    Formal approaches to the semantics of databases and database languages can have immediate and practical consequences in extending database integration technologies to include a vastly greater range...

  2. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

    Science.gov (United States)

    Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

    2014-01-01

    Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

  3. DomeHaz, a Global Hazards Database: Understanding Cyclic Dome-forming Eruptions, Contributions to Hazard Assessments, and Potential for Future Use and Integration with Existing Cyberinfrastructure

    Science.gov (United States)

    Ogburn, S. E.; Calder, E.; Loughlin, S.

    2013-12-01

    cyclicity of dome growth and pauses, the difficulty in defining eruptions at cyclically active lava domes, the identification of patterns in eruptive frequency between volcanoes of differing composition, the relationship between extrusion rates and large explosions, and the timing of large explosions in relation to dome growth. Where possible, we link these global observations to conceptual and physical models of volcanic processes. We also investigate the production of decision trees from the database for hazard analysis. Continuation of this work will include the completion of a relational database, which will be continuously maintained and updated as part of the Global Volcano Model (GVM) project. We envision DomeHaz being linked to other databases such as the mass-flows database FlowDat, and the Smithsonian GVP catalog of eruptions. A key component in creating a robust cyberinfrastructure is high-quality and complete data sets provided by the community and compiled into databases, which ideally exist as part of an informational network. This paper serves as a call for participation from individuals, research groups, and monitoring bodies for generating a global database on the hazards associated with lava dome eruptions.

  4. A Database Integrity Pattern Language

    Directory of Open Access Journals (Sweden)

    Octavian Paul ROTARU

    2004-08-01

    Full Text Available Patterns and Pattern Languages are ways to capture experience and make it re-usable for others, and describe best practices and good designs. Patterns are solutions to recurrent problems.This paper addresses the database integrity problems from a pattern perspective. Even if the number of vendors of database management systems is quite high, the number of available solutions to integrity problems is limited. They all learned from the past experience applying the same solutions over and over again.The solutions to avoid integrity threats applied to in database management systems (DBMS can be formalized as a pattern language. Constraints, transactions, locks, etc, are recurrent integrity solutions to integrity threats and therefore they should be treated accordingly, as patterns.

  5. Optimal database locks for efficient integrity checking

    DEFF Research Database (Denmark)

    Martinenghi, Davide

    2004-01-01

    In concurrent database systems, correctness of update transactions refers to the equivalent effects of the execution schedule and some serial schedule over the same set of transactions. Integrity constraints add further semantic requirements to the correctness of the database states reached upon...... the execution of update transactions. Several methods for efficient integrity checking and enforcing exist. We show in this paper how to apply one such method to automatically extend update transactions with locks and simplified consistency tests on the locked entities. All schedules produced in this way...

  6. Integrating existing software toolkits into VO system

    Science.gov (United States)

    Cui, Chenzhou; Zhao, Yong-Heng; Wang, Xiaoqian; Sang, Jian; Luo, Ze

    2004-09-01

    Virtual Observatory (VO) is a collection of interoperating data archives and software tools. Taking advantages of the latest information technologies, it aims to provide a data-intensively online research environment for astronomers all around the world. A large number of high-qualified astronomical software packages and libraries are powerful and easy of use, and have been widely used by astronomers for many years. Integrating those toolkits into the VO system is a necessary and important task for the VO developers. VO architecture greatly depends on Grid and Web services, consequently the general VO integration route is "Java Ready - Grid Ready - VO Ready". In the paper, we discuss the importance of VO integration for existing toolkits and discuss the possible solutions. We introduce two efforts in the field from China-VO project, "gImageMagick" and "Galactic abundance gradients statistical research under grid environment". We also discuss what additional work should be done to convert Grid service to VO service.

  7. [A web-based integrated clinical database for laryngeal cancer].

    Science.gov (United States)

    E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu

    2014-08-01

    To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.

  8. On Simplification of Database Integrity Constraints

    DEFF Research Database (Denmark)

    Christiansen, Henning; Martinenghi, Davide

    2006-01-01

    Without proper simplification techniques, database integrity checking can be prohibitively time consuming. Several methods have been developed for producing simplified incremental checks for each update but none until now of sufficient quality and generality for providing a true practical impact,...

  9. Loopedia, a database for loop integrals

    Science.gov (United States)

    Bogner, C.; Borowka, S.; Hahn, T.; Heinrich, G.; Jones, S. P.; Kerner, M.; von Manteuffel, A.; Michel, M.; Panzer, E.; Papara, V.

    2018-04-01

    Loopedia is a new database at loopedia.org for information on Feynman integrals, intended to provide both bibliographic information as well as results made available by the community. Its bibliometry is complementary to that of INSPIRE or arXiv in the sense that it admits searching for integrals by graph-theoretical objects, e.g. its topology.

  10. SINBAD: Shielding integral benchmark archive and database

    International Nuclear Information System (INIS)

    Hunter, H.T.; Ingersoll, D.T.; Roussin, R.W.

    1996-01-01

    SINBAD is a new electronic database developed to store a variety of radiation shielding benchmark data so that users can easily retrieve and incorporate the data into their calculations. SINBAD is an excellent data source for users who require the quality assurance necessary in developing cross-section libraries or radiation transport codes. The future needs of the scientific community are best served by the electronic database format of SINBAD and its user-friendly interface, combined with its data accuracy and integrity

  11. Integrating Variances into an Analytical Database

    Science.gov (United States)

    Sanchez, Carlos

    2010-01-01

    For this project, I enrolled in numerous SATERN courses that taught the basics of database programming. These include: Basic Access 2007 Forms, Introduction to Database Systems, Overview of Database Design, and others. My main job was to create an analytical database that can handle many stored forms and make it easy to interpret and organize. Additionally, I helped improve an existing database and populate it with information. These databases were designed to be used with data from Safety Variances and DCR forms. The research consisted of analyzing the database and comparing the data to find out which entries were repeated the most. If an entry happened to be repeated several times in the database, that would mean that the rule or requirement targeted by that variance has been bypassed many times already and so the requirement may not really be needed, but rather should be changed to allow the variance's conditions permanently. This project did not only restrict itself to the design and development of the database system, but also worked on exporting the data from the database to a different format (e.g. Excel or Word) so it could be analyzed in a simpler fashion. Thanks to the change in format, the data was organized in a spreadsheet that made it possible to sort the data by categories or types and helped speed up searches. Once my work with the database was done, the records of variances could be arranged so that they were displayed in numerical order, or one could search for a specific document targeted by the variances and restrict the search to only include variances that modified a specific requirement. A great part that contributed to my learning was SATERN, NASA's resource for education. Thanks to the SATERN online courses I took over the summer, I was able to learn many new things about computers and databases and also go more in depth into topics I already knew about.

  12. Nuclear integrated database and design advancement system

    International Nuclear Information System (INIS)

    Ha, Jae Joo; Jeong, Kwang Sub; Kim, Seung Hwan; Choi, Sun Young.

    1997-01-01

    The objective of NuIDEAS is to computerize design processes through an integrated database by eliminating the current work style of delivering hardcopy documents and drawings. The major research contents of NuIDEAS are the advancement of design processes by computerization, the establishment of design database and 3 dimensional visualization of design data. KSNP (Korea Standard Nuclear Power Plant) is the target of legacy database and 3 dimensional model, so that can be utilized in the next plant design. In the first year, the blueprint of NuIDEAS is proposed, and its prototype is developed by applying the rapidly revolutionizing computer technology. The major results of the first year research were to establish the architecture of the integrated database ensuring data consistency, and to build design database of reactor coolant system and heavy components. Also various softwares were developed to search, share and utilize the data through networks, and the detailed 3 dimensional CAD models of nuclear fuel and heavy components were constructed, and walk-through simulation using the models are developed. This report contains the major additions and modifications to the object oriented database and associated program, using methods and Javascript.. (author). 36 refs., 1 tab., 32 figs

  13. Fast mapping rapidly integrates information into existing memory networks.

    Science.gov (United States)

    Coutanche, Marc N; Thompson-Schill, Sharon L

    2014-12-01

    Successful learning involves integrating new material into existing memory networks. A learning procedure known as fast mapping (FM), thought to simulate the word-learning environment of children, has recently been linked to distinct neuroanatomical substrates in adults. This idea has suggested the (never-before tested) hypothesis that FM may promote rapid incorporation into cortical memory networks. We test this hypothesis here in 2 experiments. In our 1st experiment, we introduced 50 participants to 16 unfamiliar animals and names through FM or explicit encoding (EE) and tested participants on the training day, and again after sleep. Learning through EE produced strong declarative memories, without immediate lexical competition, as expected from slow-consolidation models. Learning through FM, however, led to almost immediate lexical competition, which continued to the next day. Additionally, the learned words began to prime related concepts on the day following FM (but not EE) training. In a 2nd experiment, we replicated the lexical integration results and determined that presenting an already-known item during learning was crucial for rapid integration through FM. The findings presented here indicate that learned items can be integrated into cortical memory networks at an accelerated rate through fast mapping. The retrieval of a related known concept, in order to infer the target of the FM question, is critical for this effect. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  14. Distributed Access View Integrated Database (DAVID) system

    Science.gov (United States)

    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. Integrated spent nuclear fuel database system

    International Nuclear Information System (INIS)

    Henline, S.P.; Klingler, K.G.; Schierman, B.H.

    1994-01-01

    The Distributed Information Systems software Unit at the Idaho National Engineering Laboratory has designed and developed an Integrated Spent Nuclear Fuel Database System (ISNFDS), which maintains a computerized inventory of all US Department of Energy (DOE) spent nuclear fuel (SNF). Commercial SNF is not included in the ISNFDS unless it is owned or stored by DOE. The ISNFDS is an integrated, single data source containing accurate, traceable, and consistent data and provides extensive data for each fuel, extensive facility data for every facility, and numerous data reports and queries

  16. High-integrity databases for helicopter operations

    Science.gov (United States)

    Pschierer, Christian; Schiefele, Jens; Lüthy, Juerg

    2009-05-01

    Helicopter Emergency Medical Service missions (HEMS) impose a high workload on pilots due to short preparation time, operations in low level flight, and landings in unknown areas. The research project PILAS, a cooperation between Eurocopter, Diehl Avionics, DLR, EADS, Euro Telematik, ESG, Jeppesen, the Universities of Darmstadt and Munich, and funded by the German government, approached this problem by researching a pilot assistance system which supports the pilots during all phases of flight. The databases required for the specified helicopter missions include different types of topological and cultural data for graphical display on the SVS system, AMDB data for operations at airports and helipads, and navigation data for IFR segments. The most critical databases for the PILAS system however are highly accurate terrain and obstacle data. While RTCA DO-276 specifies high accuracies and integrities only for the areas around airports, HEMS helicopters typically operate outside of these controlled areas and thus require highly reliable terrain and obstacle data for their designated response areas. This data has been generated by a LIDAR scan of the specified test region. Obstacles have been extracted into a vector format. This paper includes a short overview of the complete PILAS system and then focus on the generation of the required high quality databases.

  17. SIRSALE: integrated video database management tools

    Science.gov (United States)

    Brunie, Lionel; Favory, Loic; Gelas, J. P.; Lefevre, Laurent; Mostefaoui, Ahmed; Nait-Abdesselam, F.

    2002-07-01

    Video databases became an active field of research during the last decade. The main objective in such systems is to provide users with capabilities to friendly search, access and playback distributed stored video data in the same way as they do for traditional distributed databases. Hence, such systems need to deal with hard issues : (a) video documents generate huge volumes of data and are time sensitive (streams must be delivered at a specific bitrate), (b) contents of video data are very hard to be automatically extracted and need to be humanly annotated. To cope with these issues, many approaches have been proposed in the literature including data models, query languages, video indexing etc. In this paper, we present SIRSALE : a set of video databases management tools that allow users to manipulate video documents and streams stored in large distributed repositories. All the proposed tools are based on generic models that can be customized for specific applications using ad-hoc adaptation modules. More precisely, SIRSALE allows users to : (a) browse video documents by structures (sequences, scenes, shots) and (b) query the video database content by using a graphical tool, adapted to the nature of the target video documents. This paper also presents an annotating interface which allows archivists to describe the content of video documents. All these tools are coupled to a video player integrating remote VCR functionalities and are based on active network technology. So, we present how dedicated active services allow an optimized video transport for video streams (with Tamanoir active nodes). We then describe experiments of using SIRSALE on an archive of news video and soccer matches. The system has been demonstrated to professionals with a positive feedback. Finally, we discuss open issues and present some perspectives.

  18. DENdb: database of integrated human enhancers

    KAUST Repository

    Ashoor, Haitham

    2015-09-05

    Enhancers are cis-acting DNA regulatory regions that play a key role in distal control of transcriptional activities. Identification of enhancers, coupled with a comprehensive functional analysis of their properties, could improve our understanding of complex gene transcription mechanisms and gene regulation processes in general. We developed DENdb, a centralized on-line repository of predicted enhancers derived from multiple human cell-lines. DENdb integrates enhancers predicted by five different methods generating an enriched catalogue of putative enhancers for each of the analysed cell-lines. DENdb provides information about the overlap of enhancers with DNase I hypersensitive regions, ChIP-seq regions of a number of transcription factors and transcription factor binding motifs, means to explore enhancer interactions with DNA using several chromatin interaction assays and enhancer neighbouring genes. DENdb is designed as a relational database that facilitates fast and efficient searching, browsing and visualization of information.

  19. DENdb: database of integrated human enhancers

    KAUST Repository

    Ashoor, Haitham; Kleftogiannis, Dimitrios A.; Radovanovic, Aleksandar; Bajic, Vladimir B.

    2015-01-01

    Enhancers are cis-acting DNA regulatory regions that play a key role in distal control of transcriptional activities. Identification of enhancers, coupled with a comprehensive functional analysis of their properties, could improve our understanding of complex gene transcription mechanisms and gene regulation processes in general. We developed DENdb, a centralized on-line repository of predicted enhancers derived from multiple human cell-lines. DENdb integrates enhancers predicted by five different methods generating an enriched catalogue of putative enhancers for each of the analysed cell-lines. DENdb provides information about the overlap of enhancers with DNase I hypersensitive regions, ChIP-seq regions of a number of transcription factors and transcription factor binding motifs, means to explore enhancer interactions with DNA using several chromatin interaction assays and enhancer neighbouring genes. DENdb is designed as a relational database that facilitates fast and efficient searching, browsing and visualization of information.

  20. Integrated Space Asset Management Database and Modeling

    Science.gov (United States)

    MacLeod, Todd; Gagliano, Larry; Percy, Thomas; Mason, Shane

    2015-01-01

    Effective Space Asset Management is one key to addressing the ever-growing issue of space congestion. It is imperative that agencies around the world have access to data regarding the numerous active assets and pieces of space junk currently tracked in orbit around the Earth. At the center of this issues is the effective management of data of many types related to orbiting objects. As the population of tracked objects grows, so too should the data management structure used to catalog technical specifications, orbital information, and metadata related to those populations. Marshall Space Flight Center's Space Asset Management Database (SAM-D) was implemented in order to effectively catalog a broad set of data related to known objects in space by ingesting information from a variety of database and processing that data into useful technical information. Using the universal NORAD number as a unique identifier, the SAM-D processes two-line element data into orbital characteristics and cross-references this technical data with metadata related to functional status, country of ownership, and application category. The SAM-D began as an Excel spreadsheet and was later upgraded to an Access database. While SAM-D performs its task very well, it is limited by its current platform and is not available outside of the local user base. Further, while modeling and simulation can be powerful tools to exploit the information contained in SAM-D, the current system does not allow proper integration options for combining the data with both legacy and new M&S tools. This paper provides a summary of SAM-D development efforts to date and outlines a proposed data management infrastructure that extends SAM-D to support the larger data sets to be generated. A service-oriented architecture model using an information sharing platform named SIMON will allow it to easily expand to incorporate new capabilities, including advanced analytics, M&S tools, fusion techniques and user interface for

  1. Database specification for the Worldwide Port System (WPS) Regional Integrated Cargo Database (ICDB)

    Energy Technology Data Exchange (ETDEWEB)

    Faby, E.Z.; Fluker, J.; Hancock, B.R.; Grubb, J.W.; Russell, D.L. [Univ. of Tennessee, Knoxville, TN (United States); Loftis, J.P.; Shipe, P.C.; Truett, L.F. [Oak Ridge National Lab., TN (United States)

    1994-03-01

    This Database Specification for the Worldwide Port System (WPS) Regional Integrated Cargo Database (ICDB) describes the database organization and storage allocation, provides the detailed data model of the logical and physical designs, and provides information for the construction of parts of the database such as tables, data elements, and associated dictionaries and diagrams.

  2. Non-existence criteria for Laurent polynomial first integrals

    Directory of Open Access Journals (Sweden)

    Shaoyun Shi

    2003-01-01

    Full Text Available In this paper we derived some simple criteria for non-existence and partial non-existence Laurent polynomial first integrals for a general nonlinear systems of ordinary differential equations $\\dot x = f(x$, $x \\in \\mathbb{R}^n$ with $f(0 = 0$. We show that if the eigenvalues of the Jacobi matrix of the vector field $f(x$ are $\\mathbb{Z}$-independent, then the system has no nontrivial Laurent polynomial integrals.

  3. An Integrated Molecular Database on Indian Insects.

    Science.gov (United States)

    Pratheepa, Maria; Venkatesan, Thiruvengadam; Gracy, Gandhi; Jalali, Sushil Kumar; Rangheswaran, Rajagopal; Antony, Jomin Cruz; Rai, Anil

    2018-01-01

    MOlecular Database on Indian Insects (MODII) is an online database linking several databases like Insect Pest Info, Insect Barcode Information System (IBIn), Insect Whole Genome sequence, Other Genomic Resources of National Bureau of Agricultural Insect Resources (NBAIR), Whole Genome sequencing of Honey bee viruses, Insecticide resistance gene database and Genomic tools. This database was developed with a holistic approach for collecting information about phenomic and genomic information of agriculturally important insects. This insect resource database is available online for free at http://cib.res.in. http://cib.res.in/.

  4. Ontology based heterogeneous materials database integration and semantic query

    Science.gov (United States)

    Zhao, Shuai; Qian, Quan

    2017-10-01

    Materials digital data, high throughput experiments and high throughput computations are regarded as three key pillars of materials genome initiatives. With the fast growth of materials data, the integration and sharing of data is very urgent, that has gradually become a hot topic of materials informatics. Due to the lack of semantic description, it is difficult to integrate data deeply in semantic level when adopting the conventional heterogeneous database integration approaches such as federal database or data warehouse. In this paper, a semantic integration method is proposed to create the semantic ontology by extracting the database schema semi-automatically. Other heterogeneous databases are integrated to the ontology by means of relational algebra and the rooted graph. Based on integrated ontology, semantic query can be done using SPARQL. During the experiments, two world famous First Principle Computational databases, OQMD and Materials Project are used as the integration targets, which show the availability and effectiveness of our method.

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

    International Nuclear Information System (INIS)

    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.

    2009-01-01

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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

  7. Evaluation of the integrity of existing NFS waste tanks

    International Nuclear Information System (INIS)

    1977-12-01

    Various means of investigating the integrity of the existing NFS waste tanks are presented, including: visual inspection, ultrasonic testing, acoustic-emission monitoring, radiography, and forced-vibration testing. The experience that exists in performing such investigations of high-level radioactive waste tanks is documented, including: visual inspections, photography, wall-thickness measurements, and forced-vibration testing. An evaluation is made on the relative merits of the presented inspection and testing alternatives

  8. Emission & Generation Resource Integrated Database (eGRID)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Emissions & Generation Resource Integrated Database (eGRID) is an integrated source of data on environmental characteristics of electric power generation....

  9. Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases.

    Science.gov (United States)

    Lysenko, Artem; Lysenko, Atem; Hindle, Matthew Morritt; Taubert, Jan; Saqi, Mansoor; Rawlings, Christopher John

    2009-11-01

    The development of a systems based approach to problems in plant sciences requires integration of existing information resources. However, the available information is currently often incomplete and dispersed across many sources and the syntactic and semantic heterogeneity of the data is a challenge for integration. In this article, we discuss strategies for data integration and we use a graph based integration method (Ondex) to illustrate some of these challenges with reference to two example problems concerning integration of (i) metabolic pathway and (ii) protein interaction data for Arabidopsis thaliana. We quantify the degree of overlap for three commonly used pathway and protein interaction information sources. For pathways, we find that the AraCyc database contains the widest coverage of enzyme reactions and for protein interactions we find that the IntAct database provides the largest unique contribution to the integrated dataset. For both examples, however, we observe a relatively small amount of data common to all three sources. Analysis and visual exploration of the integrated networks was used to identify a number of practical issues relating to the interpretation of these datasets. We demonstrate the utility of these approaches to the analysis of groups of coexpressed genes from an individual microarray experiment, in the context of pathway information and for the combination of coexpression data with an integrated protein interaction network.

  10. IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis.

    Science.gov (United States)

    Zhang, Fan; Drabier, Renee

    2012-01-01

    Next-Generation Sequencing (NGS) technologies and Genome-Wide Association Studies (GWAS) generate millions of reads and hundreds of datasets, and there is an urgent need for a better way to accurately interpret and distill such large amounts of data. Extensive pathway and network analysis allow for the discovery of highly significant pathways from a set of disease vs. healthy samples in the NGS and GWAS. Knowledge of activation of these processes will lead to elucidation of the complex biological pathways affected by drug treatment, to patient stratification studies of new and existing drug treatments, and to understanding the underlying anti-cancer drug effects. There are approximately 141 biological human pathway resources as of Jan 2012 according to the Pathguide database. However, most currently available resources do not contain disease, drug or organ specificity information such as disease-pathway, drug-pathway, and organ-pathway associations. Systematically integrating pathway, disease, drug and organ specificity together becomes increasingly crucial for understanding the interrelationships between signaling, metabolic and regulatory pathway, drug action, disease susceptibility, and organ specificity from high-throughput omics data (genomics, transcriptomics, proteomics and metabolomics). We designed the Integrated Pathway Analysis Database for Systematic Enrichment Analysis (IPAD, http://bioinfo.hsc.unt.edu/ipad), defining inter-association between pathway, disease, drug and organ specificity, based on six criteria: 1) comprehensive pathway coverage; 2) gene/protein to pathway/disease/drug/organ association; 3) inter-association between pathway, disease, drug, and organ; 4) multiple and quantitative measurement of enrichment and inter-association; 5) assessment of enrichment and inter-association analysis with the context of the existing biological knowledge and a "gold standard" constructed from reputable and reliable sources; and 6) cross-linking of

  11. Integrated Space Asset Management Database and Modeling

    Science.gov (United States)

    Gagliano, L.; MacLeod, T.; Mason, S.; Percy, T.; Prescott, J.

    The Space Asset Management Database (SAM-D) was implemented in order to effectively track known objects in space by ingesting information from a variety of databases and performing calculations to determine the expected position of the object at a specified time. While SAM-D performs this task very well, it is limited by technology and is not available outside of the local user base. Modeling and simulation can be powerful tools to exploit the information contained in SAM-D. However, the current system does not allow proper integration options for combining the data with both legacy and new M&S tools. A more capable data management infrastructure would extend SAM-D to support the larger data sets to be generated by the COI. A service-oriented architecture model will allow it to easily expand to incorporate new capabilities, including advanced analytics, M&S tools, fusion techniques and user interface for visualizations. Based on a web-centric approach, the entire COI will be able to access the data and related analytics. In addition, tight control of information sharing policy will increase confidence in the system, which would encourage industry partners to provide commercial data. SIMON is a Government off the Shelf information sharing platform in use throughout DoD and DHS information sharing and situation awareness communities. SIMON providing fine grained control to data owners allowing them to determine exactly how and when their data is shared. SIMON supports a micro-service approach to system development, meaning M&S and analytic services can be easily built or adapted. It is uniquely positioned to fill this need as an information-sharing platform with a proven track record of successful situational awareness system deployments. Combined with the integration of new and legacy M&S tools, a SIMON-based architecture will provide a robust SA environment for the NASA SA COI that can be extended and expanded indefinitely. First Results of Coherent Uplink from a

  12. Integrating pattern mining in relational databases

    NARCIS (Netherlands)

    Calders, T.; Goethals, B.; Prado, A.; Fürnkranz, J.; Scheffer, T.; Spiliopoulou, M.

    2006-01-01

    Almost a decade ago, Imielinski and Mannila introduced the notion of Inductive Databases to manage KDD applications just as DBMSs successfully manage business applications. The goal is to follow one of the key DBMS paradigms: building optimizing compilers for ad hoc queries. During the past decade,

  13. Integration of Biodiversity Databases in Taiwan and Linkage to Global Databases

    Directory of Open Access Journals (Sweden)

    Kwang-Tsao Shao

    2007-03-01

    Full Text Available The biodiversity databases in Taiwan were dispersed to various institutions and colleges with limited amount of data by 2001. The Natural Resources and Ecology GIS Database sponsored by the Council of Agriculture, which is part of the National Geographic Information System planned by the Ministry of Interior, was the most well established biodiversity database in Taiwan. But thisThis database was, however, mainly collectingcollected the distribution data of terrestrial animals and plants within the Taiwan area. In 2001, GBIF was formed, and Taiwan joined as one of the an Associate Participant and started, starting the establishment and integration of animal and plant species databases; therefore, TaiBIF was able to co-operate with GBIF. The information of Catalog of Life, specimens, and alien species were integrated by the Darwin core. The standard. These metadata standards allowed the biodiversity information of Taiwan to connect with global databases.

  14. Database Translator (DATALATOR) for Integrated Exploitation

    Science.gov (United States)

    2010-10-31

    via the Internet to Fortune 1000 clients including Mercedes Benz , Procter & Gamble, and HP. I look forward to hearing of your successful proposal and working with you to build a successful business. Sincerely, ...testing the DATALATOR experimental prototype (IRL 4) designed to demonstrate its core functions based on Next (icneration Software technology . Die...sources, but is not directly dependent on the platform such as database technology or data formats. In other words, there is a clear air gap between

  15. On the applicability of schema integration techniques to database interoperation

    NARCIS (Netherlands)

    Vermeer, Mark W.W.; Apers, Peter M.G.

    1996-01-01

    We discuss the applicability of schema integration techniques developed for tightly-coupled database interoperation to interoperation of databases stemming from different modelling contexts. We illustrate that in such an environment, it is typically quite difficult to infer the real-world semantics

  16. Integration of Oracle and Hadoop: Hybrid Databases Affordable at Scale

    Science.gov (United States)

    Canali, L.; Baranowski, Z.; Kothuri, P.

    2017-10-01

    This work reports on the activities aimed at integrating Oracle and Hadoop technologies for the use cases of CERN database services and in particular on the development of solutions for offloading data and queries from Oracle databases into Hadoop-based systems. The goal and interest of this investigation is to increase the scalability and optimize the cost/performance footprint for some of our largest Oracle databases. These concepts have been applied, among others, to build offline copies of CERN accelerator controls and logging databases. The tested solution allows to run reports on the controls data offloaded in Hadoop without affecting the critical production database, providing both performance benefits and cost reduction for the underlying infrastructure. Other use cases discussed include building hybrid database solutions with Oracle and Hadoop, offering the combined advantages of a mature relational database system with a scalable analytics engine.

  17. Integration of functions in logic database systems

    NARCIS (Netherlands)

    Lambrichts, E.; Nees, P.; Paredaens, J.; Peelman, P.; Tanca, L.

    1990-01-01

    We extend Datalog, a logic programming language for rule-based systems, by respectively integrating types, negation and functions. This extention of Datalog is called MilAnt. Furthermore, MilAnt consistency is defined as a stronger form of consistency for functions. It is known that consistency for

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

    Science.gov (United States)

    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. An Integrated Enterprise Accelerator Database for the SLC Control System

    International Nuclear Information System (INIS)

    2002-01-01

    Since its inception in the early 1980's, the SLC Control System has been driven by a highly structured memory-resident real-time database. While efficient, its rigid structure and file-based sources makes it difficult to maintain and extract relevant information. The goal of transforming the sources for this database into a relational form is to enable it to be part of a Control System Enterprise Database that is an integrated central repository for SLC accelerator device and Control System data with links to other associated databases. We have taken the concepts developed for the NLC Enterprise Database and used them to create and load a relational model of the online SLC Control System database. This database contains data and structure to allow querying and reporting on beamline devices, their associations and parameters. In the future this will be extended to allow generation of EPICS and SLC database files, setup of applications and links to other databases such as accelerator maintenance, archive data, financial and personnel records, cabling information, documentation etc. The database is implemented using Oracle 8i. In the short term it will be updated daily in batch from the online SLC database. In the longer term, it will serve as the primary source for Control System static data, an R and D platform for the NLC, and contribute to SLC Control System operations

  20. Construction of an integrated database to support genomic sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, W.; Overbeek, R.

    1994-11-01

    The central goal of this project is to develop an integrated database to support comparative analysis of genomes including DNA sequence data, protein sequence data, gene expression data and metabolism data. In developing the logic-based system GenoBase, a broader integration of available data was achieved due to assistance from collaborators. Current goals are to easily include new forms of data as they become available and to easily navigate through the ensemble of objects described within the database. This report comments on progress made in these areas.

  1. Document control system as an integral part of RA documentation database application

    International Nuclear Information System (INIS)

    Steljic, M.M; Ljubenov, V.Lj. . E-mail address of corresponding author: milijanas@vin.bg.ac.yu; Steljic, M.M.)

    2005-01-01

    The decision about the final shutdown of the RA research reactor in Vinca Institute has been brought in 2002, and therefore the preparations for its decommissioning have begun. All activities are supervised by the International Atomic Energy Agency (IAEA), which also provides technical and experts' support. This paper describes the document control system is an integral part of the existing RA documentation database. (author)

  2. A database of immunoglobulins with integrated tools: DIGIT.

    KAUST Repository

    Chailyan, Anna; Tramontano, Anna; Marcatili, Paolo

    2011-01-01

    The DIGIT (Database of ImmunoGlobulins with Integrated Tools) database (http://biocomputing.it/digit) is an integrated resource storing sequences of annotated immunoglobulin variable domains and enriched with tools for searching and analyzing them. The annotations in the database include information on the type of antigen, the respective germline sequences and on pairing information between light and heavy chains. Other annotations, such as the identification of the complementarity determining regions, assignment of their structural class and identification of mutations with respect to the germline, are computed on the fly and can also be obtained for user-submitted sequences. The system allows customized BLAST searches and automatic building of 3D models of the domains to be performed.

  3. A database of immunoglobulins with integrated tools: DIGIT.

    KAUST Repository

    Chailyan, Anna

    2011-11-10

    The DIGIT (Database of ImmunoGlobulins with Integrated Tools) database (http://biocomputing.it/digit) is an integrated resource storing sequences of annotated immunoglobulin variable domains and enriched with tools for searching and analyzing them. The annotations in the database include information on the type of antigen, the respective germline sequences and on pairing information between light and heavy chains. Other annotations, such as the identification of the complementarity determining regions, assignment of their structural class and identification of mutations with respect to the germline, are computed on the fly and can also be obtained for user-submitted sequences. The system allows customized BLAST searches and automatic building of 3D models of the domains to be performed.

  4. Integrated testing strategies for toxicity employing new and existing technologies.

    Science.gov (United States)

    Combes, Robert D; Balls, Michael

    2011-07-01

    We have developed individual, integrated testing strategies (ITS) for predicting the toxicity of general chemicals, cosmetics, pharmaceuticals, inhaled chemicals, and nanoparticles. These ITS are based on published schemes developed previously for the risk assessment of chemicals to fulfil the requirements of REACH, which have been updated to take account of the latest developments in advanced in chemico modelling and in vitro technologies. In addition, we propose an ITS for neurotoxicity, based on the same principles, for incorporation in the other ITS. The technologies are deployed in a step-wise manner, as a basis for decision-tree approaches, incorporating weight-of-evidence stages. This means that testing can be stopped at the point where a risk assessment and/or classification can be performed, with labelling in accordance with the requirements of the regulatory authority concerned, rather than following a checklist approach to hazard identification. In addition, the strategies are intelligent, in that they are based on the fundamental premise that there is no hazard in the absence of exposure - which is why pharmacokinetic modelling plays a key role in each ITS. The new technologies include the use of complex, three-dimensional human cell tissue culture systems with in vivo-like structural, physiological and biochemical features, as well as dosing conditions. In this way, problems of inter-species extrapolation and in vitro/in vivo extrapolation are minimised. This is reflected in the ITS placing more emphasis on the use of volunteers at the whole organism testing stage, rather than on existing animal testing, which is the current situation. 2011 FRAME.

  5. INE: a rice genome database with an integrated map view.

    Science.gov (United States)

    Sakata, K; Antonio, B A; Mukai, Y; Nagasaki, H; Sakai, Y; Makino, K; Sasaki, T

    2000-01-01

    The Rice Genome Research Program (RGP) launched a large-scale rice genome sequencing in 1998 aimed at decoding all genetic information in rice. A new genome database called INE (INtegrated rice genome Explorer) has been developed in order to integrate all the genomic information that has been accumulated so far and to correlate these data with the genome sequence. A web interface based on Java applet provides a rapid viewing capability in the database. The first operational version of the database has been completed which includes a genetic map, a physical map using YAC (Yeast Artificial Chromosome) clones and PAC (P1-derived Artificial Chromosome) contigs. These maps are displayed graphically so that the positional relationships among the mapped markers on each chromosome can be easily resolved. INE incorporates the sequences and annotations of the PAC contig. A site on low quality information ensures that all submitted sequence data comply with the standard for accuracy. As a repository of rice genome sequence, INE will also serve as a common database of all sequence data obtained by collaborating members of the International Rice Genome Sequencing Project (IRGSP). The database can be accessed at http://www. dna.affrc.go.jp:82/giot/INE. html or its mirror site at http://www.staff.or.jp/giot/INE.html

  6. Efficient Integrity Checking for Databases with Recursive Views

    DEFF Research Database (Denmark)

    Martinenghi, Davide; Christiansen, Henning

    2005-01-01

    Efficient and incremental maintenance of integrity constraints involving recursive views is a difficult issue that has received some attention in the past years, but for which no widely accepted solution exists yet. In this paper a technique is proposed for compiling such integrity constraints in...... approaches have not achieved comparable optimization with the same level of generality....

  7. Toward an interactive article: integrating journals and biological databases

    Directory of Open Access Journals (Sweden)

    Marygold Steven J

    2011-05-01

    Full Text Available Abstract Background Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. Results We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD and FlyBase, and has been implemented in marking up a paper with links to multiple databases. Conclusions Our semi-automated pipeline hyperlinks articles published in GENETICS to

  8. Database of episode-integrated solar energetic proton fluences

    Science.gov (United States)

    Robinson, Zachary D.; Adams, James H.; Xapsos, Michael A.; Stauffer, Craig A.

    2018-04-01

    A new database of proton episode-integrated fluences is described. This database contains data from two different instruments on multiple satellites. The data are from instruments on the Interplanetary Monitoring Platform-8 (IMP8) and the Geostationary Operational Environmental Satellites (GOES) series. A method to normalize one set of data to one another is presented to create a seamless database spanning 1973 to 2016. A discussion of some of the characteristics that episodes exhibit is presented, including episode duration and number of peaks. As an example of what can be understood about episodes, the July 4, 2012 episode is examined in detail. The coronal mass ejections and solar flares that caused many of the fluctuations of the proton flux seen at Earth are associated with peaks in the proton flux during this episode. The reasoning for each choice is laid out to provide a reference for how CME and solar flares associations are made.

  9. Database of episode-integrated solar energetic proton fluences

    Directory of Open Access Journals (Sweden)

    Robinson Zachary D.

    2018-01-01

    Full Text Available A new database of proton episode-integrated fluences is described. This database contains data from two different instruments on multiple satellites. The data are from instruments on the Interplanetary Monitoring Platform-8 (IMP8 and the Geostationary Operational Environmental Satellites (GOES series. A method to normalize one set of data to one another is presented to create a seamless database spanning 1973 to 2016. A discussion of some of the characteristics that episodes exhibit is presented, including episode duration and number of peaks. As an example of what can be understood about episodes, the July 4, 2012 episode is examined in detail. The coronal mass ejections and solar flares that caused many of the fluctuations of the proton flux seen at Earth are associated with peaks in the proton flux during this episode. The reasoning for each choice is laid out to provide a reference for how CME and solar flares associations are made.

  10. Heterogeneous Biomedical Database Integration Using a Hybrid Strategy: A p53 Cancer Research Database

    Directory of Open Access Journals (Sweden)

    Vadim Y. Bichutskiy

    2006-01-01

    Full Text Available Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.

  11. A Support Database System for Integrated System Health Management (ISHM)

    Science.gov (United States)

    Schmalzel, John; Figueroa, Jorge F.; Turowski, Mark; Morris, John

    2007-01-01

    The development, deployment, operation and maintenance of Integrated Systems Health Management (ISHM) applications require the storage and processing of tremendous amounts of low-level data. This data must be shared in a secure and cost-effective manner between developers, and processed within several heterogeneous architectures. Modern database technology allows this data to be organized efficiently, while ensuring the integrity and security of the data. The extensibility and interoperability of the current database technologies also allows for the creation of an associated support database system. A support database system provides additional capabilities by building applications on top of the database structure. These applications can then be used to support the various technologies in an ISHM architecture. This presentation and paper propose a detailed structure and application description for a support database system, called the Health Assessment Database System (HADS). The HADS provides a shared context for organizing and distributing data as well as a definition of the applications that provide the required data-driven support to ISHM. This approach provides another powerful tool for ISHM developers, while also enabling novel functionality. This functionality includes: automated firmware updating and deployment, algorithm development assistance and electronic datasheet generation. The architecture for the HADS has been developed as part of the ISHM toolset at Stennis Space Center for rocket engine testing. A detailed implementation has begun for the Methane Thruster Testbed Project (MTTP) in order to assist in developing health assessment and anomaly detection algorithms for ISHM. The structure of this implementation is shown in Figure 1. The database structure consists of three primary components: the system hierarchy model, the historical data archive and the firmware codebase. The system hierarchy model replicates the physical relationships between

  12. Integrated solid waste management: a palliative to existing waste ...

    African Journals Online (AJOL)

    As a concept, Integrated Solid Waste Management (ISWM) is a sustainable ... on the perspective of consumers on waste generation, collection and disposal. ... to effective solid waste management in the case study area; non-sorting and ...

  13. The Center for Integrated Molecular Brain Imaging (Cimbi) database

    DEFF Research Database (Denmark)

    Knudsen, Gitte M.; Jensen, Peter S.; Erritzoe, David

    2016-01-01

    We here describe a multimodality neuroimaging containing data from healthy volunteers and patients, acquired within the Lundbeck Foundation Center for Integrated Molecular Brain Imaging (Cimbi) in Copenhagen, Denmark. The data is of particular relevance for neurobiological research questions rela...... currently contains blood and in some instances saliva samples from about 500 healthy volunteers and 300 patients with e.g., major depression, dementia, substance abuse, obesity, and impulsive aggression. Data continue to be added to the Cimbi database and biobank....

  14. An information integration system for structured documents, Web, and databases

    OpenAIRE

    Morishima, Atsuyuki

    1998-01-01

    Rapid advance in computer network technology has changed the style of computer utilization. Distributed computing resources over world-wide computer networks are available from our local computers. They include powerful computers and a variety of information sources. This change is raising more advanced requirements. Integration of distributed information sources is one of such requirements. In addition to conventional databases, structured documents have been widely used, and have increasing...

  15. Distortion-Free Watermarking Approach for Relational Database Integrity Checking

    Directory of Open Access Journals (Sweden)

    Lancine Camara

    2014-01-01

    Full Text Available Nowadays, internet is becoming a suitable way of accessing the databases. Such data are exposed to various types of attack with the aim to confuse the ownership proofing or the content protection. In this paper, we propose a new approach based on fragile zero watermarking for the authentication of numeric relational data. Contrary to some previous databases watermarking techniques which cause some distortions in the original database and may not preserve the data usability constraints, our approach simply seeks to generate the watermark from the original database. First, the adopted method partitions the database relation into independent square matrix groups. Then, group-based watermarks are securely generated and registered in a trusted third party. The integrity verification is performed by computing the determinant and the diagonal’s minor for each group. As a result, tampering can be localized up to attribute group level. Theoretical and experimental results demonstrate that the proposed technique is resilient against tuples insertion, tuples deletion, and attributes values modification attacks. Furthermore, comparison with recent related effort shows that our scheme performs better in detecting multifaceted attacks.

  16. Integrity Checking and Maintenance with Active Rules in XML Databases

    DEFF Research Database (Denmark)

    Christiansen, Henning; Rekouts, Maria

    2007-01-01

    While specification languages for integrity constraints for XML data have been considered in the literature, actual technologies and methodologies for checking and maintaining integrity are still in their infancy. Triggers, or active rules, which are widely used in previous technologies for the p...... updates, the method indicates trigger conditions and correctness criteria to be met by the trigger code supplied by a developer or possibly automatic methods. We show examples developed in the Sedna XML database system which provides a running implementation of XML triggers....

  17. DPTEdb, an integrative database of transposable elements in dioecious plants.

    Science.gov (United States)

    Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gu, Lian-Feng; Gao, Wu-Jun

    2016-01-01

    Dioecious plants usually harbor 'young' sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants.Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php. © The Author(s) 2016. Published by Oxford University Press.

  18. Database modeling to integrate macrobenthos data in Spatial Data Infrastructure

    Directory of Open Access Journals (Sweden)

    José Alberto Quintanilha

    2012-08-01

    Full Text Available Coastal zones are complex areas that include marine and terrestrial environments. Besides its huge environmental wealth, they also attracts humans because provides food, recreation, business, and transportation, among others. Some difficulties to manage these areas are related with their complexity, diversity of interests and the absence of standardization to collect and share data to scientific community, public agencies, among others. The idea to organize, standardize and share this information based on Web Atlas is essential to support planning and decision making issues. The construction of a spatial database integrating the environmental business, to be used on Spatial Data Infrastructure (SDI is illustrated by a bioindicator that indicates the quality of the sediments. The models show the phases required to build Macrobenthos spatial database based on Santos Metropolitan Region as a reference. It is concluded that, when working with environmental data the structuring of knowledge in a conceptual model is essential for their subsequent integration into the SDI. During the modeling process it can be noticed that methodological issues related to the collection process may obstruct or prejudice the integration of data from different studies of the same area. The development of a database model, as presented in this study, can be used as a reference for further research with similar goals.

  19. Integrated database for rapid mass movements in Norway

    Directory of Open Access Journals (Sweden)

    C. Jaedicke

    2009-03-01

    Full Text Available Rapid gravitational slope mass movements include all kinds of short term relocation of geological material, snow or ice. Traditionally, information about such events is collected separately in different databases covering selected geographical regions and types of movement. In Norway the terrain is susceptible to all types of rapid gravitational slope mass movements ranging from single rocks hitting roads and houses to large snow avalanches and rock slides where entire mountainsides collapse into fjords creating flood waves and endangering large areas. In addition, quick clay slides occur in desalinated marine sediments in South Eastern and Mid Norway. For the authorities and inhabitants of endangered areas, the type of threat is of minor importance and mitigation measures have to consider several types of rapid mass movements simultaneously.

    An integrated national database for all types of rapid mass movements built around individual events has been established. Only three data entries are mandatory: time, location and type of movement. The remaining optional parameters enable recording of detailed information about the terrain, materials involved and damages caused. Pictures, movies and other documentation can be uploaded into the database. A web-based graphical user interface has been developed allowing new events to be entered, as well as editing and querying for all events. An integration of the database into a GIS system is currently under development.

    Datasets from various national sources like the road authorities and the Geological Survey of Norway were imported into the database. Today, the database contains 33 000 rapid mass movement events from the last five hundred years covering the entire country. A first analysis of the data shows that the most frequent type of recorded rapid mass movement is rock slides and snow avalanches followed by debris slides in third place. Most events are recorded in the steep fjord

  20. An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database

    Directory of Open Access Journals (Sweden)

    But Paul

    2010-06-01

    Full Text Available Abstract Background Thousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials for therapy and health maintenance. Efficacies of the application is critically dependent on the use of genuine materials. For time to time, life-threatening poisoning is found because toxic adulterant or substitute is administered. DNA barcoding provides a definitive means of authentication and for conducting molecular systematics studies. Owing to the reduced cost in DNA authentication, the volume of the DNA barcodes produced for medicinal materials is on the rise and necessitates the development of an integrated DNA database. Description We have developed an integrated DNA barcode multimedia information platform- Medicinal Materials DNA Barcode Database (MMDBD for data retrieval and similarity search. MMDBD contains over 1000 species of medicinal materials listed in the Chinese Pharmacopoeia and American Herbal Pharmacopoeia. MMDBD also contains useful information of the medicinal material, including resources, adulterant information, medical parts, photographs, primers used for obtaining the barcodes and key references. MMDBD can be accessed at http://www.cuhk.edu.hk/icm/mmdbd.htm. Conclusions This work provides a centralized medicinal materials DNA barcode database and bioinformatics tools for data storage, analysis and exchange for promoting the identification of medicinal materials. MMDBD has the largest collection of DNA barcodes of medicinal materials and is a useful resource for researchers in conservation, systematic study, forensic and herbal industry.

  1. KAIKObase: An integrated silkworm genome database and data mining tool

    Directory of Open Access Journals (Sweden)

    Nagaraju Javaregowda

    2009-10-01

    Full Text Available Abstract Background The silkworm, Bombyx mori, is one of the most economically important insects in many developing countries owing to its large-scale cultivation for silk production. With the development of genomic and biotechnological tools, B. mori has also become an important bioreactor for production of various recombinant proteins of biomedical interest. In 2004, two genome sequencing projects for B. mori were reported independently by Chinese and Japanese teams; however, the datasets were insufficient for building long genomic scaffolds which are essential for unambiguous annotation of the genome. Now, both the datasets have been merged and assembled through a joint collaboration between the two groups. Description Integration of the two data sets of silkworm whole-genome-shotgun sequencing by the Japanese and Chinese groups together with newly obtained fosmid- and BAC-end sequences produced the best continuity (~3.7 Mb in N50 scaffold size among the sequenced insect genomes and provided a high degree of nucleotide coverage (88% of all 28 chromosomes. In addition, a physical map of BAC contigs constructed by fingerprinting BAC clones and a SNP linkage map constructed using BAC-end sequences were available. In parallel, proteomic data from two-dimensional polyacrylamide gel electrophoresis in various tissues and developmental stages were compiled into a silkworm proteome database. Finally, a Bombyx trap database was constructed for documenting insertion positions and expression data of transposon insertion lines. Conclusion For efficient usage of genome information for functional studies, genomic sequences, physical and genetic map information and EST data were compiled into KAIKObase, an integrated silkworm genome database which consists of 4 map viewers, a gene viewer, and sequence, keyword and position search systems to display results and data at the level of nucleotide sequence, gene, scaffold and chromosome. Integration of the

  2. Distributional, differential and integral problems: Equivalence and existence results

    Czech Academy of Sciences Publication Activity Database

    Monteiro, Giselle Antunes; Satco, B. R.

    2017-01-01

    Roč. 2017, č. 7 (2017), s. 1-26 ISSN 1417-3875 Institutional support: RVO:67985840 Keywords : derivative with respect to functions * distribution * Kurzweil-Stieltjes integral Subject RIV: BA - General Mathematics OBOR OECD: Pure mathematics Impact factor: 0.926, year: 2016 http://www.math.u-szeged.hu/ejqtde/periodica.html?periodica=1¶mtipus_ertek= publication ¶m_ertek=4753

  3. Integration of curated databases to identify genotype-phenotype associations

    Directory of Open Access Journals (Sweden)

    Li Jianrong

    2006-10-01

    Full Text Available Abstract Background The ability to rapidly characterize an unknown microorganism is critical in both responding to infectious disease and biodefense. To do this, we need some way of anticipating an organism's phenotype based on the molecules encoded by its genome. However, the link between molecular composition (i.e. genotype and phenotype for microbes is not obvious. While there have been several studies that address this challenge, none have yet proposed a large-scale method integrating curated biological information. Here we utilize a systematic approach to discover genotype-phenotype associations that combines phenotypic information from a biomedical informatics database, GIDEON, with the molecular information contained in National Center for Biotechnology Information's Clusters of Orthologous Groups database (NCBI COGs. Results Integrating the information in the two databases, we are able to correlate the presence or absence of a given protein in a microbe with its phenotype as measured by certain morphological characteristics or survival in a particular growth media. With a 0.8 correlation score threshold, 66% of the associations found were confirmed by the literature and at a 0.9 correlation threshold, 86% were positively verified. Conclusion Our results suggest possible phenotypic manifestations for proteins biochemically associated with sugar metabolism and electron transport. Moreover, we believe our approach can be extended to linking pathogenic phenotypes with functionally related proteins.

  4. Deep Time Data Infrastructure: Integrating Our Current Geologic and Biologic Databases

    Science.gov (United States)

    Kolankowski, S. M.; Fox, P. A.; Ma, X.; Prabhu, A.

    2016-12-01

    As our knowledge of Earth's geologic and mineralogical history grows, we require more efficient methods of sharing immense amounts of data. Databases across numerous disciplines have been utilized to offer extensive information on very specific Epochs of Earth's history up to its current state, i.e. Fossil record, rock composition, proteins, etc. These databases could be a powerful force in identifying previously unseen correlations such as relationships between minerals and proteins. Creating a unifying site that provides a portal to these databases will aid in our ability as a collaborative scientific community to utilize our findings more effectively. The Deep-Time Data Infrastructure (DTDI) is currently being defined as part of a larger effort to accomplish this goal. DTDI will not be a new database, but an integration of existing resources. Current geologic and related databases were identified, documentation of their schema was established and will be presented as a stage by stage progression. Through conceptual modeling focused around variables from their combined records, we will determine the best way to integrate these databases using common factors. The Deep-Time Data Infrastructure will allow geoscientists to bridge gaps in data and further our understanding of our Earth's history.

  5. Integrated olfactory receptor and microarray gene expression databases

    Directory of Open Access Journals (Sweden)

    Crasto Chiquito J

    2007-06-01

    Full Text Available Abstract Background Gene expression patterns of olfactory receptors (ORs are an important component of the signal encoding mechanism in the olfactory system since they determine the interactions between odorant ligands and sensory neurons. We have developed the Olfactory Receptor Microarray Database (ORMD to house OR gene expression data. ORMD is integrated with the Olfactory Receptor Database (ORDB, which is a key repository of OR gene information. Both databases aim to aid experimental research related to olfaction. Description ORMD is a Web-accessible database that provides a secure data repository for OR microarray experiments. It contains both publicly available and private data; accessing the latter requires authenticated login. The ORMD is designed to allow users to not only deposit gene expression data but also manage their projects/experiments. For example, contributors can choose whether to make their datasets public. For each experiment, users can download the raw data files and view and export the gene expression data. For each OR gene being probed in a microarray experiment, a hyperlink to that gene in ORDB provides access to genomic and proteomic information related to the corresponding olfactory receptor. Individual ORs archived in ORDB are also linked to ORMD, allowing users access to the related microarray gene expression data. Conclusion ORMD serves as a data repository and project management system. It facilitates the study of microarray experiments of gene expression in the olfactory system. In conjunction with ORDB, ORMD integrates gene expression data with the genomic and functional data of ORs, and is thus a useful resource for both olfactory researchers and the public.

  6. Development of mobile platform integrated with existing electronic medical records.

    Science.gov (United States)

    Kim, YoungAh; Kim, Sung Soo; Kang, Simon; Kim, Kyungduk; Kim, Jun

    2014-07-01

    This paper describes a mobile Electronic Medical Record (EMR) platform designed to manage and utilize the existing EMR and mobile application with optimized resources. We structured the mEMR to reuse services of retrieval and storage in mobile app environments that have already proven to have no problem working with EMRs. A new mobile architecture-based mobile solution was developed in four steps: the construction of a server and its architecture; screen layout and storyboard making; screen user interface design and development; and a pilot test and step-by-step deployment. This mobile architecture consists of two parts, the server-side area and the client-side area. In the server-side area, it performs the roles of service management for EMR and documents and for information exchange. Furthermore, it performs menu allocation depending on user permission and automatic clinical document architecture document conversion. Currently, Severance Hospital operates an iOS-compatible mobile solution based on this mobile architecture and provides stable service without additional resources, dealing with dynamic changes of EMR templates. The proposed mobile solution should go hand in hand with the existing EMR system, and it can be a cost-effective solution if a quality EMR system is operated steadily with this solution. Thus, we expect this example to be shared with hospitals that currently plan to deploy mobile solutions.

  7. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Kempa Stefan

    2009-05-01

    Full Text Available Abstract Background The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. Conclusion ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

  8. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.

    Science.gov (United States)

    May, Patrick; Christian, Jan-Ole; Kempa, Stefan; Walther, Dirk

    2009-05-04

    The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

  9. Integrating New Technologies and Existing Tools to Promote Programming Learning

    Directory of Open Access Journals (Sweden)

    Álvaro Santos

    2010-04-01

    Full Text Available In recent years, many tools have been proposed to reduce programming learning difficulties felt by many students. Our group has contributed to this effort through the development of several tools, such as VIP, SICAS, OOP-Anim, SICAS-COL and H-SICAS. Even though we had some positive results, the utilization of these tools doesn’t seem to significantly reduce weaker student’s difficulties. These students need stronger support to motivate them to get engaged in learning activities, inside and outside classroom. Nowadays, many technologies are available to create contexts that may help to accomplish this goal. We consider that a promising path goes through the integration of solutions. In this paper we analyze the features, strengths and weaknesses of the tools developed by our group. Based on these considerations we present a new environment, integrating different types of pedagogical approaches, resources, tools and technologies for programming learning support. With this environment, currently under development, it will be possible to review contents and lessons, based on video and screen captures. The support for collaborative tasks is another key point to improve and stimulate different models of teamwork. The platform will also allow the creation of various alternative models (learning objects for the same subject, enabling personalized learning paths adapted to each student knowledge level, needs and preferential learning styles. The learning sequences will work as a study organizer, following a suitable taxonomy, according to student’s cognitive skills. Although the main goal of this environment is to support students with more difficulties, it will provide a set of resources supporting the learning of more advanced topics. Software engineering techniques and representations, object orientation and event programming are features that will be available in order to promote the learning progress of students.

  10. GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data.

    Science.gov (United States)

    Jung, Sook; Staton, Margaret; Lee, Taein; Blenda, Anna; Svancara, Randall; Abbott, Albert; Main, Dorrie

    2008-01-01

    The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the entire Rosaceae. Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable. Most of the published Rosaceae genetic maps can be viewed and compared through CMap, the comparative map viewer. The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information. ESTs, BACs, markers and traits can be queried by various categories and the search result sites are linked to the mapping visualization tools. GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org.

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

    Science.gov (United States)

    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.

  12. Existing data sources for clinical epidemiology: Aarhus University Clinical Trial Candidate Database, Denmark.

    Science.gov (United States)

    Nørrelund, Helene; Mazin, Wiktor; Pedersen, Lars

    2014-01-01

    Denmark is facing a reduction in clinical trial activity as the pharmaceutical industry has moved trials to low-cost emerging economies. Competitiveness in industry-sponsored clinical research depends on speed, quality, and cost. Because Denmark is widely recognized as a region that generates high quality data, an enhanced ability to attract future trials could be achieved if speed can be improved by taking advantage of the comprehensive national and regional registries. A "single point-of-entry" system has been established to support collaboration between hospitals and industry. When assisting industry in early-stage feasibility assessments, potential trial participants are identified by use of registries to shorten the clinical trial startup times. The Aarhus University Clinical Trial Candidate Database consists of encrypted data from the Danish National Registry of Patients allowing an immediate estimation of the number of patients with a specific discharge diagnosis in each hospital department or outpatient specialist clinic in the Central Denmark Region. The free access to health care, thorough monitoring of patients who are in contact with the health service, completeness of registration at the hospital level, and ability to link all databases are competitive advantages in an increasingly complex clinical trial environment.

  13. Integration of a clinical trial database with a PACS

    International Nuclear Information System (INIS)

    Van Herk, M

    2014-01-01

    Many clinical trials use Electronic Case Report Forms (ECRF), e.g., from OpenClinica. Trial data is augmented if DICOM scans, dose cubes, etc. from the Picture Archiving and Communication System (PACS) are included for data mining. Unfortunately, there is as yet no structured way to collect DICOM objects in trial databases. In this paper, we obtain a tight integration of ECRF and PACS using open source software. Methods: DICOM identifiers for selected images/series/studies are stored in associated ECRF events (e.g., baseline) as follows: 1) JavaScript added to OpenClinica communicates using HTML with a gateway server inside the hospitals firewall; 2) On this gateway, an open source DICOM server runs scripts to query and select the data, returning anonymized identifiers; 3) The scripts then collects, anonymizes, zips and transmits selected data to a central trial server; 4) Here data is stored in a DICOM archive which allows authorized ECRF users to view and download the anonymous images associated with each event. Results: All integration scripts are open source. The PACS administrator configures the anonymization script and decides to use the gateway in passive (receiving) mode or in an active mode going out to the PACS to gather data. Our ECRF centric approach supports automatic data mining by iterating over the cases in the ECRF database, providing the identifiers to load images and the clinical data to correlate with image analysis results. Conclusions: Using open source software and web technology, a tight integration has been achieved between PACS and ECRF.

  14. Distributed Database Semantic Integration of Wireless Sensor Network to Access the Environmental Monitoring System

    Directory of Open Access Journals (Sweden)

    Ubaidillah Umar

    2018-06-01

    Full Text Available A wireless sensor network (WSN works continuously to gather information from sensors that generate large volumes of data to be handled and processed by applications. Current efforts in sensor networks focus more on networking and development services for a variety of applications and less on processing and integrating data from heterogeneous sensors. There is an increased need for information to become shareable across different sensors, database platforms, and applications that are not easily implemented in traditional database systems. To solve the issue of these large amounts of data from different servers and database platforms (including sensor data, a semantic sensor web service platform is needed to enable a machine to extract meaningful information from the sensor’s raw data. This additionally helps to minimize and simplify data processing and to deduce new information from existing data. This paper implements a semantic web data platform (SWDP to manage the distribution of data sensors based on the semantic database system. SWDP uses sensors for temperature, humidity, carbon monoxide, carbon dioxide, luminosity, and noise. The system uses the Sesame semantic web database for data processing and a WSN to distribute, minimize, and simplify information processing. The sensor nodes are distributed in different places to collect sensor data. The SWDP generates context information in the form of a resource description framework. The experiment results demonstrate that the SWDP is more efficient than the traditional database system in terms of memory usage and processing time.

  15. Using ontology databases for scalable query answering, inconsistency detection, and data integration

    Science.gov (United States)

    Dou, Dejing

    2011-01-01

    An ontology database is a basic relational database management system that models an ontology plus its instances. To reason over the transitive closure of instances in the subsumption hierarchy, for example, an ontology database can either unfold views at query time or propagate assertions using triggers at load time. In this paper, we use existing benchmarks to evaluate our method—using triggers—and we demonstrate that by forward computing inferences, we not only improve query time, but the improvement appears to cost only more space (not time). However, we go on to show that the true penalties were simply opaque to the benchmark, i.e., the benchmark inadequately captures load-time costs. We have applied our methods to two case studies in biomedicine, using ontologies and data from genetics and neuroscience to illustrate two important applications: first, ontology databases answer ontology-based queries effectively; second, using triggers, ontology databases detect instance-based inconsistencies—something not possible using views. Finally, we demonstrate how to extend our methods to perform data integration across multiple, distributed ontology databases. PMID:22163378

  16. Integrating the DLD dosimetry system into the Almaraz NPP Corporative Database

    International Nuclear Information System (INIS)

    Gonzalez Crego, E.; Martin Lopez-Suevos, C.

    1996-01-01

    The article discusses the experience acquired during the integration of a new MGP Instruments DLD Dosimetry System into the Almaraz NPP corporative database and general communications network, following a client-server philosophy and taking into account the computer standards of the Plant. The most important results obtained are: Integration of DLD dosimetry information into corporative databases, permitting the use of new applications Sharing of existing personnel information with the DLD dosimetry application, thereby avoiding the redundant work of introducing data and improving the quality of the information. Facilitation of maintenance, both software and hardware, of the DLD system. Maximum explotation, from the computer point of view, of the initial investment. Adaptation of the application to the applicable legislation. (Author)

  17. Dynamically Integrating OSM Data into a Borderland Database

    Directory of Open Access Journals (Sweden)

    Xiaoguang Zhou

    2015-09-01

    Full Text Available Spatial data are fundamental for borderland analyses of geography, natural resources, demography, politics, economy, and culture. As the spatial data used in borderland research usually cover the borderland regions of several neighboring countries, it is difficult for anyone research institution of government to collect them. Volunteered Geographic Information (VGI is a highly successful method for acquiring timely and detailed global spatial data at a very low cost. Therefore, VGI is a reasonable source of borderland spatial data. OpenStreetMap (OSM is known as the most successful VGI resource. However, OSM's data model is far different from the traditional geographic information model. Thus, the OSM data must be converted in the scientist’s customized data model. Because the real world changes rapidly, the converted data must be updated incrementally. Therefore, this paper presents a method used to dynamically integrate OSM data into the borderland database. In this method, a basic transformation rule base is formed by comparing the OSM Map Feature description document and the destination model definitions. Using the basic rules, the main features can be automatically converted to the destination model. A human-computer interaction model transformation and a rule/automatic-remember mechanism are developed to interactively transfer the unusual features that cannot be transferred by the basic rules to the target model and to remember the reusable rules automatically. To keep the borderland database current, the global OsmChange daily diff file is used to extract the change-only information for the research region. To extract the changed objects in the region under study, the relationship between the changed object and the research region is analyzed considering the evolution of the involved objects. In addition, five rules are determined to select the objects and integrate the changed objects with multi-versions over time. The objects

  18. TOMATOMICS: A Web Database for Integrated Omics Information in Tomato

    KAUST Repository

    Kudo, Toru; Kobayashi, Masaaki; Terashima, Shin; Katayama, Minami; Ozaki, Soichi; Kanno, Maasa; Saito, Misa; Yokoyama, Koji; Ohyanagi, Hajime; Aoki, Koh; Kubo, Yasutaka; Yano, Kentaro

    2016-01-01

    Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.

  19. TOMATOMICS: A Web Database for Integrated Omics Information in Tomato

    KAUST Repository

    Kudo, Toru

    2016-11-29

    Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.

  20. Existing data sources for clinical epidemiology: the Danish Patient Compensation Association database.

    Science.gov (United States)

    Tilma, Jens; Nørgaard, Mette; Mikkelsen, Kim Lyngby; Johnsen, Søren Paaske

    2015-01-01

    Any patient in the Danish health care system who experiences a treatment injury can make a compensation claim to the Danish Patient Compensation Association (DPCA) free of charge. The aim of this paper is to describe the DPCA database as a source of data for epidemiological research. Data to DPCA are collected prospectively on all claims and include information on patient factors and health records, system factors, and administrative data. Approval of claims is based on injury due to the principle of treatment below experienced specialist standard or intolerable, unexpected extensiveness of injury. Average processing time of a compensation claim is 6-8 months. Data collection is nationwide and started in 1992. The patient's central registration system number, a unique personal identifier, allows for data linkage to other registries such as the Danish National Patient Registry. The DPCA data are accessible for research following data usage permission and make it possible to analyze all claims or specific subgroups to identify predictors, outcomes, etc. DPCA data have until now been used only in few studies but could be a useful data source in future studies of health care-related injuries.

  1. Existing data sources for clinical epidemiology: the Danish Patient Compensation Association database

    Directory of Open Access Journals (Sweden)

    Tilma J

    2015-07-01

    Full Text Available Jens Tilma,1 Mette Nørgaard,1 Kim Lyngby Mikkelsen,2 Søren Paaske Johnsen1 1Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, 2Danish Patient Compensation Association, Copenhagen, Denmark Abstract: Any patient in the Danish health care system who experiences a treatment injury can make a compensation claim to the Danish Patient Compensation Association (DPCA free of charge. The aim of this paper is to describe the DPCA database as a source of data for epidemiological research. Data to DPCA are collected prospectively on all claims and include information on patient factors and health records, system factors, and administrative data. Approval of claims is based on injury due to the principle of treatment below experienced specialist standard or intolerable, unexpected extensiveness of injury. Average processing time of a compensation claim is 6–8 months. Data collection is nationwide and started in 1992. The patient's central registration system number, a unique personal identifier, allows for data linkage to other registries such as the Danish National Patient Registry. The DPCA data are accessible for research following data usage permission and make it possible to analyze all claims or specific subgroups to identify predictors, outcomes, etc. DPCA data have until now been used only in few studies but could be a useful data source in future studies of health care-related injuries. Keywords: public health care, treatment injuries, no-fault compensation, registries, research, Denmark

  2. Reactor core materials research and integrated material database establishment

    International Nuclear Information System (INIS)

    Ryu, Woo Seog; Jang, J. S.; Kim, D. W.

    2002-03-01

    Mainly two research areas were covered in this project. One is to establish the integrated database of nuclear materials, and the other is to study the behavior of reactor core materials, which are usually under the most severe condition in the operating plants. During the stage I of the project (for three years since 1999) in- and out of reactor properties of stainless steel, the major structural material for the core structures of PWR (Pressurized Water Reactor), were evaluated and specification of nuclear grade material was established. And the damaged core components from domestic power plants, e.g. orifice of CVCS, support pin of CRGT, etc. were investigated and the causes were revealed. To acquire more resistant materials to the nuclear environments, development of the alternative alloys was also conducted. For the integrated DB establishment, a task force team was set up including director of nuclear materials technology team, and projector leaders and relevant members from each project. The DB is now opened in public through the Internet

  3. Database and applications security integrating information security and data management

    CERN Document Server

    Thuraisingham, Bhavani

    2005-01-01

    This is the first book to provide an in-depth coverage of all the developments, issues and challenges in secure databases and applications. It provides directions for data and application security, including securing emerging applications such as bioinformatics, stream information processing and peer-to-peer computing. Divided into eight sections, each of which focuses on a key concept of secure databases and applications, this book deals with all aspects of technology, including secure relational databases, inference problems, secure object databases, secure distributed databases and emerging

  4. Databases

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte, P.D.

    Information on bibliographic as well as numeric/textual databases relevant to coastal geomorphology has been included in a tabular form. Databases cover a broad spectrum of related subjects like coastal environment and population aspects, coastline...

  5. Functional integration of automated system databases by means of artificial intelligence

    Science.gov (United States)

    Dubovoi, Volodymyr M.; Nikitenko, Olena D.; Kalimoldayev, Maksat; Kotyra, Andrzej; Gromaszek, Konrad; Iskakova, Aigul

    2017-08-01

    The paper presents approaches for functional integration of automated system databases by means of artificial intelligence. The peculiarities of turning to account the database in the systems with the usage of a fuzzy implementation of functions were analyzed. Requirements for the normalization of such databases were defined. The question of data equivalence in conditions of uncertainty and collisions in the presence of the databases functional integration is considered and the model to reveal their possible occurrence is devised. The paper also presents evaluation method of standardization of integrated database normalization.

  6. Integration of 128 channels for monitoring, acquisition and control with existing LHCD DAC system

    International Nuclear Information System (INIS)

    Joshi, Ramesh; Virani, Chetan; Wadhwani, Archana; Sharma, P.K.

    2015-01-01

    Lower Hybrid Current Drive (LHCD) data acquisition system needs to be upgraded for additional channel requirement. The existing VME based DAC has been used since long with 32 analog input channels for data monitoring and control. Additional 128 channels require integrating with existing DAC. There are four layers of waveguides which deliver final output power into tokamak. Each layer requires 32 channels for power measurement. For the same requirement 128 analog input channels have been integrated with the help of carrier board and IP modules. Acromag IP330 modules have been procured and finally integrated with additional carrier board with existing VME hardware. Each module provides 32 analog input channels. Device driver has been developed for each module and integrated with existing program. LHCD DAC system has been upgraded with additional 128 channels requirement. It has been successfully testing with recent SST-1 campaign. (author)

  7. Development of an integrated database management system to evaluate integrity of flawed components of nuclear power plant

    International Nuclear Information System (INIS)

    Mun, H. L.; Choi, S. N.; Jang, K. S.; Hong, S. Y.; Choi, J. B.; Kim, Y. J.

    2001-01-01

    The object of this paper is to develop an NPP-IDBMS(Integrated DataBase Management System for Nuclear Power Plants) for evaluating the integrity of components of nuclear power plant using relational data model. This paper describes the relational data model, structure and development strategy for the proposed NPP-IDBMS. The NPP-IDBMS consists of database, database management system and interface part. The database part consists of plant, shape, operating condition, material properties and stress database, which are required for the integrity evaluation of each component in nuclear power plants. For the development of stress database, an extensive finite element analysis was performed for various components considering operational transients. The developed NPP-IDBMS will provide efficient and accurate way to evaluate the integrity of flawed components

  8. Existence and computation of equilibria of first-price auctions with integral valuations and bids

    DEFF Research Database (Denmark)

    Escamocher, Guillaume; Miltersen, Peter Bro; Santillan, Rocio

    2009-01-01

    We consider existence and computation of symmetric Pure Strategy Nash Equilibrium (PSNE) in single-item, sealed-bid, first-price auctions with integral valuations and bids. For the most general case, we show that existence of PSNE is NP-hard. Then, we present algorithmic results for the case...

  9. Databases

    Directory of Open Access Journals (Sweden)

    Nick Ryan

    2004-01-01

    Full Text Available Databases are deeply embedded in archaeology, underpinning and supporting many aspects of the subject. However, as well as providing a means for storing, retrieving and modifying data, databases themselves must be a result of a detailed analysis and design process. This article looks at this process, and shows how the characteristics of data models affect the process of database design and implementation. The impact of the Internet on the development of databases is examined, and the article concludes with a discussion of a range of issues associated with the recording and management of archaeological data.

  10. Design of Integrated Database on Mobile Information System: A Study of Yogyakarta Smart City App

    Science.gov (United States)

    Nurnawati, E. K.; Ermawati, E.

    2018-02-01

    An integration database is a database which acts as the data store for multiple applications and thus integrates data across these applications (in contrast to an Application Database). An integration database needs a schema that takes all its client applications into account. The benefit of the schema that sharing data among applications does not require an extra layer of integration services on the applications. Any changes to data made in a single application are made available to all applications at the time of database commit - thus keeping the applications’ data use better synchronized. This study aims to design and build an integrated database that can be used by various applications in a mobile device based system platforms with the based on smart city system. The built-in database can be used by various applications, whether used together or separately. The design and development of the database are emphasized on the flexibility, security, and completeness of attributes that can be used together by various applications to be built. The method used in this study is to choice of the appropriate database logical structure (patterns of data) and to build the relational-database models (Design Databases). Test the resulting design with some prototype apps and analyze system performance with test data. The integrated database can be utilized both of the admin and the user in an integral and comprehensive platform. This system can help admin, manager, and operator in managing the application easily and efficiently. This Android-based app is built based on a dynamic clientserver where data is extracted from an external database MySQL. So if there is a change of data in the database, then the data on Android applications will also change. This Android app assists users in searching of Yogyakarta (as smart city) related information, especially in culture, government, hotels, and transportation.

  11. MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status

    NARCIS (Netherlands)

    Attimonelli, M.; Altamura, N.; Benne, R.; Brennicke, A.; Cooper, J. M.; D'Elia, D.; Montalvo, A.; Pinto, B.; de Robertis, M.; Golik, P.; Knoop, V.; Lanave, C.; Lazowska, J.; Licciulli, F.; Malladi, B. S.; Memeo, F.; Monnerot, M.; Pasimeni, R.; Pilbout, S.; Schapira, A. H.; Sloof, P.; Saccone, C.

    2000-01-01

    MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces

  12. Integrating heterogeneous databases in clustered medic care environments using object-oriented technology

    Science.gov (United States)

    Thakore, Arun K.; Sauer, Frank

    1994-05-01

    The organization of modern medical care environments into disease-related clusters, such as a cancer center, a diabetes clinic, etc., has the side-effect of introducing multiple heterogeneous databases, often containing similar information, within the same organization. This heterogeneity fosters incompatibility and prevents the effective sharing of data amongst applications at different sites. Although integration of heterogeneous databases is now feasible, in the medical arena this is often an ad hoc process, not founded on proven database technology or formal methods. In this paper we illustrate the use of a high-level object- oriented semantic association method to model information found in different databases into an integrated conceptual global model that integrates the databases. We provide examples from the medical domain to illustrate an integration approach resulting in a consistent global view, without attacking the autonomy of the underlying databases.

  13. Brassica ASTRA: an integrated database for Brassica genomic research.

    Science.gov (United States)

    Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

    2005-01-01

    Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

  14. Using XML technology for the ontology-based semantic integration of life science databases.

    Science.gov (United States)

    Philippi, Stephan; Köhler, Jacob

    2004-06-01

    Several hundred internet accessible life science databases with constantly growing contents and varying areas of specialization are publicly available via the internet. Database integration, consequently, is a fundamental prerequisite to be able to answer complex biological questions. Due to the presence of syntactic, schematic, and semantic heterogeneities, large scale database integration at present takes considerable efforts. As there is a growing apprehension of extensible markup language (XML) as a means for data exchange in the life sciences, this article focuses on the impact of XML technology on database integration in this area. In detail, a general architecture for ontology-driven data integration based on XML technology is introduced, which overcomes some of the traditional problems in this area. As a proof of concept, a prototypical implementation of this architecture based on a native XML database and an expert system shell is described for the realization of a real world integration scenario.

  15. Secondary Analysis and Integration of Existing Data to Elucidate the Genetic Architecture of Cancer Risk and Related Outcomes, R21 | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    This funding opportunity announcement (FOA) encourages applications that propose to conduct secondary data analysis and integration of existing datasets and database resources, with the ultimate aim to elucidate the genetic architecture of cancer risk and related outcomes. The goal of this initiative is to address key scientific questions relevant to cancer epidemiology by supporting the analysis of existing genetic or genomic datasets, possibly in combination with environmental, outcomes, behavioral, lifestyle, and molecular profiles data.

  16. Secondary Analysis and Integration of Existing Data to Elucidate the Genetic Architecture of Cancer Risk and Related Outcomes, R01 | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    This funding opportunity announcement (FOA) encourages applications that propose to conduct secondary data analysis and integration of existing datasets and database resources, with the ultimate aim to elucidate the genetic architecture of cancer risk and related outcomes. The goal of this initiative is to address key scientific questions relevant to cancer epidemiology by supporting the analysis of existing genetic or genomic datasets, possibly in combination with environmental, outcomes, behavioral, lifestyle, and molecular profiles data.

  17. STAR Online Meta-Data Collection Framework: Integration with the Pre-existing Controls Infrastructure

    Science.gov (United States)

    Arkhipkin, D.; Lauret, J.

    2017-10-01

    One of the STAR experiment’s modular Messaging Interface and Reliable Architecture framework (MIRA) integration goals is to provide seamless and automatic connections with the existing control systems. After an initial proof of concept and operation of the MIRA system as a parallel data collection system for online use and real-time monitoring, the STAR Software and Computing group is now working on the integration of Experimental Physics and Industrial Control System (EPICS) with MIRA’s interfaces. This integration goals are to allow functional interoperability and, later on, to replace the existing/legacy Detector Control System components at the service level. In this report, we describe the evolutionary integration process and, as an example, will discuss the EPICS Alarm Handler conversion. We review the complete upgrade procedure starting with the integration of EPICS-originated alarm signals propagation into MIRA, followed by the replacement of the existing operator interface based on Motif Editor and Display Manager (MEDM) with modern portable web-based Alarm Handler interface. To achieve this aim, we have built an EPICS-to-MQTT [8] bridging service, and recreated the functionality of the original Alarm Handler using low-latency web messaging technologies. The integration of EPICS alarm handling into our messaging framework allowed STAR to improve the DCS alarm awareness of existing STAR DAQ and RTS services, which use MIRA as a primary source of experiment control information.

  18. A semantic data dictionary method for database schema integration in CIESIN

    Science.gov (United States)

    Hinds, N.; Huang, Y.; Ravishankar, C.

    1993-08-01

    CIESIN (Consortium for International Earth Science Information Network) is funded by NASA to investigate the technology necessary to integrate and facilitate the interdisciplinary use of Global Change information. A clear of this mission includes providing a link between the various global change data sets, in particular the physical sciences and the human (social) sciences. The typical scientist using the CIESIN system will want to know how phenomena in an outside field affects his/her work. For example, a medical researcher might ask: how does air-quality effect emphysema? This and many similar questions will require sophisticated semantic data integration. The researcher who raised the question may be familiar with medical data sets containing emphysema occurrences. But this same investigator may know little, if anything, about the existance or location of air-quality data. It is easy to envision a system which would allow that investigator to locate and perform a ``join'' on two data sets, one containing emphysema cases and the other containing air-quality levels. No such system exists today. One major obstacle to providing such a system will be overcoming the heterogeneity which falls into two broad categories. ``Database system'' heterogeneity involves differences in data models and packages. ``Data semantic'' heterogeneity involves differences in terminology between disciplines which translates into data semantic issues, and varying levels of data refinement, from raw to summary. Our work investigates a global data dictionary mechanism to facilitate a merged data service. Specially, we propose using a semantic tree during schema definition to aid in locating and integrating heterogeneous databases.

  19. Integr8: enhanced inter-operability of European molecular biology databases.

    Science.gov (United States)

    Kersey, P J; Morris, L; Hermjakob, H; Apweiler, R

    2003-01-01

    The increasing production of molecular biology data in the post-genomic era, and the proliferation of databases that store it, require the development of an integrative layer in database services to facilitate the synthesis of related information. The solution of this problem is made more difficult by the absence of universal identifiers for biological entities, and the breadth and variety of available data. Integr8 was modelled using UML (Universal Modelling Language). Integr8 is being implemented as an n-tier system using a modern object-oriented programming language (Java). An object-relational mapping tool, OJB, is being used to specify the interface between the upper layers and an underlying relational database. The European Bioinformatics Institute is launching the Integr8 project. Integr8 will be an automatically populated database in which we will maintain stable identifiers for biological entities, describe their relationships with each other (in accordance with the central dogma of biology), and store equivalences between identified entities in the source databases. Only core data will be stored in Integr8, with web links to the source databases providing further information. Integr8 will provide the integrative layer of the next generation of bioinformatics services from the EBI. Web-based interfaces will be developed to offer gene-centric views of the integrated data, presenting (where known) the links between genome, proteome and phenotype.

  20. DEVELOPING FLEXIBLE APPLICATIONS WITH XML AND DATABASE INTEGRATION

    Directory of Open Access Journals (Sweden)

    Hale AS

    2004-04-01

    Full Text Available In recent years the most popular subject in Information System area is Enterprise Application Integration (EAI. It can be defined as a process of forming a standart connection between different systems of an organization?s information system environment. The incorporating, gaining and marriage of corporations are the major reasons of popularity in Enterprise Application Integration. The main purpose is to solve the application integrating problems while similar systems in such corporations continue working together for a more time. With the help of XML technology, it is possible to find solutions to the problems of application integration either within the corporation or between the corporations.

  1. Existence Results for Some Nonlinear Functional-Integral Equations in Banach Algebra with Applications

    Directory of Open Access Journals (Sweden)

    Lakshmi Narayan Mishra

    2016-04-01

    Full Text Available In the present manuscript, we prove some results concerning the existence of solutions for some nonlinear functional-integral equations which contains various integral and functional equations that considered in nonlinear analysis and its applications. By utilizing the techniques of noncompactness measures, we operate the fixed point theorems such as Darbo's theorem in Banach algebra concerning the estimate on the solutions. The results obtained in this paper extend and improve essentially some known results in the recent literature. We also provide an example of nonlinear functional-integral equation to show the ability of our main result.

  2. Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.

    Science.gov (United States)

    Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

    2011-07-01

    Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.

  3. Coordinate Systems Integration for Craniofacial Database from Multimodal Devices

    Directory of Open Access Journals (Sweden)

    Deni Suwardhi

    2005-05-01

    Full Text Available This study presents a data registration method for craniofacial spatial data of different modalities. The data consists of three dimensional (3D vector and raster data models. The data is stored in object relational database. The data capture devices are Laser scanner, CT (Computed Tomography scan and CR (Close Range Photogrammetry. The objective of the registration is to transform the data from various coordinate systems into a single 3-D Cartesian coordinate system. The standard error of the registration obtained from multimodal imaging devices using 3D affine transformation is in the ranged of 1-2 mm. This study is a step forward for storing the craniofacial spatial data in one reference system in database.

  4. M4FT-16LL080302052-Update to Thermodynamic Database Development and Sorption Database Integration

    Energy Technology Data Exchange (ETDEWEB)

    Zavarin, Mavrik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Glenn T. Seaborg Inst.. Physical and Life Sciences; Wolery, T. J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Akima Infrastructure Services, LLC; Atkins-Duffin, C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Global Security

    2016-08-16

    This progress report (Level 4 Milestone Number M4FT-16LL080302052) summarizes research conducted at Lawrence Livermore National Laboratory (LLNL) within the Argillite Disposal R&D Work Package Number FT-16LL08030205. The focus of this research is the thermodynamic modeling of Engineered Barrier System (EBS) materials and properties and development of thermodynamic databases and models to evaluate the stability of EBS materials and their interactions with fluids at various physico-chemical conditions relevant to subsurface repository environments. The development and implementation of equilibrium thermodynamic models are intended to describe chemical and physical processes such as solubility, sorption, and diffusion.

  5. Large-scale integration of wind power into the existing Chinese energy system

    DEFF Research Database (Denmark)

    Liu, Wen; Lund, Henrik; Mathiesen, Brian Vad

    2011-01-01

    stability, the maximum feasible wind power penetration in the existing Chinese energy system is approximately 26% from both technical and economic points of view. A fuel efficiency decrease occurred when increasing wind power penetration in the system, due to its rigid power supply structure and the task......This paper presents the ability of the existing Chinese energy system to integrate wind power and explores how the Chinese energy system needs to prepare itself in order to integrate more fluctuating renewable energy in the future. With this purpose in mind, a model of the Chinese energy system has...... been constructed by using EnergyPLAN based on the year 2007, which has then been used for investigating three issues. Firstly, the accuracy of the model itself has been examined and then the maximum feasible wind power penetration in the existing energy system has been identified. Finally, barriers...

  6. MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.

    Science.gov (United States)

    Kwon, Taejoon; Choi, Hyungwon; Vogel, Christine; Nesvizhskii, Alexey I; Marcotte, Edward M

    2011-07-01

    Shotgun proteomics using mass spectrometry is a powerful method for protein identification but suffers limited sensitivity in complex samples. Integrating peptide identifications from multiple database search engines is a promising strategy to increase the number of peptide identifications and reduce the volume of unassigned tandem mass spectra. Existing methods pool statistical significance scores such as p-values or posterior probabilities of peptide-spectrum matches (PSMs) from multiple search engines after high scoring peptides have been assigned to spectra, but these methods lack reliable control of identification error rates as data are integrated from different search engines. We developed a statistically coherent method for integrative analysis, termed MSblender. MSblender converts raw search scores from search engines into a probability score for every possible PSM and properly accounts for the correlation between search scores. The method reliably estimates false discovery rates and identifies more PSMs than any single search engine at the same false discovery rate. Increased identifications increment spectral counts for most proteins and allow quantification of proteins that would not have been quantified by individual search engines. We also demonstrate that enhanced quantification contributes to improve sensitivity in differential expression analyses.

  7. Integration of existing systematic reviews into new reviews: identification of guidance needs

    Science.gov (United States)

    2014-01-01

    Background An exponential increase in the number of systematic reviews published, and constrained resources for new reviews, means that there is an urgent need for guidance on explicitly and transparently integrating existing reviews into new systematic reviews. The objectives of this paper are: 1) to identify areas where existing guidance may be adopted or adapted, and 2) to suggest areas for future guidance development. Methods We searched documents and websites from healthcare focused systematic review organizations to identify and, where available, to summarize relevant guidance on the use of existing systematic reviews. We conducted informational interviews with members of Evidence-based Practice Centers (EPCs) to gather experiences in integrating existing systematic reviews, including common issues and challenges, as well as potential solutions. Results There was consensus among systematic review organizations and the EPCs about some aspects of incorporating existing systematic reviews into new reviews. Current guidance may be used in assessing the relevance of prior reviews and in scanning references of prior reviews to identify studies for a new review. However, areas of challenge remain. Areas in need of guidance include how to synthesize, grade the strength of, and present bodies of evidence composed of primary studies and existing systematic reviews. For instance, empiric evidence is needed regarding how to quality check data abstraction and when and how to use study-level risk of bias assessments from prior reviews. Conclusions There remain areas of uncertainty for how to integrate existing systematic reviews into new reviews. Methods research and consensus processes among systematic review organizations are needed to develop guidance to address these challenges. PMID:24956937

  8. Integrated Strategic Tracking and Recruiting Database (iSTAR) Data Inventory

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Integrated Strategic Tracking and Recruiting Database (iSTAR) Data Inventory contains measured and modeled partnership and contact data. It is comprised of basic...

  9. IMG: the integrated microbial genomes database and comparative analysis system

    Science.gov (United States)

    Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2012-01-01

    The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. IMG's data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp). PMID:22194640

  10. Cost benefit analysis of power plant database integration

    International Nuclear Information System (INIS)

    Wilber, B.E.; Cimento, A.; Stuart, R.

    1988-01-01

    A cost benefit analysis of plant wide data integration allows utility management to evaluate integration and automation benefits from an economic perspective. With this evaluation, the utility can determine both the quantitative and qualitative savings that can be expected from data integration. The cost benefit analysis is then a planning tool which helps the utility to develop a focused long term implementation strategy that will yield significant near term benefits. This paper presents a flexible cost benefit analysis methodology which is both simple to use and yields accurate, verifiable results. Included in this paper is a list of parameters to consider, a procedure for performing the cost savings analysis, and samples of this procedure when applied to a utility. A case study is presented involving a specific utility where this procedure was applied. Their uses of the cost-benefit analysis are also described

  11. Development of Integrated PSA Database and Application Technology

    Energy Technology Data Exchange (ETDEWEB)

    Han, Sang Hoon; Park, Jin Hee; Kim, Seung Hwan; Choi, Sun Yeong; Jung, Woo Sik; Jeong, Kwang Sub; Ha Jae Joo; Yang, Joon Eon; Min Kyung Ran; Kim, Tae Woon

    2005-04-15

    The purpose of this project is to develop 1) the reliability database framework, 2) the methodology for the reactor trip and abnormal event analysis, and 3) the prototype PSA information DB system. We already have a part of the reactor trip and component reliability data. In this study, we extend the collection of data up to 2002. We construct the pilot reliability database for common cause failure and piping failure data. A reactor trip or a component failure may have an impact on the safety of a nuclear power plant. We perform the precursor analysis for such events that occurred in the KSNP, and to develop a procedure for the precursor analysis. A risk monitor provides a mean to trace the changes in the risk following the changes in the plant configurations. We develop a methodology incorporating the model of secondary system related to the reactor trip into the risk monitor model. We develop a prototype PSA information system for the UCN 3 and 4 PSA models where information for the PSA is inputted into the system such as PSA reports, analysis reports, thermal-hydraulic analysis results, system notebooks, and so on. We develop a unique coherent BDD method to quantify a fault tree and the fastest fault tree quantification engine FTREX. We develop quantification software for a full PSA model and a one top model.

  12. Building an integrated neurodegenerative disease database at an academic health center.

    Science.gov (United States)

    Xie, Sharon X; Baek, Young; Grossman, Murray; Arnold, Steven E; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M-Y; Trojanowski, John Q

    2011-07-01

    It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration. These comparative studies rely on powerful database tools to quickly generate data sets that match diverse and complementary criteria set by them. In this article, we present a novel integrated neurodegenerative disease (INDD) database, which was developed at the University of Pennsylvania (Penn) with the help of a consortium of Penn investigators. Because the work of these investigators are based on Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration, it allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used the Microsoft SQL server as a platform, with built-in "backwards" functionality to provide Access as a frontend client to interface with the database. We used PHP Hypertext Preprocessor to create the "frontend" web interface and then used a master lookup table to integrate individual neurodegenerative disease databases. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Using the INDD database, we compared the results of a biomarker study with those using an alternative approach by querying individual databases separately. We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies on several neurodegenerative diseases. Copyright © 2011 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

  13. SolveDB: Integrating Optimization Problem Solvers Into SQL Databases

    DEFF Research Database (Denmark)

    Siksnys, Laurynas; Pedersen, Torben Bach

    2016-01-01

    for optimization problems, (2) an extensible infrastructure for integrating different solvers, and (3) query optimization techniques to achieve the best execution performance and/or result quality. Extensive experiments with the PostgreSQL-based implementation show that SolveDB is a versatile tool offering much...

  14. Sustaining high energy efficiency in existing processes with advanced process integration technology

    International Nuclear Information System (INIS)

    Zhang, Nan; Smith, Robin; Bulatov, Igor; Klemeš, Jiří Jaromír

    2013-01-01

    Highlights: ► Process integration with better modelling and more advanced solution methods. ► Operational changes for better environmental performance through optimisation. ► Identification of process integration technology for operational optimisation. ► Systematic implementation procedure of process integration technology. ► A case study with crude oil distillation to demonstrate the operational flexibility. -- Abstract: To reduce emissions in the process industry, much emphasis has been put on making step changes in emission reduction, by developing new process technology and making renewable energy more affordable. However, the energy saving potential of existing systems cannot be simply ignored. In recent years, there have been significant advances in process integration technology with better modelling techniques and more advanced solution methods. These methods have been applied to the new design and retrofit studies in the process industry. Here attempts are made to apply these technologies to improve the environmental performance of existing facilities with operational changes. An industrial project was carried out to demonstrate the importance and effectiveness of exploiting the operational flexibility for energy conservation. By applying advanced optimisation technique to integrate the operation of distillation and heat recovery in a crude oil distillation unit, the energy consumption was reduced by 8% without capital expenditure. It shows that with correctly identified technology and the proper execution procedure, significant energy savings and emission reduction can be achieved very quickly without major capital expenditure. This allows the industry to improve its economic and environment performance at the same time.

  15. Representing clinical communication knowledge through database management system integration.

    Science.gov (United States)

    Khairat, Saif; Craven, Catherine; Gong, Yang

    2012-01-01

    Clinical communication failures are considered the leading cause of medical errors [1]. The complexity of the clinical culture and the significant variance in training and education levels form a challenge to enhancing communication within the clinical team. In order to improve communication, a comprehensive understanding of the overall communication process in health care is required. In an attempt to further understand clinical communication, we conducted a thorough methodology literature review to identify strengths and limitations of previous approaches [2]. Our research proposes a new data collection method to study the clinical communication activities among Intensive Care Unit (ICU) clinical teams with a primary focus on the attending physician. In this paper, we present the first ICU communication instrument, and, we introduce the use of database management system to aid in discovering patterns and associations within our ICU communications data repository.

  16. Twelve recommendations for integrating existing systematic reviews into new reviews: EPC guidance.

    Science.gov (United States)

    Robinson, Karen A; Chou, Roger; Berkman, Nancy D; Newberry, Sydne J; Fu, Rongwei; Hartling, Lisa; Dryden, Donna; Butler, Mary; Foisy, Michelle; Anderson, Johanna; Motu'apuaka, Makalapua; Relevo, Rose; Guise, Jeanne-Marie; Chang, Stephanie

    2016-02-01

    As time and cost constraints in the conduct of systematic reviews increase, the need to consider the use of existing systematic reviews also increases. We developed guidance on the integration of systematic reviews into new reviews. A workgroup of methodologists from Evidence-based Practice Centers developed consensus-based recommendations. Discussions were informed by a literature scan and by interviews with organizations that conduct systematic reviews. Twelve recommendations were developed addressing selecting reviews, assessing risk of bias, qualitative and quantitative synthesis, and summarizing and assessing body of evidence. We provide preliminary guidance for an efficient and unbiased approach to integrating existing systematic reviews with primary studies in a new review. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. On integration of plug-in hybrid electric vehicles into existing power system structures

    International Nuclear Information System (INIS)

    Galus, Matthias D.; Zima, Marek; Andersson, Goeran

    2010-01-01

    Plug-in hybrid electric vehicles (PHEVs) represent one option for the electrification of private mobility. In order to efficiently integrate PHEVs into power systems, existing organizational structures need to be considered. Based on procedures of power systems planning and operation, actors are identified whose operational activities will be affected by PHEV integration. Potential changes and challenges in the actors' long- and short term planning activities are discussed. Further, a PHEV operation state description is developed which defines vehicle operation states from the power system point of view integrating uncontrolled, controlled recharging and vehicle to grid (V2G) utilization in one single framework. Future PHEV managing entities, such as aggregators, can use this framework for planning and operation activities including load management and V2G. This operational state description could provide a solution for future short term planning challenges of PHEVs and an aegis for various routes of current research, which to date have been weakly linked to each other.

  18. Integration of published information into a resistance-associated mutation database for Mycobacterium tuberculosis.

    Science.gov (United States)

    Salamon, Hugh; Yamaguchi, Ken D; Cirillo, Daniela M; Miotto, Paolo; Schito, Marco; Posey, James; Starks, Angela M; Niemann, Stefan; Alland, David; Hanna, Debra; Aviles, Enrique; Perkins, Mark D; Dolinger, David L

    2015-04-01

    Tuberculosis remains a major global public health challenge. Although incidence is decreasing, the proportion of drug-resistant cases is increasing. Technical and operational complexities prevent Mycobacterium tuberculosis drug susceptibility phenotyping in the vast majority of new and retreatment cases. The advent of molecular technologies provides an opportunity to obtain results rapidly as compared to phenotypic culture. However, correlations between genetic mutations and resistance to multiple drugs have not been systematically evaluated. Molecular testing of M. tuberculosis sampled from a typical patient continues to provide a partial picture of drug resistance. A database of phenotypic and genotypic testing results, especially where prospectively collected, could document statistically significant associations and may reveal new, predictive molecular patterns. We examine the feasibility of integrating existing molecular and phenotypic drug susceptibility data to identify associations observed across multiple studies and demonstrate potential for well-integrated M. tuberculosis mutation data to reveal actionable findings. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. System/subsystem specifications for the Worldwide Port System (WPS) Regional Integrated Cargo Database (ICDB)

    Energy Technology Data Exchange (ETDEWEB)

    Rollow, J.P.; Shipe, P.C.; Truett, L.F. [Oak Ridge National Lab., TN (United States); Faby, E.Z.; Fluker, J.; Grubb, J.; Hancock, B.R. [Univ. of Tennessee, Knoxville, TN (United States); Ferguson, R.A. [Science Applications International Corp., Oak Ridge, TN (United States)

    1995-11-20

    A system is being developed by the Military Traffic Management Command (MTMC) to provide data integration and worldwide management and tracking of surface cargo movements. The Integrated Cargo Database (ICDB) will be a data repository for the WPS terminal-level system, will be a primary source of queries and cargo traffic reports, will receive data from and provide data to other MTMC and non-MTMC systems, will provide capabilities for processing Advance Transportation Control and Movement Documents (ATCMDs), and will process and distribute manifests. This System/Subsystem Specifications for the Worldwide Port System Regional ICDB documents the system/subsystem functions, provides details of the system/subsystem analysis in order to provide a communication link between developers and operational personnel, and identifies interfaces with other systems and subsystems. It must be noted that this report is being produced near the end of the initial development phase of ICDB, while formal software testing is being done. Following the initial implementation of the ICDB system, maintenance contractors will be in charge of making changes and enhancing software modules. Formal testing and user reviews may indicate the need for additional software units or changes to existing ones. This report describes the software units that are components of this ICDB system as of August 1995.

  20. Improving Microbial Genome Annotations in an Integrated Database Context

    Science.gov (United States)

    Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Anderson, Iain; Mavromatis, Konstantinos; Kyrpides, Nikos C.; Ivanova, Natalia N.

    2013-01-01

    Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/. PMID:23424620

  1. Improving microbial genome annotations in an integrated database context.

    Directory of Open Access Journals (Sweden)

    I-Min A Chen

    Full Text Available Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.

  2. Construction, database integration, and application of an Oenothera EST library.

    Science.gov (United States)

    Mrácek, Jaroslav; Greiner, Stephan; Cho, Won Kyong; Rauwolf, Uwe; Braun, Martha; Umate, Pavan; Altstätter, Johannes; Stoppel, Rhea; Mlcochová, Lada; Silber, Martina V; Volz, Stefanie M; White, Sarah; Selmeier, Renate; Rudd, Stephen; Herrmann, Reinhold G; Meurer, Jörg

    2006-09-01

    Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges. The genus Oenothera represents a unique, at present the only available, resource to study the role of the compartmentalized plant genome in diversification of populations and speciation processes. An integrated approach involving cDNA cloning, EST sequencing, and bioinformatic data mining was chosen using Oenothera elata with the genetic constitution nuclear genome AA with plastome type I. The Gene Ontology system grouped 1621 unique gene products into 17 different functional categories. Application of arrays generated from a selected fraction of ESTs revealed significantly differing expression profiles among closely related Oenothera species possessing the potential to generate fertile and incompatible plastid/nuclear hybrids (hybrid bleaching). Furthermore, the EST library provides a valuable source of PCR-based polymorphic molecular markers that are instrumental for genotyping and molecular mapping approaches.

  3. MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases.

    Science.gov (United States)

    Townend, Gillian S; Ehrhart, Friederike; van Kranen, Henk J; Wilkinson, Mark; Jacobsen, Annika; Roos, Marco; Willighagen, Egon L; van Enckevort, David; Evelo, Chris T; Curfs, Leopold M G

    2018-04-27

    Rett syndrome (RTT) is a monogenic rare disorder that causes severe neurological problems. In most cases, it results from a loss-of-function mutation in the gene encoding methyl-CPG-binding protein 2 (MECP2). Currently, about 900 unique MECP2 variations (benign and pathogenic) have been identified and it is suspected that the different mutations contribute to different levels of disease severity. For researchers and clinicians, it is important that genotype-phenotype information is available to identify disease-causing mutations for diagnosis, to aid in clinical management of the disorder, and to provide counseling for parents. In this study, 13 genotype-phenotype databases were surveyed for their general functionality and availability of RTT-specific MECP2 variation data. For each database, we investigated findability and interoperability alongside practical user functionality, and type and amount of genetic and phenotype data. The main conclusions are that, as well as being challenging to find these databases and specific MECP2 variants held within, interoperability is as yet poorly developed and requires effort to search across databases. Nevertheless, we found several thousand online database entries for MECP2 variations and their associated phenotypes, diagnosis, or predicted variant effects, which is a good starting point for researchers and clinicians who want to provide, annotate, and use the data. © 2018 The Authors. Human Mutation published by Wiley Periodicals, Inc.

  4. CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002.

    Science.gov (United States)

    Yang, Yaohua; Feng, Jie; Li, Tao; Ge, Feng; Zhao, Jindong

    2015-01-01

    Cyanobacteria are an important group of organisms that carry out oxygenic photosynthesis and play vital roles in both the carbon and nitrogen cycles of the Earth. The annotated genome of Synechococcus sp. PCC 7002, as an ideal model cyanobacterium, is available. A series of transcriptomic and proteomic studies of Synechococcus sp. PCC 7002 cells grown under different conditions have been reported. However, no database of such integrated omics studies has been constructed. Here we present CyanOmics, a database based on the results of Synechococcus sp. PCC 7002 omics studies. CyanOmics comprises one genomic dataset, 29 transcriptomic datasets and one proteomic dataset and should prove useful for systematic and comprehensive analysis of all those data. Powerful browsing and searching tools are integrated to help users directly access information of interest with enhanced visualization of the analytical results. Furthermore, Blast is included for sequence-based similarity searching and Cluster 3.0, as well as the R hclust function is provided for cluster analyses, to increase CyanOmics's usefulness. To the best of our knowledge, it is the first integrated omics analysis database for cyanobacteria. This database should further understanding of the transcriptional patterns, and proteomic profiling of Synechococcus sp. PCC 7002 and other cyanobacteria. Additionally, the entire database framework is applicable to any sequenced prokaryotic genome and could be applied to other integrated omics analysis projects. Database URL: http://lag.ihb.ac.cn/cyanomics. © The Author(s) 2015. Published by Oxford University Press.

  5. Development of integrated parameter database for risk assessment at the Rokkasho Reprocessing Plant

    International Nuclear Information System (INIS)

    Tamauchi, Yoshikazu

    2011-01-01

    A study to develop a parameter database for Probabilistic Safety Assessment (PSA) for the application of risk information on plant operation and maintenance activity is important because the transparency, consistency, and traceability of parameters are needed to explanation adequacy of the evaluation to third parties. Application of risk information for the plant operation and maintenance activity, equipment reliability data, human error rate, and 5 factors of 'five-factor formula' for estimation of the amount of radioactive material discharge (source term) are key inputs. As a part of the infrastructure development for the risk information application, we developed the integrated parameter database, 'R-POD' (Rokkasho reprocessing Plant Omnibus parameter Database) on the trial basis for the PSA of the Rokkasho Reprocessing Plant. This database consists primarily of the following 3 parts, 1) an equipment reliability database, 2) a five-factor formula database, and 3) a human reliability database. The underpinning for explaining the validity of the risk assessment can be improved by developing this database. Furthermore, this database is an important tool for the application of risk information, because it provides updated data by incorporating the accumulated operation experiences of the Rokkasho reprocessing plant. (author)

  6. The Integration of DCS I/O to an Existing PLC

    Science.gov (United States)

    Sadhukhan, Debashis; Mihevic, John

    2013-01-01

    At the NASA Glenn Research Center (GRC), Existing Programmable Logic Controller (PLC) I/O was replaced with Distributed Control System (DCS) I/O, while keeping the existing PLC sequence Logic. The reason for integration of the PLC logic and DCS I/O, along with the evaluation of the resulting system is the subject of this paper. The pros and cons of the old system and new upgrade are described, including operator workstation screen update times. Detail of the physical layout and the communication between the PLC, the DCS I/O and the operator workstations are illustrated. The complex characteristics of a central process control system and the plan to remove the PLC processors in future upgrades is also discussed.

  7. On the existence of solutions for Volterra integral inclusions in Banach spaces

    Directory of Open Access Journals (Sweden)

    Evgenios P. Avgerinos

    1993-01-01

    Full Text Available In this paper we examine a class of nonlinear integral inclusions defined in a separable Banach space. For this class of inclusions of Volterra type we establish two existence results, one for inclusions with a convex-valued orientor field and the other for inclusions with nonconvex-valued orientor field. We present conditions guaranteeing that the multivalued map that represents the right-hand side of the inclusion is α-condensing using for the proof of our results a known fixed point theorem for α-condensing maps.

  8. CTDB: An Integrated Chickpea Transcriptome Database for Functional and Applied Genomics

    OpenAIRE

    Verma, Mohit; Kumar, Vinay; Patel, Ravi K.; Garg, Rohini; Jain, Mukesh

    2015-01-01

    Chickpea is an important grain legume used as a rich source of protein in human diet. The narrow genetic diversity and limited availability of genomic resources are the major constraints in implementing breeding strategies and biotechnological interventions for genetic enhancement of chickpea. We developed an integrated Chickpea Transcriptome Database (CTDB), which provides the comprehensive web interface for visualization and easy retrieval of transcriptome data in chickpea. The database fea...

  9. Integrating existing radiation monitors into a microprocessor-based display system

    International Nuclear Information System (INIS)

    Kalita, R, S.; Bartucci, C.M.; Mason, R.G.; Greaves, C.

    1992-01-01

    Plantwide digital radiation monitoring systems (RMSs) have been generally installed as part of the original design for newer nuclear reactors. For older plants, area and process radiation monitors were either analog or a combination of analog and digital but were not part of an integrated system design. At some plants, individual monitors have been replaced or modified, resulting in a rainbow of different monitors and vendors being represented at the plant. Usually at some point, consideration is given to replacing these monitors with a state-of-the-art RMS to improve overall reliability and achieve the benefits of sound human factors engineering. This can be a very costly project in terms of expenditures for engineering, equipment, construction, startup, and time. When human engineering deficiencies (HEDs) became an issue at Zion station, Commonwealth Edison elected to install a computer-based radiation monitoring display system (RMDS) that would interface existing raidation monitors. After reviewing the existing as-built RMS configuration and internal circuits of the various monitors, it was concluded that a microprocessor-based RMDS could be successfully designed and installed that would solve the HEDs and would tie the older analog channels into a system configuration. Although in many cases, internal modifications were made to existing RMS monitors, the RMDS upgrade allowed the existing RMS monitors to retain their original functionality and location

  10. GDR (Genome Database for Rosaceae: integrated web resources for Rosaceae genomics and genetics research

    Directory of Open Access Journals (Sweden)

    Ficklin Stephen

    2004-09-01

    Full Text Available Abstract Background Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. Description The Genome Database for Rosaceae (GDR is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. Conclusions The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.

  11. GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research.

    Science.gov (United States)

    Jung, Sook; Jesudurai, Christopher; Staton, Margaret; Du, Zhidian; Ficklin, Stephen; Cho, Ilhyung; Abbott, Albert; Tomkins, Jeffrey; Main, Dorrie

    2004-09-09

    Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.

  12. Integration of TGS and CTEN assays using the CTENFIT analysis and databasing program

    International Nuclear Information System (INIS)

    Estep, R.

    2000-01-01

    The CTEN F IT program, written for Windows 9x/NT in C++, performs databasing and analysis of combined thermal/epithermal neutron (CTEN) passive and active neutron assay data and integrates that with isotopics results and gamma-ray data from methods such as tomographic gamma scanning (TGS). The binary database is reflected in a companion Excel database that allows extensive customization via Visual Basic for Applications macros. Automated analysis options make the analysis of the data transparent to the assay system operator. Various record browsers and information displays simplified record keeping tasks

  13. Integrated Controlling System and Unified Database for High Throughput Protein Crystallography Experiments

    International Nuclear Information System (INIS)

    Gaponov, Yu.A.; Igarashi, N.; Hiraki, M.; Sasajima, K.; Matsugaki, N.; Suzuki, M.; Kosuge, T.; Wakatsuki, S.

    2004-01-01

    An integrated controlling system and a unified database for high throughput protein crystallography experiments have been developed. Main features of protein crystallography experiments (purification, crystallization, crystal harvesting, data collection, data processing) were integrated into the software under development. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data that are stored in a central data server) in a MySQL relational database. The database contains four mutually linked hierarchical trees describing protein crystals, data collection of protein crystal and experimental data processing. A database editor was designed and developed. The editor supports basic database functions to view, create, modify and delete user records in the database. Two search engines were realized: direct search of necessary information in the database and object oriented search. The system is based on TCP/IP secure UNIX sockets with four predefined sending and receiving behaviors, which support communications between all connected servers and clients with remote control functions (creating and modifying data for experimental conditions, data acquisition, viewing experimental data, and performing data processing). Two secure login schemes were designed and developed: a direct method (using the developed Linux clients with secure connection) and an indirect method (using the secure SSL connection using secure X11 support from any operating system with X-terminal and SSH support). A part of the system has been implemented on a new MAD beam line, NW12, at the Photon Factory Advanced Ring for general user experiments

  14. A perspective for biomedical data integration: Design of databases for flow cytometry

    Directory of Open Access Journals (Sweden)

    Lakoumentas John

    2008-02-01

    Full Text Available Abstract Background The integration of biomedical information is essential for tackling medical problems. We describe a data model in the domain of flow cytometry (FC allowing for massive management, analysis and integration with other laboratory and clinical information. The paper is concerned with the proper translation of the Flow Cytometry Standard (FCS into a relational database schema, in a way that facilitates end users at either doing research on FC or studying specific cases of patients undergone FC analysis Results The proposed database schema provides integration of data originating from diverse acquisition settings, organized in a way that allows syntactically simple queries that provide results significantly faster than the conventional implementations of the FCS standard. The proposed schema can potentially achieve up to 8 orders of magnitude reduction in query complexity and up to 2 orders of magnitude reduction in response time for data originating from flow cytometers that record 256 colours. This is mainly achieved by managing to maintain an almost constant number of data-mining procedures regardless of the size and complexity of the stored information. Conclusion It is evident that using single-file data storage standards for the design of databases without any structural transformations significantly limits the flexibility of databases. Analysis of the requirements of a specific domain for integration and massive data processing can provide the necessary schema modifications that will unlock the additional functionality of a relational database.

  15. Integration of a PAFC-Cogeneration Plant into an existing District-Heating-System

    International Nuclear Information System (INIS)

    Wagner, Ulrich; Geiger, Bernd; Grohmann, Juergen

    1999-01-01

    The Studiengesellschaft Brennstoffzellen e. V. assigned in the middle of 1995 the Institutions ''Lehrstuhl fir Energiewirtschaft mid Kraftwerkstechnik (IfE)'' to design a concept to integrate an ONSI-PAFC Model C in an existing district heating system. The fuel cell generates about 200 kW electrical and 215 kW thermal power consuming 500 kW natural gas. In the case of complete use of thermal power the fuel cell surpasses the efficiency of conventional systems by about 30 %. The possibilities to install the fuel cell were investigated at three locations, two housing areas, one with 36.000 m2 the other with 60.000 m2 heated area, and one indoor pool. The heating systems are representative of the Federal Republic of Germany. It turned out that the integration of the fuel cell into the existing heating system might be difficult at each location, either the annual consumption of thermal energy was too low or the heating system was operating at a temperature level reducing the usable thermal power of the fuel cell. After further studies the larger housing area was selected, with the intention of using the thermal power of the fuel cell during the whole year and to get high thermal load factors. Some difficulties are caused by the temperature level of the heating system, which is 70/55 o C. (author)

  16. A District Approach to Building Renovation for the Integral Energy Redevelopment of Existing Residential Areas

    Directory of Open Access Journals (Sweden)

    Mira Conci

    2017-05-01

    Full Text Available Building energy renovation quotas are not currently being met due to unfavorable conditions such as complex building regulations, limited investment incentives, historical preservation priorities, and technical limitations. The traditional strategy has been to incrementally lower the energy consumption of the building stock, instead of raising the efficiency of the energy supply through a broader use of renewable sources. This strategy requires an integral redefinition of the approach to energy building renovations. The joint project SWIVT elaborates on a district redevelopment strategy that combines a reduction in the energy demand of existing buildings and their physical interconnection within a local micro-grid and heating network. The district is equipped with energy generation and distribution technologies as well as hybrid thermal and electrical energy storage systems, steered by an optimizing energy management controller. This strategy is explored through three scenarios designed for an existing residential area in Darmstadt, Germany, and benchmarked against measured data. Presented findings show that a total primary energy balance at least 30% lower than that of a standard building renovation can be achieved by a cluster of buildings with different thermal qualities and connected energy generation, conversion, and storage systems, with only minimal physical intervention to existing buildings.

  17. LmSmdB: an integrated database for metabolic and gene regulatory network in Leishmania major and Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Priyanka Patel

    2016-03-01

    Full Text Available A database that integrates all the information required for biological processing is essential to be stored in one platform. We have attempted to create one such integrated database that can be a one stop shop for the essential features required to fetch valuable result. LmSmdB (L. major and S. mansoni database is an integrated database that accounts for the biological networks and regulatory pathways computationally determined by integrating the knowledge of the genome sequences of the mentioned organisms. It is the first database of its kind that has together with the network designing showed the simulation pattern of the product. This database intends to create a comprehensive canopy for the regulation of lipid metabolism reaction in the parasite by integrating the transcription factors, regulatory genes and the protein products controlled by the transcription factors and hence operating the metabolism at genetic level. Keywords: L.major, S.mansoni, Regulatory networks, Transcription factors, Database

  18. KaBOB: ontology-based semantic integration of biomedical databases.

    Science.gov (United States)

    Livingston, Kevin M; Bada, Michael; Baumgartner, William A; Hunter, Lawrence E

    2015-04-23

    The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing resources. Despite ongoing work moving toward shared data formats and linked identifiers, significant problems persist in semantic data integration in order to establish shared identity and shared meaning across heterogeneous biomedical data sources. We present five processes for semantic data integration that, when applied collectively, solve seven key problems. These processes include making explicit the differences between biomedical concepts and database records, aggregating sets of identifiers denoting the same biomedical concepts across data sources, and using declaratively represented forward-chaining rules to take information that is variably represented in source databases and integrating it into a consistent biomedical representation. We demonstrate these processes and solutions by presenting KaBOB (the Knowledge Base Of Biomedicine), a knowledge base of semantically integrated data from 18 prominent biomedical databases using common representations grounded in Open Biomedical Ontologies. An instance of KaBOB with data about humans and seven major model organisms can be built using on the order of 500 million RDF triples. All source code for building KaBOB is available under an open-source license. KaBOB is an integrated knowledge base of biomedical data representationally based in prominent, actively maintained Open Biomedical Ontologies, thus enabling queries of the underlying data in terms of biomedical concepts (e.g., genes and gene products, interactions and processes) rather than features of source-specific data schemas or file formats. KaBOB resolves many of the issues that routinely plague biomedical researchers intending to work with data from multiple data sources and provides a platform for ongoing data integration and development and for

  19. CTDB: An Integrated Chickpea Transcriptome Database for Functional and Applied Genomics.

    Directory of Open Access Journals (Sweden)

    Mohit Verma

    Full Text Available Chickpea is an important grain legume used as a rich source of protein in human diet. The narrow genetic diversity and limited availability of genomic resources are the major constraints in implementing breeding strategies and biotechnological interventions for genetic enhancement of chickpea. We developed an integrated Chickpea Transcriptome Database (CTDB, which provides the comprehensive web interface for visualization and easy retrieval of transcriptome data in chickpea. The database features many tools for similarity search, functional annotation (putative function, PFAM domain and gene ontology search and comparative gene expression analysis. The current release of CTDB (v2.0 hosts transcriptome datasets with high quality functional annotation from cultivated (desi and kabuli types and wild chickpea. A catalog of transcription factor families and their expression profiles in chickpea are available in the database. The gene expression data have been integrated to study the expression profiles of chickpea transcripts in major tissues/organs and various stages of flower development. The utilities, such as similarity search, ortholog identification and comparative gene expression have also been implemented in the database to facilitate comparative genomic studies among different legumes and Arabidopsis. Furthermore, the CTDB represents a resource for the discovery of functional molecular markers (microsatellites and single nucleotide polymorphisms between different chickpea types. We anticipate that integrated information content of this database will accelerate the functional and applied genomic research for improvement of chickpea. The CTDB web service is freely available at http://nipgr.res.in/ctdb.html.

  20. An object-oriented language-database integration model: The composition filters approach

    NARCIS (Netherlands)

    Aksit, Mehmet; Bergmans, Lodewijk; Vural, Sinan; Vural, S.

    1991-01-01

    This paper introduces a new model, based on so-called object-composition filters, that uniformly integrates database-like features into an object-oriented language. The focus is on providing persistent dynamic data structures, data sharing, transactions, multiple views and associative access,

  1. An Object-Oriented Language-Database Integration Model: The Composition-Filters Approach

    NARCIS (Netherlands)

    Aksit, Mehmet; Bergmans, Lodewijk; Vural, S.; Vural, Sinan; Lehrmann Madsen, O.

    1992-01-01

    This paper introduces a new model, based on so-called object-composition filters, that uniformly integrates database-like features into an object-oriented language. The focus is on providing persistent dynamic data structures, data sharing, transactions, multiple views and associative access,

  2. Psychological Contract Development: An Integration of Existing Knowledge to Form a Temporal Model

    Directory of Open Access Journals (Sweden)

    Kelly Windle

    2014-07-01

    Full Text Available The psychological contract has received substantial theoretical attention over the past two decades as a popular framework within which to examine contemporary employment relationships. Previous research mostly examines breach and violation of the psychological contract and its impact on employee organization outcomes. Few studies have employed longitudinal, prospective research designs to investigate the psychological contract and as a result, psychological contract content and formation are incompletely understood. It is argued that employment relationships may be better proactively managed with greater understanding of formation and changes in the psychological contract. We examine existing psychological contract literature to identify five key factors proposed to contribute to the formation of psychological contracts. We extend the current research by integrating these factors for the first time into a temporal model of psychological contract development.

  3. Critical assessment of human metabolic pathway databases: a stepping stone for future integration

    Directory of Open Access Journals (Sweden)

    Stobbe Miranda D

    2011-10-01

    Full Text Available Abstract Background Multiple pathway databases are available that describe the human metabolic network and have proven their usefulness in many applications, ranging from the analysis and interpretation of high-throughput data to their use as a reference repository. However, so far the various human metabolic networks described by these databases have not been systematically compared and contrasted, nor has the extent to which they differ been quantified. For a researcher using these databases for particular analyses of human metabolism, it is crucial to know the extent of the differences in content and their underlying causes. Moreover, the outcomes of such a comparison are important for ongoing integration efforts. Results We compared the genes, EC numbers and reactions of five frequently used human metabolic pathway databases. The overlap is surprisingly low, especially on reaction level, where the databases agree on 3% of the 6968 reactions they have combined. Even for the well-established tricarboxylic acid cycle the databases agree on only 5 out of the 30 reactions in total. We identified the main causes for the lack of overlap. Importantly, the databases are partly complementary. Other explanations include the number of steps a conversion is described in and the number of possible alternative substrates listed. Missing metabolite identifiers and ambiguous names for metabolites also affect the comparison. Conclusions Our results show that each of the five networks compared provides us with a valuable piece of the puzzle of the complete reconstruction of the human metabolic network. To enable integration of the networks, next to a need for standardizing the metabolite names and identifiers, the conceptual differences between the databases should be resolved. Considerable manual intervention is required to reach the ultimate goal of a unified and biologically accurate model for studying the systems biology of human metabolism. Our comparison

  4. Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database

    Directory of Open Access Journals (Sweden)

    Belmamoune Mounia

    2008-06-01

    Full Text Available The Gene Expression Management System (GEMS is a database system for patterns of gene expression. These patterns result from systematic whole-mount fluorescent in situ hybridization studies on zebrafish embryos. GEMS is an integrative platform that addresses one of the important challenges of developmental biology: how to integrate genetic data that underpin morphological changes during embryogenesis. Our motivation to build this system was by the need to be able to organize and compare multiple patterns of gene expression at tissue level. Integration with other developmental and biomolecular databases will further support our understanding of development. The GEMS operates in concert with a database containing a digital atlas of zebrafish embryo; this digital atlas of zebrafish development has been conceived prior to the expansion of the GEMS. The atlas contains 3D volume models of canonical stages of zebrafish development in which in each volume model element is annotated with an anatomical term. These terms are extracted from a formal anatomical ontology, i.e. the Developmental Anatomy Ontology of Zebrafish (DAOZ. In the GEMS, anatomical terms from this ontology together with terms from the Gene Ontology (GO are also used to annotate patterns of gene expression and in this manner providing mechanisms for integration and retrieval . The annotations are the glue for integration of patterns of gene expression in GEMS as well as in other biomolecular databases. At the one hand, zebrafish anatomy terminology allows gene expression data within GEMS to be integrated with phenotypical data in the 3D atlas of zebrafish development. At the other hand, GO terms extend GEMS expression patterns integration to a wide range of bioinformatics resources.

  5. Integrating UNIX workstation into existing online data acquisition systems for Fermilab experiments

    International Nuclear Information System (INIS)

    Oleynik, G.

    1991-03-01

    With the availability of cost effective computing prior from multiple vendors of UNIX workstations, experiments at Fermilab are adding such computers to their VMS based online data acquisition systems. In anticipation of this trend, we have extended the software products available in our widely used VAXONLINE and PANDA data acquisition software systems, to provide support for integrating these workstations into existing distributed online systems. The software packages we are providing pave the way for the smooth migration of applications from the current Data Acquisition Host and Monitoring computers running the VMS operating systems, to UNIX based computers of various flavors. We report on software for Online Event Distribution from VAXONLINE and PANDA, integration of Message Reporting Facilities, and a framework under UNIX for experiments to monitor and view the raw event data produced at any level in their DA system. We have developed software that allows host UNIX computers to communicate with intelligent front-end embedded read-out controllers and processor boards running the pSOS operating system. Both RS-232 and Ethernet control paths are supported. This enables calibration and hardware monitoring applications to be migrated to these platforms. 6 refs., 5 figs

  6. Integration of first-principles methods and crystallographic database searches for new ferroelectrics: Strategies and explorations

    International Nuclear Information System (INIS)

    Bennett, Joseph W.; Rabe, Karin M.

    2012-01-01

    In this concept paper, the development of strategies for the integration of first-principles methods with crystallographic database mining for the discovery and design of novel ferroelectric materials is discussed, drawing on the results and experience derived from exploratory investigations on three different systems: (1) the double perovskite Sr(Sb 1/2 Mn 1/2 )O 3 as a candidate semiconducting ferroelectric; (2) polar derivatives of schafarzikite MSb 2 O 4 ; and (3) ferroelectric semiconductors with formula M 2 P 2 (S,Se) 6 . A variety of avenues for further research and investigation are suggested, including automated structure type classification, low-symmetry improper ferroelectrics, and high-throughput first-principles searches for additional representatives of structural families with desirable functional properties. - Graphical abstract: Integration of first-principles methods with crystallographic database mining, for the discovery and design of novel ferroelectric materials, could potentially lead to new classes of multifunctional materials. Highlights: ► Integration of first-principles methods and database mining. ► Minor structural families with desirable functional properties. ► Survey of polar entries in the Inorganic Crystal Structural Database.

  7. VaProS: a database-integration approach for protein/genome information retrieval

    KAUST Repository

    Gojobori, Takashi; Ikeo, Kazuho; Katayama, Yukie; Kawabata, Takeshi; Kinjo, Akira R.; Kinoshita, Kengo; Kwon, Yeondae; Migita, Ohsuke; Mizutani, Hisashi; Muraoka, Masafumi; Nagata, Koji; Omori, Satoshi; Sugawara, Hideaki; Yamada, Daichi; Yura, Kei

    2016-01-01

    Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.

  8. VaProS: a database-integration approach for protein/genome information retrieval

    KAUST Repository

    Gojobori, Takashi

    2016-12-24

    Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.

  9. Automatic single questionnaire intensity (SQI, EMS98 scale) estimation using ranking models built on the existing BCSF database

    Science.gov (United States)

    Schlupp, A.; Sira, C.; Schmitt, K.; Schaming, M.

    2013-12-01

    In charge of intensity estimations in France, BCSF has collected and manually analyzed more than 47000 online individual macroseismic questionnaires since 2000 up to intensity VI. These macroseismic data allow us to estimate one SQI value (Single Questionnaire Intensity) for each form following the EMS98 scale. The reliability of the automatic intensity estimation is important as they are today used for automatic shakemaps communications and crisis management. Today, the automatic intensity estimation at BCSF is based on the direct use of thumbnails selected on a menu by the witnesses. Each thumbnail corresponds to an EMS-98 intensity value, allowing us to quickly issue an intensity map of the communal intensity by averaging the SQIs at each city. Afterwards an expert, to determine a definitive SQI, manually analyzes each form. This work is time consuming and not anymore suitable considering the increasing number of testimonies at BCSF. Nevertheless, it can take into account incoherent answers. We tested several automatic methods (USGS algorithm, Correlation coefficient, Thumbnails) (Sira et al. 2013, IASPEI) and compared them with 'expert' SQIs. These methods gave us medium score (between 50 to 60% of well SQI determined and 35 to 40% with plus one or minus one intensity degree). The best fit was observed with the thumbnails. Here, we present new approaches based on 3 statistical ranking methods as 1) Multinomial logistic regression model, 2) Discriminant analysis DISQUAL and 3) Support vector machines (SVMs). The two first methods are standard methods, while the third one is more recent. Theses methods could be applied because the BCSF has already in his database more then 47000 forms and because their questions and answers are well adapted for a statistical analysis. The ranking models could then be used as automatic method constrained on expert analysis. The performance of the automatic methods and the reliability of the estimated SQI can be evaluated thanks to

  10. Quality controls in integrative approaches to detect errors and inconsistencies in biological databases

    Directory of Open Access Journals (Sweden)

    Ghisalberti Giorgio

    2010-12-01

    Full Text Available Numerous biomolecular data are available, but they are scattered in many databases and only some of them are curated by experts. Most available data are computationally derived and include errors and inconsistencies. Effective use of available data in order to derive new knowledge hence requires data integration and quality improvement. Many approaches for data integration have been proposed. Data warehousing seams to be the most adequate when comprehensive analysis of integrated data is required. This makes it the most suitable also to implement comprehensive quality controls on integrated data. We previously developed GFINDer (http://www.bioinformatics.polimi.it/GFINDer/, a web system that supports scientists in effectively using available information. It allows comprehensive statistical analysis and mining of functional and phenotypic annotations of gene lists, such as those identified by high-throughput biomolecular experiments. GFINDer backend is composed of a multi-organism genomic and proteomic data warehouse (GPDW. Within the GPDW, several controlled terminologies and ontologies, which describe gene and gene product related biomolecular processes, functions and phenotypes, are imported and integrated, together with their associations with genes and proteins of several organisms. In order to ease maintaining updated the GPDW and to ensure the best possible quality of data integrated in subsequent updating of the data warehouse, we developed several automatic procedures. Within them, we implemented numerous data quality control techniques to test the integrated data for a variety of possible errors and inconsistencies. Among other features, the implemented controls check data structure and completeness, ontological data consistency, ID format and evolution, unexpected data quantification values, and consistency of data from single and multiple sources. We use the implemented controls to analyze the quality of data available from several

  11. MAGIC Database and Interfaces: An Integrated Package for Gene Discovery and Expression

    Directory of Open Access Journals (Sweden)

    Lee H. Pratt

    2006-03-01

    Full Text Available The rapidly increasing rate at which biological data is being produced requires a corresponding growth in relational databases and associated tools that can help laboratories contend with that data. With this need in mind, we describe here a Modular Approach to a Genomic, Integrated and Comprehensive (MAGIC Database. This Oracle 9i database derives from an initial focus in our laboratory on gene discovery via production and analysis of expressed sequence tags (ESTs, and subsequently on gene expression as assessed by both EST clustering and microarrays. The MAGIC Gene Discovery portion of the database focuses on information derived from DNA sequences and on its biological relevance. In addition to MAGIC SEQ-LIMS, which is designed to support activities in the laboratory, it contains several additional subschemas. The latter include MAGIC Admin for database administration, MAGIC Sequence for sequence processing as well as sequence and clone attributes, MAGIC Cluster for the results of EST clustering, MAGIC Polymorphism in support of microsatellite and single-nucleotide-polymorphism discovery, and MAGIC Annotation for electronic annotation by BLAST and BLAT. The MAGIC Microarray portion is a MIAME-compliant database with two components at present. These are MAGIC Array-LIMS, which makes possible remote entry of all information into the database, and MAGIC Array Analysis, which provides data mining and visualization. Because all aspects of interaction with the MAGIC Database are via a web browser, it is ideally suited not only for individual research laboratories but also for core facilities that serve clients at any distance.

  12. Towards the integration of sustainable infrastructure into the existing built environment

    Directory of Open Access Journals (Sweden)

    Dimitrijević Branka

    2013-01-01

    Full Text Available The construction sector in the United Kingdom is dominated by small and medium size enterprises (SMEs which have less than 250 employees and usually do not have research capacities to develop a range of low carbon innovations applicable in the construction sector. Various European and national funding programmes have addressed this problem by providing funding for research collaboration between universities and SMEs. The paper provides a selection of the outputs of academic/industry research, undertaken by seven Scottish universities through the project CIC Start Online from September 2009 until February 2013, related to low carbon planning, building design, technologies, construction, refurbishment and performance. The studies either contributed to the further development of existing products or processes, or tested new products or processes, often developed for a specific project with a potential for application in future projects. Online dissemination of the project outcomes has assisted in attracting membership across Scotland, the United Kingdom and internationally. Along with the low carbon building products and technologies, new low carbon infrastructure is being planned and developed in order to provide connections and services for energy generation from renewables, energy storage and decentralised distribution, water management (harvesting, saving and reuse, waste management (reduction, reuse and to-energy, transport (electric vehicles, cycling and walking and information communication technology (ICT for monitoring and managing infrastructure systems. The second part of the paper outlines how innovations for integration of sustainable infrastructure into the existing built environment will be supported through the follow-on joint project of nine Scottish universities, named Mainstreaming Innovation.

  13. Use of Graph Database for the Integration of Heterogeneous Biological Data.

    Science.gov (United States)

    Yoon, Byoung-Ha; Kim, Seon-Kyu; Kim, Seon-Young

    2017-03-01

    Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data.

  14. A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila

    Directory of Open Access Journals (Sweden)

    Parrish Jodi R

    2006-04-01

    Full Text Available Abstract Background Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis. One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to many existing and emerging data sets. Description Here we describe a comprehensive database of Drosophila gene and protein interactions collected from a variety of sources, including low and high throughput screens, genetic interactions, and computational predictions. We also present a program for exploring multiple interaction data sets and for combining data from different sources. The program, referred to as the Interaction Map (IM Browser, is a web-based application for searching and visualizing interaction data stored in a relational database system. Use of the application requires no downloads and minimal user configuration or training, thereby enabling rapid initial access to interaction data. IM Browser was designed to readily accommodate and integrate new types of interaction data as it becomes available. Moreover, all information associated with interaction measurements or predictions and the genes or proteins involved are accessible to the user. This allows combined searches and analyses based on either common or technique-specific attributes

  15. Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

    Science.gov (United States)

    Chiba, Hirokazu; Nishide, Hiroyo; Uchiyama, Ikuo

    2015-01-01

    Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic Web technology, aiming at the integration of numerous genomic data and various types of biological information. To formalize the structure of the ortholog information in the Semantic Web, we have constructed the Ortholog Ontology (OrthO). While the OrthO is a compact ontology for general use, it is designed to be extended to the description of database-specific concepts. On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) and made it available through the SPARQL endpoint, which accepts arbitrary queries specified by users. In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub. Besides, the ortholog information from different data sources can be compared with each other using the OrthO as a shared ontology. Here we show some examples demonstrating that the ortholog information described in RDF can be used to link various biological data such as taxonomy information and Gene Ontology. Thus, the ortholog database using the Semantic Web technology can contribute to biological knowledge discovery through integrative data analysis.

  16. The Kembs project: environmental integration of a large existing hydropower scheme

    International Nuclear Information System (INIS)

    Garnier, Alain; Barillier, Agnes

    2015-01-01

    The environment was a major issue for the Kembs re-licensing process on the upper Rhine River. Since 1932, Kembs dam derives water from the Rhine River to the 'Grand Canal d'Alsace' (GCA) which is equipped with four hydropower plants (max. diverted flow: 1400 m 3 /s, 630 MW, 3760 GWh/y). The Old Rhine River downstream of the dam is 50 km long and has been strongly affected by works (dikes) since the 19. century for flood protection and navigation, and then by the construction of the dam. Successive engineering works induced morphological simplification and stabilization of the channel pattern from a formerly braided form to a single incised channel, generating ecological alterations. As the Kembs hydroelectric scheme concerns three countries (France, Germany and Switzerland) with various regulations and views on how to manage with environment, EDF undertook an integrated environmental approach instead of a strict 'impact/mitigation' balance that took 10 years to develop. Therefore, the project simultaneously acts on complementary compartments of the aquatic, riparian and terrestrial environment, to benefit from the synergies that exist between them; a new power plant (8,5 MW, 28 GWh/y) is built to limit the energetic losses and to ensure various functions thereby increasing the overall environmental gain. (authors)

  17. Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize.

    Science.gov (United States)

    Kelley, Rowena Y; Gresham, Cathy; Harper, Jonathan; Bridges, Susan M; Warburton, Marilyn L; Hawkins, Leigh K; Pechanova, Olga; Peethambaran, Bela; Pechan, Tibor; Luthe, Dawn S; Mylroie, J E; Ankala, Arunkanth; Ozkan, Seval; Henry, W B; Williams, W P

    2010-10-07

    Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database

  18. Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

    Science.gov (United States)

    Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

    2015-01-01

    The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/. © The Author(s) 2015. Published by Oxford University Press.

  19. Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow.

    Science.gov (United States)

    Stockton, David B; Santamaria, Fidel

    2017-10-01

    We developed software tools to download, extract features, and organize the Cell Types Database from the Allen Brain Institute (ABI) in order to integrate its whole cell patch clamp characterization data into the automated modeling/data analysis cycle. To expand the potential user base we employed both Python and MATLAB. The basic set of tools downloads selected raw data and extracts cell, sweep, and spike features, using ABI's feature extraction code. To facilitate data manipulation we added a tool to build a local specialized database of raw data plus extracted features. Finally, to maximize automation, we extended our NeuroManager workflow automation suite to include these tools plus a separate investigation database. The extended suite allows the user to integrate ABI experimental and modeling data into an automated workflow deployed on heterogeneous computer infrastructures, from local servers, to high performance computing environments, to the cloud. Since our approach is focused on workflow procedures our tools can be modified to interact with the increasing number of neuroscience databases being developed to cover all scales and properties of the nervous system.

  20. dbPAF: an integrative database of protein phosphorylation in animals and fungi.

    Science.gov (United States)

    Ullah, Shahid; Lin, Shaofeng; Xu, Yang; Deng, Wankun; Ma, Lili; Zhang, Ying; Liu, Zexian; Xue, Yu

    2016-03-24

    Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. Recent progresses in phosphoproteomic identifications have generated a flood of phosphorylation sites, while the integration of these sites is an urgent need. In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. Based on the new data set, we computationally detected significantly over-represented sequence motifs around phosphorylation sites, predicted potential kinases that are responsible for the modification of collected phospho-sites, and evolutionarily analyzed phosphorylation conservation states across different species. Besides to be largely consistent with previous reports, our results also proposed new features of phospho-regulation. Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. The dbPAF database was implemented in PHP + MySQL and freely available at http://dbpaf.biocuckoo.org.

  1. Integration of the ATLAS tag database with data management and analysis components

    International Nuclear Information System (INIS)

    Cranshaw, J; Malon, D; Doyle, A T; Kenyon, M J; McGlone, H; Nicholson, C

    2008-01-01

    The ATLAS Tag Database is an event-level metadata system, designed to allow efficient identification and selection of interesting events for user analysis. By making first-level cuts using queries on a relational database, the size of an analysis input sample could be greatly reduced and thus the time taken for the analysis reduced. Deployment of such a Tag database is underway, but to be most useful it needs to be integrated with the distributed data management (DDM) and distributed analysis (DA) components. This means addressing the issue that the DDM system at ATLAS groups files into datasets for scalability and usability, whereas the Tag Database points to events in files. It also means setting up a system which could prepare a list of input events and use both the DDM and DA systems to run a set of jobs. The ATLAS Tag Navigator Tool (TNT) has been developed to address these issues in an integrated way and provide a tool that the average physicist can use. Here, the current status of this work is presented and areas of future work are highlighted

  2. Integration of the ATLAS tag database with data management and analysis components

    Energy Technology Data Exchange (ETDEWEB)

    Cranshaw, J; Malon, D [Argonne National Laboratory, Argonne, IL 60439 (United States); Doyle, A T; Kenyon, M J; McGlone, H; Nicholson, C [Department of Physics and Astronomy, University of Glasgow, Glasgow, G12 8QQ, Scotland (United Kingdom)], E-mail: c.nicholson@physics.gla.ac.uk

    2008-07-15

    The ATLAS Tag Database is an event-level metadata system, designed to allow efficient identification and selection of interesting events for user analysis. By making first-level cuts using queries on a relational database, the size of an analysis input sample could be greatly reduced and thus the time taken for the analysis reduced. Deployment of such a Tag database is underway, but to be most useful it needs to be integrated with the distributed data management (DDM) and distributed analysis (DA) components. This means addressing the issue that the DDM system at ATLAS groups files into datasets for scalability and usability, whereas the Tag Database points to events in files. It also means setting up a system which could prepare a list of input events and use both the DDM and DA systems to run a set of jobs. The ATLAS Tag Navigator Tool (TNT) has been developed to address these issues in an integrated way and provide a tool that the average physicist can use. Here, the current status of this work is presented and areas of future work are highlighted.

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

    International Nuclear Information System (INIS)

    Quock, D.E.R.; Cianciarulo, M.B.

    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.

  4. The Future of Asset Management for Human Space Exploration: Supply Classification and an Integrated Database

    Science.gov (United States)

    Shull, Sarah A.; Gralla, Erica L.; deWeck, Olivier L.; Shishko, Robert

    2006-01-01

    One of the major logistical challenges in human space exploration is asset management. This paper presents observations on the practice of asset management in support of human space flight to date and discusses a functional-based supply classification and a framework for an integrated database that could be used to improve asset management and logistics for human missions to the Moon, Mars and beyond.

  5. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

    OpenAIRE

    May, P.; Christian, J.O.; Kempa, S.; Walther, D.

    2009-01-01

    Abstract Background The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results In the fra...

  6. CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002

    OpenAIRE

    Yang, Yaohua; Feng, Jie; Li, Tao; Ge, Feng; Zhao, Jindong

    2015-01-01

    Cyanobacteria are an important group of organisms that carry out oxygenic photosynthesis and play vital roles in both the carbon and nitrogen cycles of the Earth. The annotated genome of Synechococcus sp. PCC 7002, as an ideal model cyanobacterium, is available. A series of transcriptomic and proteomic studies of Synechococcus sp. PCC 7002 cells grown under different conditions have been reported. However, no database of such integrated omics studies has been constructed. Here we present Cyan...

  7. Automated granularity to integrate digital information: the "Antarctic Treaty Searchable Database" case study

    Directory of Open Access Journals (Sweden)

    Paul Arthur Berkman

    2006-06-01

    Full Text Available Access to information is necessary, but not sufficient in our digital era. The challenge is to objectively integrate digital resources based on user-defined objectives for the purpose of discovering information relationships that facilitate interpretations and decision making. The Antarctic Treaty Searchable Database (http://aspire.nvi.net, which is in its sixth edition, provides an example of digital integration based on the automated generation of information granules that can be dynamically combined to reveal objective relationships within and between digital information resources. This case study further demonstrates that automated granularity and dynamic integration can be accomplished simply by utilizing the inherent structure of the digital information resources. Such information integration is relevant to library and archival programs that require long-term preservation of authentic digital resources.

  8. Integrating Environmental and Human Health Databases in the Great Lakes Basin: Themes, Challenges and Future Directions

    Directory of Open Access Journals (Sweden)

    Kate L. Bassil

    2015-03-01

    Full Text Available Many government, academic and research institutions collect environmental data that are relevant to understanding the relationship between environmental exposures and human health. Integrating these data with health outcome data presents new challenges that are important to consider to improve our effective use of environmental health information. Our objective was to identify the common themes related to the integration of environmental and health data, and suggest ways to address the challenges and make progress toward more effective use of data already collected, to further our understanding of environmental health associations in the Great Lakes region. Environmental and human health databases were identified and reviewed using literature searches and a series of one-on-one and group expert consultations. Databases identified were predominantly environmental stressors databases, with fewer found for health outcomes and human exposure. Nine themes or factors that impact integration were identified: data availability, accessibility, harmonization, stakeholder collaboration, policy and strategic alignment, resource adequacy, environmental health indicators, and data exchange networks. The use and cost effectiveness of data currently collected could be improved by strategic changes to data collection and access systems to provide better opportunities to identify and study environmental exposures that may impact human health.

  9. Integrated data acquisition, storage, retrieval and processing using the COMPASS DataBase (CDB)

    Energy Technology Data Exchange (ETDEWEB)

    Urban, J., E-mail: urban@ipp.cas.cz [Institute of Plasma Physics AS CR, v.v.i., Za Slovankou 3, 182 00 Praha 8 (Czech Republic); Pipek, J.; Hron, M. [Institute of Plasma Physics AS CR, v.v.i., Za Slovankou 3, 182 00 Praha 8 (Czech Republic); Janky, F.; Papřok, R.; Peterka, M. [Institute of Plasma Physics AS CR, v.v.i., Za Slovankou 3, 182 00 Praha 8 (Czech Republic); Department of Surface and Plasma Science, Faculty of Mathematics and Physics, Charles University in Prague, V Holešovičkách 2, 180 00 Praha 8 (Czech Republic); Duarte, A.S. [Instituto de Plasmas e Fusão Nuclear, Instituto Superior Técnico, Universidade Técnica de Lisboa, 1049-001 Lisboa (Portugal)

    2014-05-15

    Highlights: • CDB is used as a new data storage solution for the COMPASS tokamak. • The software is light weight, open, fast and easily extensible and scalable. • CDB seamlessly integrates with any data acquisition system. • Rich metadata are stored for physics signals. • Data can be processed automatically, based on dependence rules. - Abstract: We present a complex data handling system for the COMPASS tokamak, operated by IPP ASCR Prague, Czech Republic [1]. The system, called CDB (COMPASS DataBase), integrates different data sources as an assortment of data acquisition hardware and software from different vendors is used. Based on widely available open source technologies wherever possible, CDB is vendor and platform independent and it can be easily scaled and distributed. The data is directly stored and retrieved using a standard NAS (Network Attached Storage), hence independent of the particular technology; the description of the data (the metadata) is recorded in a relational database. Database structure is general and enables the inclusion of multi-dimensional data signals in multiple revisions (no data is overwritten). This design is inherently distributed as the work is off-loaded to the clients. Both NAS and database can be implemented and optimized for fast local access as well as secure remote access. CDB is implemented in Python language; bindings for Java, C/C++, IDL and Matlab are provided. Independent data acquisitions systems as well as nodes managed by FireSignal [2] are all integrated using CDB. An automated data post-processing server is a part of CDB. Based on dependency rules, the server executes, in parallel if possible, prescribed post-processing tasks.

  10. IntPath--an integrated pathway gene relationship database for model organisms and important pathogens.

    Science.gov (United States)

    Zhou, Hufeng; Jin, Jingjing; Zhang, Haojun; Yi, Bo; Wozniak, Michal; Wong, Limsoon

    2012-01-01

    Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Pathway gene relationships are crucial information for guidance, prediction, reference and assessment in biochemistry, computational biology, and medicine. Many well-established databases--e.g., KEGG, WikiPathways, and BioCyc--are dedicated to collecting pathway data for public access. However, the effectiveness of these databases is hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. In this paper, we overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc). We build a database that not only hosts our integrated pathway gene relationship data for public access but also maintains the necessary updates in the long run. This public repository is named IntPath (Integrated Pathway gene relationship database for model organisms and important pathogens). Four organisms--S. cerevisiae, M. tuberculosis H37Rv, H. Sapiens and M. musculus--are included in this version (V2.0) of IntPath. IntPath uses the "full unification" approach to ensure no deletion and no introduced noise in this process. Therefore, IntPath contains much richer pathway-gene and pathway-gene pair relationships and much larger number of non-redundant genes and gene pairs than any of the single-source databases. The gene relationships of each gene (measured by average node degree) per pathway are significantly richer. The gene relationships in each pathway (measured by average number of gene pairs per pathway) are also considerably richer in the integrated pathways. Moderate manual curation are involved to get rid of errors and noises from source data (e.g., the gene ID errors in WikiPathways and

  11. Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

    Directory of Open Access Journals (Sweden)

    Bradley Michael E

    2006-02-01

    Full Text Available Abstract Background When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. Results The precomputed Magnum database offers a solution to this problem for ca. 1,800 full-length protein families with at least one crystal structure. The Magnum deliverables include 1 multiple sequence alignments, 2 mapping of alignment sites to crystal structure sites, 3 phylogenetic trees, 4 inferred ancestral sequences at internal tree nodes, and 5 amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accurate models of how proteins divergently evolve, or genealogies, and correctly integrated these with the structural data. To demonstrate Magnum's capabilities, we asked for amino acid replacements requiring three nucleotide substitutions, located at internal protein structure sites, and occurring on short phylogenetic tree branches. In the cellular retinoid binding protein family a site that potentially modulates ligand binding affinity was discovered. Recruitment of cellular retinol binding protein to function as a lens crystallin in the diurnal gecko afforded another opportunity to showcase the predictive value of a browsable database containing branch replacement patterns integrated with protein structures. Conclusion We integrated two areas of protein science, evolution and structure, on a large scale and created a precomputed database, known as Magnum, which is the first freely available resource of its kind. Magnum provides evolutionary and structural

  12. PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine.

    Directory of Open Access Journals (Sweden)

    Ji-Hyun Lee

    Full Text Available Despite the growing attention given to Traditional Medicine (TM worldwide, there is no well-known, publicly available, integrated bio-pharmacological Traditional Korean Medicine (TKM database for researchers in drug discovery. In this study, we have constructed PharmDB-K, which offers comprehensive information relating to TKM-associated drugs (compound, disease indication, and protein relationships. To explore the underlying molecular interaction of TKM, we integrated fourteen different databases, six Pharmacopoeias, and literature, and established a massive bio-pharmacological network for TKM and experimentally validated some cases predicted from the PharmDB-K analyses. Currently, PharmDB-K contains information about 262 TKMs, 7,815 drugs, 3,721 diseases, 32,373 proteins, and 1,887 side effects. One of the unique sets of information in PharmDB-K includes 400 indicator compounds used for standardization of herbal medicine. Furthermore, we are operating PharmDB-K via phExplorer (a network visualization software and BioMart (a data federation framework for convenient search and analysis of the TKM network. Database URL: http://pharmdb-k.org, http://biomart.i-pharm.org.

  13. MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore.

    Science.gov (United States)

    Ren, Jian; Liu, Zexian; Gao, Xinjiao; Jin, Changjiang; Ye, Mingliang; Zou, Hanfa; Wen, Longping; Zhang, Zhaolei; Xue, Yu; Yao, Xuebiao

    2010-01-01

    During cell division/mitosis, a specific subset of proteins is spatially and temporally assembled into protein super complexes in three distinct regions, i.e. centrosome/spindle pole, kinetochore/centromere and midbody/cleavage furrow/phragmoplast/bud neck, and modulates cell division process faithfully. Although many experimental efforts have been carried out to investigate the characteristics of these proteins, no integrated database was available. Here, we present the MiCroKit database (http://microkit.biocuckoo.org) of proteins that localize in midbody, centrosome and/or kinetochore. We collected into the MiCroKit database experimentally verified microkit proteins from the scientific literature that have unambiguous supportive evidence for subcellular localization under fluorescent microscope. The current version of MiCroKit 3.0 provides detailed information for 1489 microkit proteins from seven model organisms, including Saccharomyces cerevisiae, Schizasaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Xenopus laevis, Mus musculus and Homo sapiens. Moreover, the orthologous information was provided for these microkit proteins, and could be a useful resource for further experimental identification. The online service of MiCroKit database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0).

  14. Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing

    Science.gov (United States)

    Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E.; de Magalhães, João Pedro

    2013-01-01

    The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology. PMID:23193293

  15. FY1995 transduction method and CAD database systems for integrated design; 1995 nendo transduction ho to CAD database togo sekkei shien system

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    Transduction method developed by the research coordinator and Prof. Muroga is one of the most popular methods to design large-scale integrated circuits, and thus used by major design tool companies in USA and Japan. The major objectives of the research is to improve capability and utilize its reusable property by combining with CAD databases. Major results of the project is as follows, (1) Improvement of Transduction method : Efficiency, capability and the maximum circuit size are improved. Error compensation method is also improved. (2) Applications to new logic elements : Transduction method is modified to cope with wired logic and FPGAs. (3) CAD databases : One of the major advantages of Transduction methods is 'reusability' of already designed circuits. It is suitable to combine with CAD databases. We design CAD databases suitable for cooperative design using Transduction method. (4) Program development : Programs for Windows95 and developed for distribution. (NEDO)

  16. FY1995 transduction method and CAD database systems for integrated design; 1995 nendo transduction ho to CAD database togo sekkei shien system

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    Transduction method developed by the research coordinator and Prof. Muroga is one of the most popular methods to design large-scale integrated circuits, and thus used by major design tool companies in USA and Japan. The major objectives of the research is to improve capability and utilize its reusable property by combining with CAD databases. Major results of the project is as follows, (1) Improvement of Transduction method : Efficiency, capability and the maximum circuit size are improved. Error compensation method is also improved. (2) Applications to new logic elements : Transduction method is modified to cope with wired logic and FPGAs. (3) CAD databases : One of the major advantages of Transduction methods is 'reusability' of already designed circuits. It is suitable to combine with CAD databases. We design CAD databases suitable for cooperative design using Transduction method. (4) Program development : Programs for Windows95 and developed for distribution. (NEDO)

  17. MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

    Science.gov (United States)

    Hayashi, Takanori; Matsuzaki, Yuri; Yanagisawa, Keisuke; Ohue, Masahito; Akiyama, Yutaka

    2018-05-08

    Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on

  18. BEopt-CA (Ex): A Tool for Optimal Integration of EE, DR and PV in Existing California Homes

    Energy Technology Data Exchange (ETDEWEB)

    Christensen, Craig [National Renewable Energy Lab. (NREL), Golden, CO (United States); Horowitz, Scott [National Renewable Energy Lab. (NREL), Golden, CO (United States); Maguire, Jeff [National Renewable Energy Lab. (NREL), Golden, CO (United States); Velasco, Paulo Tabrares [National Renewable Energy Lab. (NREL), Golden, CO (United States); Springer, David [Davis Energy Group, Davis, CA (United States); Coates, Peter [Davis Energy Group, Davis, CA (United States); Bell, Christy [Davis Energy Group, Davis, CA (United States); Price, Snuller [Energy & Environmental Economics, San Francisco, CA (United States); Sreedharan, Priya [Energy & Environmental Economics, San Francisco, CA (United States); Pickrell, Katie [Energy & Environmental Economics, San Francisco, CA (United States)

    2014-04-01

    This project targeted the development of a software tool, BEopt-CA (Ex) (Building Energy Optimization Tool for California Existing Homes), that aims to facilitate balanced integration of energy efficiency (EE), demand response (DR), and photovoltaics (PV) in the residential retrofit1 market. The intent is to provide utility program managers and contractors in the EE/DR/PV marketplace with a means of balancing the integration of EE, DR, and PV

  19. Neutron metrology file NMF-90. An integrated database for performing neutron spectrum adjustment calculations

    International Nuclear Information System (INIS)

    Kocherov, N.P.

    1996-01-01

    The Neutron Metrology File NMF-90 is an integrated database for performing neutron spectrum adjustment (unfolding) calculations. It contains 4 different adjustment codes, the dosimetry reaction cross-section library IRDF-90/NMF-G with covariances files, 6 input data sets for reactor benchmark neutron fields and a number of utility codes for processing and plotting the input and output data. The package consists of 9 PC HD diskettes and manuals for the codes. It is distributed by the Nuclear Data Section of the IAEA on request free of charge. About 10 MB of diskspace is needed to install and run a typical reactor neutron dosimetry unfolding problem. (author). 8 refs

  20. Planning the future of JPL's management and administrative support systems around an integrated database

    Science.gov (United States)

    Ebersole, M. M.

    1983-01-01

    JPL's management and administrative support systems have been developed piece meal and without consistency in design approach over the past twenty years. These systems are now proving to be inadequate to support effective management of tasks and administration of the Laboratory. New approaches are needed. Modern database management technology has the potential for providing the foundation for more effective administrative tools for JPL managers and administrators. Plans for upgrading JPL's management and administrative systems over a six year period evolving around the development of an integrated management and administrative data base are discussed.

  1. Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets

    Directory of Open Access Journals (Sweden)

    Lemoine Nicholas R

    2007-11-01

    Full Text Available Abstract Background Pancreatic cancer is the 5th leading cause of cancer death in both males and females. In recent years, a wealth of gene and protein expression studies have been published broadening our understanding of pancreatic cancer biology. Due to the explosive growth in publicly available data from multiple different sources it is becoming increasingly difficult for individual researchers to integrate these into their current research programmes. The Pancreatic Expression database, a generic web-based system, is aiming to close this gap by providing the research community with an open access tool, not only to mine currently available pancreatic cancer data sets but also to include their own data in the database. Description Currently, the database holds 32 datasets comprising 7636 gene expression measurements extracted from 20 different published gene or protein expression studies from various pancreatic cancer types, pancreatic precursor lesions (PanINs and chronic pancreatitis. The pancreatic data are stored in a data management system based on the BioMart technology alongside the human genome gene and protein annotations, sequence, homologue, SNP and antibody data. Interrogation of the database can be achieved through both a web-based query interface and through web services using combined criteria from pancreatic (disease stages, regulation, differential expression, expression, platform technology, publication and/or public data (antibodies, genomic region, gene-related accessions, ontology, expression patterns, multi-species comparisons, protein data, SNPs. Thus, our database enables connections between otherwise disparate data sources and allows relatively simple navigation between all data types and annotations. Conclusion The database structure and content provides a powerful and high-speed data-mining tool for cancer research. It can be used for target discovery i.e. of biomarkers from body fluids, identification and analysis

  2. Integrating query of relational and textual data in clinical databases: a case study.

    Science.gov (United States)

    Fisk, John M; Mutalik, Pradeep; Levin, Forrest W; Erdos, Joseph; Taylor, Caroline; Nadkarni, Prakash

    2003-01-01

    The authors designed and implemented a clinical data mart composed of an integrated information retrieval (IR) and relational database management system (RDBMS). Using commodity software, which supports interactive, attribute-centric text and relational searches, the mart houses 2.8 million documents that span a five-year period and supports basic IR features such as Boolean searches, stemming, and proximity and fuzzy searching. Results are relevance-ranked using either "total documents per patient" or "report type weighting." Non-curated medical text has a significant degree of malformation with respect to spelling and punctuation, which creates difficulties for text indexing and searching. Presently, the IR facilities of RDBMS packages lack the features necessary to handle such malformed text adequately. A robust IR+RDBMS system can be developed, but it requires integrating RDBMSs with third-party IR software. RDBMS vendors need to make their IR offerings more accessible to non-programmers.

  3. Integrated Storage and Management of Vector and Raster Data Based on Oracle Database

    Directory of Open Access Journals (Sweden)

    WU Zheng

    2017-05-01

    Full Text Available At present, there are many problems in the storage and management of multi-source heterogeneous spatial data, such as the difficulty of transferring, the lack of unified storage and the low efficiency. By combining relational database and spatial data engine technology, an approach for integrated storage and management of vector and raster data is proposed on the basis of Oracle in this paper. This approach establishes an integrated storage model on vector and raster data and optimizes the retrieval mechanism at first, then designs a framework for the seamless data transfer, finally realizes the unified storage and efficient management of multi-source heterogeneous data. By comparing experimental results with the international leading similar software ArcSDE, it is proved that the proposed approach has higher data transfer performance and better query retrieval efficiency.

  4. CPLA 1.0: an integrated database of protein lysine acetylation.

    Science.gov (United States)

    Liu, Zexian; Cao, Jun; Gao, Xinjiao; Zhou, Yanhong; Wen, Longping; Yang, Xiangjiao; Yao, Xuebiao; Ren, Jian; Xue, Yu

    2011-01-01

    As a reversible post-translational modification (PTM) discovered decades ago, protein lysine acetylation was known for its regulation of transcription through the modification of histones. Recent studies discovered that lysine acetylation targets broad substrates and especially plays an essential role in cellular metabolic regulation. Although acetylation is comparable with other major PTMs such as phosphorylation, an integrated resource still remains to be developed. In this work, we presented the compendium of protein lysine acetylation (CPLA) database for lysine acetylated substrates with their sites. From the scientific literature, we manually collected 7151 experimentally identified acetylation sites in 3311 targets. We statistically studied the regulatory roles of lysine acetylation by analyzing the Gene Ontology (GO) and InterPro annotations. Combined with protein-protein interaction information, we systematically discovered a potential human lysine acetylation network (HLAN) among histone acetyltransferases (HATs), substrates and histone deacetylases (HDACs). In particular, there are 1862 triplet relationships of HAT-substrate-HDAC retrieved from the HLAN, at least 13 of which were previously experimentally verified. The online services of CPLA database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0). The CPLA database is freely available for all users at: http://cpla.biocuckoo.org.

  5. EVpedia: an integrated database of high-throughput data for systemic analyses of extracellular vesicles

    Directory of Open Access Journals (Sweden)

    Dae-Kyum Kim

    2013-03-01

    Full Text Available Secretion of extracellular vesicles is a general cellular activity that spans the range from simple unicellular organisms (e.g. archaea; Gram-positive and Gram-negative bacteria to complex multicellular ones, suggesting that this extracellular vesicle-mediated communication is evolutionarily conserved. Extracellular vesicles are spherical bilayered proteolipids with a mean diameter of 20–1,000 nm, which are known to contain various bioactive molecules including proteins, lipids, and nucleic acids. Here, we present EVpedia, which is an integrated database of high-throughput datasets from prokaryotic and eukaryotic extracellular vesicles. EVpedia provides high-throughput datasets of vesicular components (proteins, mRNAs, miRNAs, and lipids present on prokaryotic, non-mammalian eukaryotic, and mammalian extracellular vesicles. In addition, EVpedia also provides an array of tools, such as the search and browse of vesicular components, Gene Ontology enrichment analysis, network analysis of vesicular proteins and mRNAs, and a comparison of vesicular datasets by ortholog identification. Moreover, publications on extracellular vesicle studies are listed in the database. This free web-based database of EVpedia (http://evpedia.info might serve as a fundamental repository to stimulate the advancement of extracellular vesicle studies and to elucidate the novel functions of these complex extracellular organelles.

  6. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

    Science.gov (United States)

    Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Naville, Magali; Nitta, Kazuhiro R; Piette, Jacques; Reeves, Wendy; Scornavacca, Céline; Simion, Paul; Vincentelli, Renaud; Bellec, Maelle; Aicha, Sameh Ben; Fagotto, Marie; Guéroult-Bellone, Marion; Haeussler, Maximilian; Jacox, Edwin; Lowe, Elijah K; Mendez, Mickael; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Brown, C Titus; Cambillau, Christian; Christiaen, Lionel; Delsuc, Frédéric; Douzery, Emmanuel; Dumollard, Rémi; Kusakabe, Takehiro; Nakai, Kenta; Nishida, Hiroki; Satou, Yutaka; Swalla, Billie; Veeman, Michael; Volff, Jean-Nicolas; Lemaire, Patrick

    2018-01-04

    ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Work-life integration in neuropsychology: a review of the existing literature and preliminary recommendations.

    Science.gov (United States)

    Feigon, Maia; Block, Cady; Guidotti Breting, Leslie; Boxley, Laura; Dawson, Erica; Cobia, Derin

    2018-02-01

    The purpose of the current review paper is to identify and describe challenges to work-life integration in neuropsychology, and from this review extrapolate an initial set of recommendations and present a set of scenarios in which the recommendations might apply in the hopes of improving quality of life for current and prospective neuropsychologists. Specific areas of focus include diversity, early and mid-career transitions, and potential barriers to advancement in specific practice settings. A broad review was conducted of extant literature on work-life integration. There is scant scientific literature in this area that is specific to neuropsychologists, or even psychology as a whole. Subsequently, the majority of this review was collected from more developed literatures in business and medical fields. The authors then provided recommendations based on experiences in their respective careers. Attempts were made to promote generalizability of recommendations for neuropsychologists in different settings. Evidence supports a potentially adverse impact on quality of life and overall life satisfaction when work and personal lives conflict. This manuscript identifies some of the potential risks when work and life responsibilities are not well integrated. It is anticipated this will serve as a catalyst for future studies on work-life integration in the field of neuropsychology, specifically.

  8. Integration of PV modules in existing Romanian buildings from rural areas

    Energy Technology Data Exchange (ETDEWEB)

    Fara, S.; Finta, D. [IPA SA Research Development, Engineering and Manufacturing for Automation Equipment and Systems, Bucharest (Romania); Fara, L.; Comaneci, D. [Polytechnic Univ. of Bucharest (Romania); Dabija, A.M. [Univ. of Architecture and Urbanism Ion Mincu, Bucharest (Romania); Tulcan-Paulescu, E. [West Univ. of Timisoara, Timisoara (Romania)

    2010-07-01

    Romania has launched a national research project to promote the use of distributed solar architecture and the use of BIPV systems. These systems include solar tunnels and active solar photovoltaic (PV) systems installed on the roofs and facades of buildings in rural areas. In contrast to other EU states, Romania does not have a photovoltaic building construction branch. The number of isolated cases are insufficient to identify a starting point regarding the PV market in the building industry. The main objective of the project is to demonstrate the efficiency of integrating various PV elements in buildings from rural areas, to test them and to make them known so that they can be used on a large scale. This will be accomplished by installing new products on 2 buildings in Bucharest and in 1 building in Timisoara. The PV modules will be integrated with the architecture. One of the buildings will be a historical building while the other 2 will be new buildings with different typologies. The installed power for each building will be of about 1.000 Wp, including some technologies with PV modules.

  9. Existing Approaches to Chemical, Biological, Radiological, and Nuclear (CBRN) Education and Training for Health Professionals: Findings from an Integrative Literature Review.

    Science.gov (United States)

    Kako, Mayumi; Hammad, Karen; Mitani, Satoko; Arbon, Paul

    2018-04-01

    This review was conducted to explore the literature to determine the availability, content, and evaluation of existing chemical, biological, radiological, and nuclear (CBRN) education programs for health professionals. An integrative review of the international literature describing disaster education for CBRN (2004-2016) was conducted. The following relevant databases were searched: Proquest, Pubmed, Science Direct, Scopus, Journals @ OVID, Google Scholar, Medline, and Ichuschi ver. 5 (Japanese database for health professionals). The search terms used were: "disaster," "chemical," "biological," "radiological," "nuclear," "CBRN," "health professional education," and "method." The following Medical Subject Headings (MeSH) terms, "education," "nursing," "continuing," "disasters," "disaster planning," and "bioterrorism," were used wherever possible and appropriate. The retrieved articles were narratively analyzed according to availability, content, and method. The content was thematically analyzed to provide an overview of the core content of the training. The literature search identified 619 potentially relevant articles for this study. Duplicates (n=104) were removed and 87 articles were identified for title review. In total, 67 articles were discarded, yielding 20 articles for all-text review, following 11 studies were retained for analysis, including one Japanese study. All articles published in English were from the USA, apart from the two studies located in Japan and Sweden. The most typical content in the selected literature was CBRN theory (n=11), followed by studies based on incident command (n=8), decontamination (n=7), disaster management (n=7), triage (n=7), personal protective equipment (PPE) use (n = 5), and post-training briefing (n=3). While the CBRN training course requires the participants to gain specific skills and knowledge, proposed training courses should be effectively constructed to include approaches such as scenario-based simulations

  10. Integrating stations from the North America Gravity Database into a local GPS-based land gravity survey

    Science.gov (United States)

    Shoberg, Thomas G.; Stoddard, Paul R.

    2013-01-01

    The ability to augment local gravity surveys with additional gravity stations from easily accessible national databases can greatly increase the areal coverage and spatial resolution of a survey. It is, however, necessary to integrate such data seamlessly with the local survey. One challenge to overcome in integrating data from national databases is that these data are typically of unknown quality. This study presents a procedure for the evaluation and seamless integration of gravity data of unknown quality from a national database with data from a local Global Positioning System (GPS)-based survey. The starting components include the latitude, longitude, elevation and observed gravity at each station location. Interpolated surfaces of the complete Bouguer anomaly are used as a means of quality control and comparison. The result is an integrated dataset of varying quality with many stations having GPS accuracy and other reliable stations of unknown origin, yielding a wider coverage and greater spatial resolution than either survey alone.

  11. Whistleblowing: An integrative literature review of data-based studies involving nurses.

    Science.gov (United States)

    Jackson, Debra; Hickman, Louise D; Hutchinson, Marie; Andrew, Sharon; Smith, James; Potgieter, Ingrid; Cleary, Michelle; Peters, Kath

    2014-01-01

    Abstract Aim: To summarise and critique the research literature about whistleblowing and nurses. Whistleblowing is identified as a crucial issue in maintenance of healthcare standards and nurses are frequently involved in whistleblowing events. Despite the importance of this issue, to our knowledge an evaluation of this body of the data-based literature has not been undertaken. An integrative literature review approach was used to summarise and critique the research literature. A comprehensive search of five databases including Medline, CINAHL, PubMed and Health Science: Nursing/Academic Edition, and Google, were searched using terms including: 'Whistleblow*,' 'nurs*.' In addition, relevant journals were examined, as well as reference lists of retrieved papers. Papers published during the years 2007-2013 were selected for inclusion. Fifteen papers were identified, capturing data from nurses in seven countries. The findings in this review demonstrate a growing body of research for the nursing profession at large to engage and respond appropriately to issues involving suboptimal patient care or organisational wrongdoing. Nursing plays a key role in maintaining practice standards and in reporting care that is unacceptable although the repercussions to nurses who raise concerns are insupportable. Overall, whistleblowing and how it influences the individual, their family, work colleagues, nursing practice and policy overall, requires further national and international research attention.

  12. Smart CCP. Integration of CCP data in the existing infrastructure of a grid operator; Smart KKS. Integration von KKS-Daten in die bestehende Infrastruktur eines Netzbetreibers

    Energy Technology Data Exchange (ETDEWEB)

    Deiss, Rainer [EnBW Regional AG, Stuttgart (Germany); Mueller, Matthias [RBS wave GmbH, Stuttgart (Germany)

    2012-07-01

    The ever growing importance of the cathodic corrosion protection (CCP) requires a much greater integration of the CCP data in the existing infrastructure of a grid operator. The necessary technical adjustments to CCP current protection devices and CCP remote monitoring systems easily can be done with the help of embedded systems.

  13. Bio-optical data integration based on a 4 D database system approach

    Science.gov (United States)

    Imai, N. N.; Shimabukuro, M. H.; Carmo, A. F. C.; Alcantara, E. H.; Rodrigues, T. W. P.; Watanabe, F. S. Y.

    2015-04-01

    Bio-optical characterization of water bodies requires spatio-temporal data about Inherent Optical Properties and Apparent Optical Properties which allow the comprehension of underwater light field aiming at the development of models for monitoring water quality. Measurements are taken to represent optical properties along a column of water, and then the spectral data must be related to depth. However, the spatial positions of measurement may differ since collecting instruments vary. In addition, the records should not refer to the same wavelengths. Additional difficulty is that distinct instruments store data in different formats. A data integration approach is needed to make these large and multi source data sets suitable for analysis. Thus, it becomes possible, even automatically, semi-empirical models evaluation, preceded by preliminary tasks of quality control. In this work it is presented a solution, in the stated scenario, based on spatial - geographic - database approach with the adoption of an object relational Database Management System - DBMS - due to the possibilities to represent all data collected in the field, in conjunction with data obtained by laboratory analysis and Remote Sensing images that have been taken at the time of field data collection. This data integration approach leads to a 4D representation since that its coordinate system includes 3D spatial coordinates - planimetric and depth - and the time when each data was taken. It was adopted PostgreSQL DBMS extended by PostGIS module to provide abilities to manage spatial/geospatial data. It was developed a prototype which has the mainly tools an analyst needs to prepare the data sets for analysis.

  14. Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases.

    Science.gov (United States)

    Barbosa-Silva, A; Pafilis, E; Ortega, J M; Schneider, R

    2007-12-11

    Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS). The library has been written using SOAP definitions, and permits the programmatic communication through webservices with the SRS. The interactions are possible by invoking the methods described in WSDL by exchanging XML messages. The current functions available in the library have been built to access specific data stored in any of the 90 different databases (such as UNIPROT, KEGG and GO) using the same query syntax format. The inclusion of the described functions in the source of scripts written in PHP enables them as webservice clients to the SRS server. The functions permit one to query the whole content of any SRS database, to list specific records in these databases, to get specific fields from the records, and to link any record among any pair of linked databases. The case study presented exemplifies the library usage to retrieve information regarding registries of a Plant Defense Mechanisms database. The Plant Defense Mechanisms database is currently being developed, and the proposal of SRS.php library usage is to enable the data acquisition for the further warehousing tasks related to its setup and maintenance.

  15. Integration of solar process heat into an existing thermal desalination plant in Qatar

    Science.gov (United States)

    Dieckmann, S.; Krishnamoorthy, G.; Aboumadi, M.; Pandian, Y.; Dersch, J.; Krüger, D.; Al-Rasheed, A. S.; Krüger, J.; Ottenburger, U.

    2016-05-01

    The water supply of many countries in the Middle East relies mainly on water desalination. In Qatar, the water network is completely fed with water from desalination plants. One of these power and desalination plants is located in Ras Abu Fontas, 20 km south of the capital Doha. The heat required for thermal desalination is provided by steam which is generated in waste heat recovery boilers (HRB) connected to gas turbines. Additionally, gas fired boilers or auxiliary firing in the HRBs are used in order to decouple the water generation from the electricity generation. In Ras Abu Fontas some auxiliary boilers run 24/7 because the HRB capacity does not match the demand of the desalination units. This paper contains the techno-economic analysis of two large-scale commercial solar field options, which could reduce the fuel consumption significantly. Both options employ parabolic trough technology with a nominal saturated steam output of 350 t/h at 15 bar (198°C, 240 MW). The first option uses direct steam generation without storage while the second relies on common thermal oil in combination with a molten salt thermal storage with 6 hours full-load capacity. The economic benefit of the integration of solar power depends mainly on the cost of the fossil alternative, and thus the price (respectively opportunity costs) of natural gas. At a natural gas price of 8 US-/MMBtu the internal rate of return on equity (IRR) is expected at about 5%.

  16. Creating integrative work: a qualitative study of how massage therapists work with existing clients.

    Science.gov (United States)

    Fortune, Luann Drolc; Hymel, Glenn M

    2015-01-01

    As one of the most often used complementary treatments, massage is increasingly positioned as an essential component of integrative medicine. Recent studies evaluate the clinical efficacy of massage therapy, but few studies explore how massage therapists (MTs) execute their work and exercise clinical reasoning in natural settings. To gain foundational knowledge about clinical reasoning and applied knowledge, this study examined how 10 MTs executed an entire session with established clients. Results support translational research design and inform educators. Ethnomethodology and phenomenology informed the qualitative design. Data were collected by videotaping actual sessions and interviewing the participants immediately afterward while viewing the videos. Computer-aided analysis identified data patterns for thematic interpretation. The MTs shared tacit knowledge that directed their work: a) maintaining a primarily biomechanical focus, b) prerequisite safe touch, c) multitasking not allowed, d) MTs assume physical risk, and e) the work affects multiple bodily systems. The MTs sensed effectiveness experientially by adopting common tactics: a) visualizing the manual engagement points, b) assuming the client controlled the physiological release, and c) educating the client. Within these commonalities, they operationalized their work in complex and singular ways, with the particular client relationship critical to structuring the session and evaluating the outcome. MTs viewed their work primarily as a biomechanical intervention, but understood therapeutic massage as serving multiple functions. Process-oriented clinical reasoning mirrored models found in psychotherapy and was informed by experience, intuition, and training, which resulted in an intentionally holistic approach. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Integrated Testing Strategy (ITS) - Opportunities to better use existing data and guide future testing in toxicology.

    Science.gov (United States)

    Jaworska, Joanna; Hoffmann, Sebastian

    2010-01-01

    The topic of Integrated Testing Strategies (ITS) has attracted considerable attention, and not only because it is supposed to be a central element of REACH, the ambitious European chemical regulation effort. Although what ITSs are supposed to do seems unambiguous, i.e. speeding up hazard and risk assessment while reducing testing costs, not much has been said, except basic conceptual proposals, about the methodologies that would allow execution of these concepts. Although a pressing concern, the topic of ITS has drawn mostly general reviews, broad concepts, and the expression of a clear need for more research on ITS. Published research in the field remains scarce. Solutions for ITS design emerge slowly, most likely due to the methodological challenges of the task, and perhaps also to it its complexity and the need for multidisciplinary collaboration. Along with the challenge, ITS offer a unique opportunity to contribute to the Toxicology of the 21st century by providing frameworks and tools to actually implement 21st century toxicology data in the chemical management and decision making processes. Further, ITS have the potential to significantly contribute to a modernization of the science of risk assessment. Therefore, to advance ITS research we propose a methodical approach to their design and will discuss currently available approaches as well as challenges to overcome. To this end, we define a framework for ITS that will inform toxicological decisions in a systematic, transparent, and consistent way. We review conceptual requirements for ITS developed earlier and present a roadmap to an operational framework that should be probabilistic, hypothesis-driven, and adaptive. Furthermore, we define properties an ITS should have in order to meet the identified requirements and differentiate them from evidence synthesis. Making use of an ITS for skin sensitization, we demonstrate how the proposed ITS concepts can be implemented.

  18. An integrated photogrammetric and spatial database management system for producing fully structured data using aerial and remote sensing images.

    Science.gov (United States)

    Ahmadi, Farshid Farnood; Ebadi, Hamid

    2009-01-01

    3D spatial data acquired from aerial and remote sensing images by photogrammetric techniques is one of the most accurate and economic data sources for GIS, map production, and spatial data updating. However, there are still many problems concerning storage, structuring and appropriate management of spatial data obtained using these techniques. According to the capabilities of spatial database management systems (SDBMSs); direct integration of photogrammetric and spatial database management systems can save time and cost of producing and updating digital maps. This integration is accomplished by replacing digital maps with a single spatial database. Applying spatial databases overcomes the problem of managing spatial and attributes data in a coupled approach. This management approach is one of the main problems in GISs for using map products of photogrammetric workstations. Also by the means of these integrated systems, providing structured spatial data, based on OGC (Open GIS Consortium) standards and topological relations between different feature classes, is possible at the time of feature digitizing process. In this paper, the integration of photogrammetric systems and SDBMSs is evaluated. Then, different levels of integration are described. Finally design, implementation and test of a software package called Integrated Photogrammetric and Oracle Spatial Systems (IPOSS) is presented.

  19. An Integrated Photogrammetric and Spatial Database Management System for Producing Fully Structured Data Using Aerial and Remote Sensing Images

    Directory of Open Access Journals (Sweden)

    Farshid Farnood Ahmadi

    2009-03-01

    Full Text Available 3D spatial data acquired from aerial and remote sensing images by photogrammetric techniques is one of the most accurate and economic data sources for GIS, map production, and spatial data updating. However, there are still many problems concerning storage, structuring and appropriate management of spatial data obtained using these techniques. According to the capabilities of spatial database management systems (SDBMSs; direct integration of photogrammetric and spatial database management systems can save time and cost of producing and updating digital maps. This integration is accomplished by replacing digital maps with a single spatial database. Applying spatial databases overcomes the problem of managing spatial and attributes data in a coupled approach. This management approach is one of the main problems in GISs for using map products of photogrammetric workstations. Also by the means of these integrated systems, providing structured spatial data, based on OGC (Open GIS Consortium standards and topological relations between different feature classes, is possible at the time of feature digitizing process. In this paper, the integration of photogrammetric systems and SDBMSs is evaluated. Then, different levels of integration are described. Finally design, implementation and test of a software package called Integrated Photogrammetric and Oracle Spatial Systems (IPOSS is presented.

  20. PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data.

    Science.gov (United States)

    Spannagl, Manuel; Nussbaumer, Thomas; Bader, Kai; Gundlach, Heidrun; Mayer, Klaus F X

    2017-01-01

    Plant Genome and Systems Biology (PGSB), formerly Munich Institute for Protein Sequences (MIPS) PlantsDB, is a database framework for the integration and analysis of plant genome data, developed and maintained for more than a decade now. Major components of that framework are genome databases and analysis resources focusing on individual (reference) genomes providing flexible and intuitive access to data. Another main focus is the integration of genomes from both model and crop plants to form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny). Data exchange and integrated search functionality with/over many plant genome databases is provided within the transPLANT project.

  1. Analysis and databasing software for integrated tomographic gamma scanner (TGS) and passive-active neutron (PAN) assay systems

    International Nuclear Information System (INIS)

    Estep, R.J.; Melton, S.G.; Buenafe, C.

    2000-01-01

    The CTEN-FIT program, written for Windows 9x/NT in C++,performs databasing and analysis of combined thermal/epithermal neutron (CTEN) passive and active neutron assay data and integrates that with isotopics results and gamma-ray data from methods such as tomographic gamma scanning (TGS). The binary database is reflected in a companion Excel database that allows extensive customization via Visual Basic for Applications macros. Automated analysis options make the analysis of the data transparent to the assay system operator. Various record browsers and information displays simplify record keeping tasks

  2. Updates on drug-target network; facilitating polypharmacology and data integration by growth of DrugBank database.

    Science.gov (United States)

    Barneh, Farnaz; Jafari, Mohieddin; Mirzaie, Mehdi

    2016-11-01

    Network pharmacology elucidates the relationship between drugs and targets. As the identified targets for each drug increases, the corresponding drug-target network (DTN) evolves from solely reflection of the pharmaceutical industry trend to a portrait of polypharmacology. The aim of this study was to evaluate the potentials of DrugBank database in advancing systems pharmacology. We constructed and analyzed DTN from drugs and targets associations in the DrugBank 4.0 database. Our results showed that in bipartite DTN, increased ratio of identified targets for drugs augmented density and connectivity of drugs and targets and decreased modular structure. To clear up the details in the network structure, the DTNs were projected into two networks namely, drug similarity network (DSN) and target similarity network (TSN). In DSN, various classes of Food and Drug Administration-approved drugs with distinct therapeutic categories were linked together based on shared targets. Projected TSN also showed complexity because of promiscuity of the drugs. By including investigational drugs that are currently being tested in clinical trials, the networks manifested more connectivity and pictured the upcoming pharmacological space in the future years. Diverse biological processes and protein-protein interactions were manipulated by new drugs, which can extend possible target combinations. We conclude that network-based organization of DrugBank 4.0 data not only reveals the potential for repurposing of existing drugs, also allows generating novel predictions about drugs off-targets, drug-drug interactions and their side effects. Our results also encourage further effort for high-throughput identification of targets to build networks that can be integrated into disease networks. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  3. Autism genetic database (AGD: a comprehensive database including autism susceptibility gene-CNVs integrated with known noncoding RNAs and fragile sites

    Directory of Open Access Journals (Sweden)

    Talebizadeh Zohreh

    2009-09-01

    Full Text Available Abstract Background Autism is a highly heritable complex neurodevelopmental disorder, therefore identifying its genetic basis has been challenging. To date, numerous susceptibility genes and chromosomal abnormalities have been reported in association with autism, but most discoveries either fail to be replicated or account for a small effect. Thus, in most cases the underlying causative genetic mechanisms are not fully understood. In the present work, the Autism Genetic Database (AGD was developed as a literature-driven, web-based, and easy to access database designed with the aim of creating a comprehensive repository for all the currently reported genes and genomic copy number variations (CNVs associated with autism in order to further facilitate the assessment of these autism susceptibility genetic factors. Description AGD is a relational database that organizes data resulting from exhaustive literature searches for reported susceptibility genes and CNVs associated with autism. Furthermore, genomic information about human fragile sites and noncoding RNAs was also downloaded and parsed from miRBase, snoRNA-LBME-db, piRNABank, and the MIT/ICBP siRNA database. A web client genome browser enables viewing of the features while a web client query tool provides access to more specific information for the features. When applicable, links to external databases including GenBank, PubMed, miRBase, snoRNA-LBME-db, piRNABank, and the MIT siRNA database are provided. Conclusion AGD comprises a comprehensive list of susceptibility genes and copy number variations reported to-date in association with autism, as well as all known human noncoding RNA genes and fragile sites. Such a unique and inclusive autism genetic database will facilitate the evaluation of autism susceptibility factors in relation to known human noncoding RNAs and fragile sites, impacting on human diseases. As a result, this new autism database offers a valuable tool for the research

  4. Design Integration of Man-Machine Interface (MMI) Display Drawings and MMI Database

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yong Jun; Seo, Kwang Rak; Song, Jeong Woog; Kim, Dae Ho; Han, Jung A [KEPCO Engineering and Construction Co., Deajeon (Korea, Republic of)

    2016-10-15

    The conventional Main Control Room (MCR) was designed using hardwired controllers and analog indications mounted on control boards for control and acquisition of plant information. This is compared with advanced MCR design where Flat Panel Displays (FPDs) with soft controls and mimic displays are used. The advanced design needs MMI display drawings replacing the conventional control board layout drawings and component lists. The data is linked to related object of the MMI displays. Compilation of the data into the DB is generally done manually, which tends to introduce errors and discrepancies. Also, updating and managing is difficult due to a huge number of entries in the DB and the update must closely track the changes in the associated drawing. Therefore, automating the DB update whenever a related drawing is updated would be quite beneficial. An attempt is made to develop a new method to integrate the MMIS display drawing design and the DB management. This would significantly reduce the amount of errors and improve design quality. The design integration of the MMI Display drawing and MMI DB is explained briefly but concisely in this paper. The existing method involved individually and separately inputting design data for the MMI display drawings. This caused to the potential problem of data discrepancies and errors as well as the update time lag between related drawings and the DB. This led to development of an integration of design process which automates the design data input activity.

  5. OECD/NEA data bank scientific and integral experiments databases in support of knowledge preservation and transfer

    International Nuclear Information System (INIS)

    Sartori, E.; Kodeli, I.; Mompean, F.J.; Briggs, J.B.; Gado, J.; Hasegawa, A.; D'hondt, P.; Wiesenack, W.; Zaetta, A.

    2004-01-01

    The OECD/Nuclear Energy Data Bank was established by its member countries as an institution to allow effective sharing of knowledge and its basic underlying information and data in key areas of nuclear science and technology. The activities as regards preserving and transferring knowledge consist of the: 1) Acquisition of basic nuclear data, computer codes and experimental system data needed over a wide range of nuclear and radiation applications; 2) Independent verification and validation of these data using quality assurance methods, adding value through international benchmark exercises, workshops and meetings and by issuing relevant reports with conclusions and recommendations, as well as by organising training courses to ensure their qualified and competent use; 3) Dissemination of the different products to authorised establishments in member countries and collecting and integrating user feedback. Of particular importance has been the establishment of basic and integral experiments databases and the methodology developed with the aim of knowledge preservation and transfer. Databases established thus far include: 1) IRPhE - International Reactor Physics Experimental Benchmarks Evaluations, 2) SINBAD - a radiation shielding experiments database (nuclear reactors, fusion neutronics and accelerators), 3) IFPE - International Fuel Performance Benchmark Experiments Database, 4) TDB - The Thermochemical Database Project, 5) ICSBE - International Nuclear Criticality Safety Benchmark Evaluations, 6) CCVM - CSNI Code Validation Matrix of Thermal-hydraulic Codes for LWR LOCA and Transients. This paper will concentrate on knowledge preservation and transfer concepts and methods related to some of the integral experiments and TDB. (author)

  6. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics

    Science.gov (United States)

    Schoof, Heiko; Ernst, Rebecca; Nazarov, Vladimir; Pfeifer, Lukas; Mewes, Hans-Werner; Mayer, Klaus F. X.

    2004-01-01

    Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the annotated genetic elements of Arabidopsis must be linked to diverse biological data and higher order information such as metabolic or regulatory pathways. The MIPS Arabidopsis thaliana database MAtDB aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops. The genome sequence as a common backbone serves as a scaffold for the integration of data, while, in a complementary effort, these data are enhanced through the application of state-of-the-art bioinformatics tools. This information is visualized on a genome-wide and a gene-by-gene basis with access both for web users and applications. This report updates the information given in a previous report and provides an outlook on further developments. The MAtDB web interface can be accessed at http://mips.gsf.de/proj/thal/db. PMID:14681437

  7. ViralORFeome: an integrated database to generate a versatile collection of viral ORFs.

    Science.gov (United States)

    Pellet, J; Tafforeau, L; Lucas-Hourani, M; Navratil, V; Meyniel, L; Achaz, G; Guironnet-Paquet, A; Aublin-Gex, A; Caignard, G; Cassonnet, P; Chaboud, A; Chantier, T; Deloire, A; Demeret, C; Le Breton, M; Neveu, G; Jacotot, L; Vaglio, P; Delmotte, S; Gautier, C; Combet, C; Deleage, G; Favre, M; Tangy, F; Jacob, Y; Andre, P; Lotteau, V; Rabourdin-Combe, C; Vidalain, P O

    2010-01-01

    Large collections of protein-encoding open reading frames (ORFs) established in a versatile recombination-based cloning system have been instrumental to study protein functions in high-throughput assays. Such 'ORFeome' resources have been developed for several organisms but in virology, plasmid collections covering a significant fraction of the virosphere are still needed. In this perspective, we present ViralORFeome 1.0 (http://www.viralorfeome.com), an open-access database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway(R) system. ViralORFeome provides a convenient interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to validate the sequence of generated constructs and to browse established collections of virus ORFs. Most importantly, ViralORFeome has been designed to manage all possible variants or mutants of a given ORF so that the cloning procedure can be applied to any emerging virus strain. A subset of plasmid constructs generated with ViralORFeome platform has been tested with success for heterologous protein expression in different expression systems at proteome scale. ViralORFeome should provide our community with a framework to establish a large collection of virus ORF clones, an instrumental resource to determine functions, activities and binding partners of viral proteins.

  8. SPAN: A Network Providing Integrated, End-to-End, Sensor-to-Database Solutions for Environmental Sciences

    Science.gov (United States)

    Benzel, T.; Cho, Y. H.; Deschon, A.; Gullapalli, S.; Silva, F.

    2009-12-01

    In recent years, advances in sensor network technology have shown great promise to revolutionize environmental data collection. Still, wide spread adoption of these systems by domain experts has been lacking, and these have remained the purview of the engineers who design them. While there are many data logging options for basic data collection in the field currently, scientists are often required to visit the deployment sites to retrieve their data and manually import it into spreadsheets. Some advanced commercial software systems do allow scientists to collect data remotely, but most of these systems only allow point-to-point access, and require proprietary hardware. Furthermore, these commercial solutions preclude the use of sensors from other manufacturers or integration with internet based database repositories and compute engines. Therefore, scientists often must download and manually reformat their data before uploading it to the repositories if they wish to share their data. We present an open-source, low-cost, extensible, turnkey solution called Sensor Processing and Acquisition Network (SPAN) which provides a robust and flexible sensor network service. At the deployment site, SPAN leverages low-power generic embedded processors to integrate variety of commercially available sensor hardware to the network of environmental observation systems. By bringing intelligence close to the sensed phenomena, we can remotely control configuration and re-use, establish rules to trigger sensor activity, manage power requirements, and control the two-way flow of sensed data as well as control information to the sensors. Key features of our design include (1) adoption of a hardware agnostic architecture: our solutions are compatible with several programmable platforms, sensor systems, communication devices and protocols. (2) information standardization: our system supports several popular communication protocols and data formats, and (3) extensible data support: our

  9. NOAA's Integrated Tsunami Database: Data for improved forecasts, warnings, research, and risk assessments

    Science.gov (United States)

    Stroker, Kelly; Dunbar, Paula; Mungov, George; Sweeney, Aaron; McCullough, Heather; Carignan, Kelly

    2015-04-01

    The National Oceanic and Atmospheric Administration (NOAA) has primary responsibility in the United States for tsunami forecast, warning, research, and supports community resiliency. NOAA's National Geophysical Data Center (NGDC) and co-located World Data Service for Geophysics provide a unique collection of data enabling communities to ensure preparedness and resilience to tsunami hazards. Immediately following a damaging or fatal tsunami event there is a need for authoritative data and information. The NGDC Global Historical Tsunami Database (http://www.ngdc.noaa.gov/hazard/) includes all tsunami events, regardless of intensity, as well as earthquakes and volcanic eruptions that caused fatalities, moderate damage, or generated a tsunami. The long-term data from these events, including photographs of damage, provide clues to what might happen in the future. NGDC catalogs the information on global historical tsunamis and uses these data to produce qualitative tsunami hazard assessments at regional levels. In addition to the socioeconomic effects of a tsunami, NGDC also obtains water level data from the coasts and the deep-ocean at stations operated by the NOAA/NOS Center for Operational Oceanographic Products and Services, the NOAA Tsunami Warning Centers, and the National Data Buoy Center (NDBC) and produces research-quality data to isolate seismic waves (in the case of the deep-ocean sites) and the tsunami signal. These water-level data provide evidence of sea-level fluctuation and possible inundation events. NGDC is also building high-resolution digital elevation models (DEMs) to support real-time forecasts, implemented at 75 US coastal communities. After a damaging or fatal event NGDC begins to collect and integrate data and information from many organizations into the hazards databases. Sources of data include our NOAA partners, the U.S. Geological Survey, the UNESCO Intergovernmental Oceanographic Commission (IOC) and International Tsunami Information Center

  10. Performance Analysis of an Integrated Heat Pump with Air-Conditioning System for the Existing Hospital Building Application

    Directory of Open Access Journals (Sweden)

    Chen-Yu Chiang

    2017-03-01

    Full Text Available In this study, a complete evaluation procedure of energy-saving and efficiency improvement for a large-scale hospital retrofit project has been established and successfully validated in Taiwan. The retrofit scheme, in integrating the alternative hot water system, namely, a water source heat pump (WSHP, with the existing HVAC (Heating, Ventilating, and Air-Conditioning system, enables the capability to meet the cooling and hot water demand simultaneously with a larger safety margin as well as saving energy. In addition, it has been found that the integrated system provides a new source for cooling which can be utilized as a system redundancy in avoiding system shutdown. This is very useful when considering in specific areas in the hospital, such as intensive care unit, or operation rooms, where cooling should not be interrupted on any occasion. In this study, it is validated that the coefficient of performance (COP of the newly added WSHP system, under heating and cooling mode, is 3.62 and 2.62, respectively. The recorded annual cost reduction by this integrated system is $102,564, with a payback of 1.2 years. The hospital after retrofit has been operating safer, with more redundancy, and more energy-efficient which warrants tremendous potential for implementation in the industry.

  11. The human interactome knowledge base (hint-kb): An integrative human protein interaction database enriched with predicted protein–protein interaction scores using a novel hybrid technique

    KAUST Repository

    Theofilatos, Konstantinos A.

    2013-07-12

    Proteins are the functional components of many cellular processes and the identification of their physical protein–protein interactions (PPIs) is an area of mature academic research. Various databases have been developed containing information about experimentally and computationally detected human PPIs as well as their corresponding annotation data. However, these databases contain many false positive interactions, are partial and only a few of them incorporate data from various sources. To overcome these limitations, we have developed HINT-KB (http://biotools.ceid.upatras.gr/hint-kb/), a knowledge base that integrates data from various sources, provides a user-friendly interface for their retrieval, cal-culatesasetoffeaturesofinterest and computesaconfidence score for every candidate protein interaction. This confidence score is essential for filtering the false positive interactions which are present in existing databases, predicting new protein interactions and measuring the frequency of each true protein interaction. For this reason, a novel machine learning hybrid methodology, called (Evolutionary Kalman Mathematical Modelling—EvoKalMaModel), was used to achieve an accurate and interpretable scoring methodology. The experimental results indicated that the proposed scoring scheme outperforms existing computational methods for the prediction of PPIs.

  12. Managing Consistency Anomalies in Distributed Integrated Databases with Relaxed ACID Properties

    DEFF Research Database (Denmark)

    Frank, Lars; Ulslev Pedersen, Rasmus

    2014-01-01

    In central databases the consistency of data is normally implemented by using the ACID (Atomicity, Consistency, Isolation and Durability) properties of a DBMS (Data Base Management System). This is not possible if distributed and/or mobile databases are involved and the availability of data also...... has to be optimized. Therefore, we will in this paper use so called relaxed ACID properties across different locations. The objective of designing relaxed ACID properties across different database locations is that the users can trust the data they use even if the distributed database temporarily...... is inconsistent. It is also important that disconnected locations can operate in a meaningful way in socalled disconnected mode. A database is DBMS consistent if its data complies with the consistency rules of the DBMS's metadata. If the database is DBMS consistent both when a transaction starts and when it has...

  13. Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

    KAUST Repository

    Komatsu, Setsuko

    2017-05-10

    The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

  14. Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

    Science.gov (United States)

    Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

    2017-06-23

    The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from

  15. Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

    KAUST Repository

    Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

    2017-01-01

    The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

  16. Development of an Integrated Natural Barrier Database System for Site Evaluation of a Deep Geologic Repository in Korea - 13527

    International Nuclear Information System (INIS)

    Jung, Haeryong; Lee, Eunyong; Jeong, YiYeong; Lee, Jeong-Hwan

    2013-01-01

    Korea Radioactive-waste Management Corporation (KRMC) established in 2009 has started a new project to collect information on long-term stability of deep geological environments on the Korean Peninsula. The information has been built up in the integrated natural barrier database system available on web (www.deepgeodisposal.kr). The database system also includes socially and economically important information, such as land use, mining area, natural conservation area, population density, and industrial complex, because some of this information is used as exclusionary criteria during the site selection process for a deep geological repository for safe and secure containment and isolation of spent nuclear fuel and other long-lived radioactive waste in Korea. Although the official site selection process has not been started yet in Korea, current integrated natural barrier database system and socio-economic database is believed that the database system will be effectively utilized to narrow down the number of sites where future investigation is most promising in the site selection process for a deep geological repository and to enhance public acceptance by providing readily-available relevant scientific information on deep geological environments in Korea. (authors)

  17. An Autonomic Framework for Integrating Security and Quality of Service Support in Databases

    Science.gov (United States)

    Alomari, Firas

    2013-01-01

    The back-end databases of multi-tiered applications are a major data security concern for enterprises. The abundance of these systems and the emergence of new and different threats require multiple and overlapping security mechanisms. Therefore, providing multiple and diverse database intrusion detection and prevention systems (IDPS) is a critical…

  18. European Vegetation Archive (EVA): an integrated database of European vegetation plots

    DEFF Research Database (Denmark)

    Chytrý, M; Hennekens, S M; Jiménez-Alfaro, B

    2015-01-01

    vegetation- plot databases on a single software platform. Data storage in EVA does not affect on-going independent development of the contributing databases, which remain the property of the data contributors. EVA uses a prototype of the database management software TURBOVEG 3 developed for joint management......The European Vegetation Archive (EVA) is a centralized database of European vegetation plots developed by the IAVS Working Group European Vegetation Survey. It has been in development since 2012 and first made available for use in research projects in 2014. It stores copies of national and regional...... data source for large-scale analyses of European vegetation diversity both for fundamental research and nature conservation applications. Updated information on EVA is available online at http://euroveg.org/eva-database....

  19. A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis.

    Science.gov (United States)

    Faria-Blanc, Nuno; Mortimer, Jenny C; Dupree, Paul

    2018-01-01

    Yeast have long been known to possess a cell wall integrity (CWI) system, and recently an analogous system has been described for the primary walls of plants (PCWI) that leads to changes in plant growth and cell wall composition. A similar system has been proposed to exist for secondary cell walls (SCWI). However, there is little data to support this. Here, we analyzed the stem transcriptome of a set of cell wall biosynthetic mutants in order to investigate whether cell wall damage, in this case caused by aberrant xylan synthesis, activates a signaling cascade or changes in cell wall synthesis gene expression. Our data revealed remarkably few changes to the transcriptome. We hypothesize that this is because cells undergoing secondary cell wall thickening have entered a committed programme leading to cell death, and therefore a SCWI system would have limited impact. The absence of transcriptomic responses to secondary cell wall alterations may facilitate engineering of the secondary cell wall of plants.

  20. The NCBI BioSystems database.

    Science.gov (United States)

    Geer, Lewis Y; Marchler-Bauer, Aron; Geer, Renata C; Han, Lianyi; He, Jane; He, Siqian; Liu, Chunlei; Shi, Wenyao; Bryant, Stephen H

    2010-01-01

    The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets.

  1. A Reaction Database for Small Molecule Pharmaceutical Processes Integrated with Process Information

    Directory of Open Access Journals (Sweden)

    Emmanouil Papadakis

    2017-10-01

    Full Text Available This article describes the development of a reaction database with the objective to collect data for multiphase reactions involved in small molecule pharmaceutical processes with a search engine to retrieve necessary data in investigations of reaction-separation schemes, such as the role of organic solvents in reaction performance improvement. The focus of this reaction database is to provide a data rich environment with process information available to assist during the early stage synthesis of pharmaceutical products. The database is structured in terms of reaction classification of reaction types; compounds participating in the reaction; use of organic solvents and their function; information for single step and multistep reactions; target products; reaction conditions and reaction data. Information for reactor scale-up together with information for the separation and other relevant information for each reaction and reference are also available in the database. Additionally, the retrieved information obtained from the database can be evaluated in terms of sustainability using well-known “green” metrics published in the scientific literature. The application of the database is illustrated through the synthesis of ibuprofen, for which data on different reaction pathways have been retrieved from the database and compared using “green” chemistry metrics.

  2. Multilingual access to full text databases; Acces multilingue aux bases de donnees en texte integral

    Energy Technology Data Exchange (ETDEWEB)

    Fluhr, C; Radwan, K [Institut National des Sciences et Techniques Nucleaires (INSTN), Centre d` Etudes de Saclay, 91 - Gif-sur-Yvette (France)

    1990-05-01

    Many full text databases are available in only one language, or more, they may contain documents in different languages. Even if the user is able to understand the language of the documents in the database, it could be easier for him to express his need in his own language. For the case of databases containing documents in different languages, it is more simple to formulate the query in one language only and to retrieve documents in different languages. This paper present the developments and the first experiments of multilingual search, applied to french-english pair, for text data in nuclear field, based on the system SPIRIT. After reminding the general problems of full text databases search by queries formulated in natural language, we present the methods used to reformulate the queries and show how they can be expanded for multilingual search. The first results on data in nuclear field are presented (AFCEN norms and INIS abstracts). 4 refs.

  3. An Integrated Database of Unit Training Performance: Description an Lessons Learned

    National Research Council Canada - National Science Library

    Leibrecht, Bruce

    1997-01-01

    The Army Research Institute (ARI) has developed a prototype relational database for processing and archiving unit performance data from home station, training area, simulation based, and Combat Training Center training exercises...

  4. A Comprehensive Database and Analysis Framework To Incorporate Multiscale Data Types and Enable Integrated Analysis of Bioactive Polyphenols.

    Science.gov (United States)

    Ho, Lap; Cheng, Haoxiang; Wang, Jun; Simon, James E; Wu, Qingli; Zhao, Danyue; Carry, Eileen; Ferruzzi, Mario G; Faith, Jeremiah; Valcarcel, Breanna; Hao, Ke; Pasinetti, Giulio M

    2018-03-05

    The development of a given botanical preparation for eventual clinical application requires extensive, detailed characterizations of the chemical composition, as well as the biological availability, biological activity, and safety profiles of the botanical. These issues are typically addressed using diverse experimental protocols and model systems. Based on this consideration, in this study we established a comprehensive database and analysis framework for the collection, collation, and integrative analysis of diverse, multiscale data sets. Using this framework, we conducted an integrative analysis of heterogeneous data from in vivo and in vitro investigation of a complex bioactive dietary polyphenol-rich preparation (BDPP) and built an integrated network linking data sets generated from this multitude of diverse experimental paradigms. We established a comprehensive database and analysis framework as well as a systematic and logical means to catalogue and collate the diverse array of information gathered, which is securely stored and added to in a standardized manner to enable fast query. We demonstrated the utility of the database in (1) a statistical ranking scheme to prioritize response to treatments and (2) in depth reconstruction of functionality studies. By examination of these data sets, the system allows analytical querying of heterogeneous data and the access of information related to interactions, mechanism of actions, functions, etc., which ultimately provide a global overview of complex biological responses. Collectively, we present an integrative analysis framework that leads to novel insights on the biological activities of a complex botanical such as BDPP that is based on data-driven characterizations of interactions between BDPP-derived phenolic metabolites and their mechanisms of action, as well as synergism and/or potential cancellation of biological functions. Out integrative analytical approach provides novel means for a systematic integrative

  5. Higher renewable energy integration into the existing energy system of Finland – Is there any maximum limit?

    International Nuclear Information System (INIS)

    Zakeri, Behnam; Syri, Sanna; Rinne, Samuli

    2015-01-01

    Finland is to increase the share of RES (renewable energy sources) up to 38% in final energy consumption by 2020. While benefiting from local biomass resources Finnish energy system is deemed to achieve this goal, increasing the share of other intermittent renewables is under development, namely wind power and solar energy. Yet the maximum flexibility of the existing energy system in integration of renewable energy is not investigated, which is an important step before undertaking new renewable energy obligations. This study aims at filling this gap by hourly analysis and comprehensive modeling of the energy system including electricity, heat, and transportation, by employing EnergyPLAN tool. Focusing on technical and economic implications, we assess the maximum potential of different RESs separately (including bioenergy, hydropower, wind power, solar heating and PV, and heat pumps), as well as an optimal mix of different technologies. Furthermore, we propose a new index for assessing the maximum flexibility of energy systems in absorbing variable renewable energy. The results demonstrate that wind energy can be harvested at maximum levels of 18–19% of annual power demand (approx. 16 TWh/a), without major enhancements in the flexibility of energy infrastructure. With today's energy demand, the maximum feasible renewable energy for Finland is around 44–50% by an optimal mix of different technologies, which promises 35% reduction in carbon emissions from 2012's level. Moreover, Finnish energy system is flexible to augment the share of renewables in gross electricity consumption up to 69–72%, at maximum. Higher shares of RES calls for lower energy consumption (energy efficiency) and more flexibility in balancing energy supply and consumption (e.g. by energy storage). - Highlights: • By hourly analysis, we model the whole energy system of Finland. • With existing energy infrastructure, RES (renewable energy sources) in primary energy cannot go beyond 50%.

  6. DMPD: Signal integration between IFNgamma and TLR signalling pathways in macrophages. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 16920490 Signal integration between IFNgamma and TLR signalling pathways in macroph...tml) (.csml) Show Signal integration between IFNgamma and TLR signalling pathways in macrophages. PubmedID 16920490 Title Signal inte...gration between IFNgamma and TLR signalling pathways in

  7. Implementation of an anonymisation tool for clinical trials using a clinical trial processor integrated with an existing trial patient data information system

    NARCIS (Netherlands)

    Aryanto, Kadek Y. E.; Broekema, Andre; Oudkerk, Matthijs; van Ooijen, Peter M. A.

    To present an adapted Clinical Trial Processor (CTP) test set-up for receiving, anonymising and saving Digital Imaging and Communications in Medicine (DICOM) data using external input from the original database of an existing clinical study information system to guide the anonymisation process. Two

  8. YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

    Science.gov (United States)

    Colangelo, Christopher M; Shifman, Mark; Cheung, Kei-Hoi; Stone, Kathryn L; Carriero, Nicholas J; Gulcicek, Erol E; Lam, TuKiet T; Wu, Terence; Bjornson, Robert D; Bruce, Can; Nairn, Angus C; Rinehart, Jesse; Miller, Perry L; Williams, Kenneth R

    2015-02-01

    We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  9. Integrated application of the database for airborne geophysical survey achievement information

    International Nuclear Information System (INIS)

    Ji Zengxian; Zhang Junwei

    2006-01-01

    The paper briefly introduces the database of information for airborne geophysical survey achievements. This database was developed on the platform of Microsoft Windows System with the technical methods of Visual C++ 6.0 and MapGIS. It is an information management system concerning airborne geophysical surveying achievements with perfect functions in graphic display, graphic cutting and output, query of data, printing of documents and reports, maintenance of database, etc. All information of airborne geophysical survey achievements in nuclear industry from 1972 to 2003 was embedded in. Based on regional geological map and Meso-Cenozoic basin map, the detailed statistical information of each airborne survey area, each airborne radioactive anomalous point and high field point can be presented visually by combining geological or basin research result. The successful development of this system will provide a fairly good base and platform for management of archives and data of airborne geophysical survey achievements in nuclear industry. (authors)

  10. Data integration and knowledge discovery in biomedical databases. Reliable information from unreliable sources

    Directory of Open Access Journals (Sweden)

    A Mitnitski

    2003-01-01

    Full Text Available To better understand information about human health from databases we analyzed three datasets collected for different purposes in Canada: a biomedical database of older adults, a large population survey across all adult ages, and vital statistics. Redundancy in the variables was established, and this led us to derive a generalized (macroscopic state variable, being a fitness/frailty index that reflects both individual and group health status. Evaluation of the relationship between fitness/frailty and the mortality rate revealed that the latter could be expressed in terms of variables generally available from any cross-sectional database. In practical terms, this means that the risk of mortality might readily be assessed from standard biomedical appraisals collected for other purposes.

  11. Follicle Online: an integrated database of follicle assembly, development and ovulation.

    Science.gov (United States)

    Hua, Juan; Xu, Bo; Yang, Yifan; Ban, Rongjun; Iqbal, Furhan; Cooke, Howard J; Zhang, Yuanwei; Shi, Qinghua

    2015-01-01

    Folliculogenesis is an important part of ovarian function as it provides the oocytes for female reproductive life. Characterizing genes/proteins involved in folliculogenesis is fundamental for understanding the mechanisms associated with this biological function and to cure the diseases associated with folliculogenesis. A large number of genes/proteins associated with folliculogenesis have been identified from different species. However, no dedicated public resource is currently available for folliculogenesis-related genes/proteins that are validated by experiments. Here, we are reporting a database 'Follicle Online' that provides the experimentally validated gene/protein map of the folliculogenesis in a number of species. Follicle Online is a web-based database system for storing and retrieving folliculogenesis-related experimental data. It provides detailed information for 580 genes/proteins (from 23 model organisms, including Homo sapiens, Mus musculus, Rattus norvegicus, Mesocricetus auratus, Bos Taurus, Drosophila and Xenopus laevis) that have been reported to be involved in folliculogenesis, POF (premature ovarian failure) and PCOS (polycystic ovary syndrome). The literature was manually curated from more than 43,000 published articles (till 1 March 2014). The Follicle Online database is implemented in PHP + MySQL + JavaScript and this user-friendly web application provides access to the stored data. In summary, we have developed a centralized database that provides users with comprehensive information about genes/proteins involved in folliculogenesis. This database can be accessed freely and all the stored data can be viewed without any registration. Database URL: http://mcg.ustc.edu.cn/sdap1/follicle/index.php © The Author(s) 2015. Published by Oxford University Press.

  12. Social Gerontology--Integrative and Territorial Aspects: A Citation Analysis of Subject Scatter and Database Coverage

    Science.gov (United States)

    Lasda Bergman, Elaine M.

    2011-01-01

    To determine the mix of resources used in social gerontology research, a citation analysis was conducted. A representative sample of citations was selected from three prominent gerontology journals and information was added to determine subject scatter and database coverage for the cited materials. Results indicate that a significant portion of…

  13. Influenza research database: an integrated bioinformatics resource for influenza virus research

    Science.gov (United States)

    The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics, an...

  14. Development and implementation of a custom integrated database with dashboards to assist with hematopathology specimen triage and traffic

    Directory of Open Access Journals (Sweden)

    Elizabeth M Azzato

    2014-01-01

    Full Text Available Background: At some institutions, including ours, bone marrow aspirate specimen triage is complex, with hematopathology triage decisions that need to be communicated to downstream ancillary testing laboratories and many specimen aliquot transfers that are handled outside of the laboratory information system (LIS. We developed a custom integrated database with dashboards to facilitate and streamline this workflow. Methods: We developed user-specific dashboards that allow entry of specimen information by technologists in the hematology laboratory, have custom scripting to present relevant information for the hematopathology service and ancillary laboratories and allow communication of triage decisions from the hematopathology service to other laboratories. These dashboards are web-accessible on the local intranet and accessible from behind the hospital firewall on a computer or tablet. Secure user access and group rights ensure that relevant users can edit or access appropriate records. Results: After database and dashboard design, two-stage beta-testing and user education was performed, with the first focusing on technologist specimen entry and the second on downstream users. Commonly encountered issues and user functionality requests were resolved with database and dashboard redesign. Final implementation occurred within 6 months of initial design; users report improved triage efficiency and reduced need for interlaboratory communications. Conclusions: We successfully developed and implemented a custom database with dashboards that facilitates and streamlines our hematopathology bone marrow aspirate triage. This provides an example of a possible solution to specimen communications and traffic that are outside the purview of a standard LIS.

  15. A Local Action Plan (PAL to Combat Desertification in Apulia Region: Functional Integration of Existing Territorial Programs

    Directory of Open Access Journals (Sweden)

    Claudia Trotta

    2010-10-01

    Full Text Available In 2006-2007, the Italian National Committee to Combat Drought and Desertification promoted the execution of local action plans in some of the Italian regions. The aims of these plans were: to carry out specific actions at a local scale; to promote the integration of local policies; to involve the local communities in proposing strategies to be adopted; to harmonize the procedures among institutions in charge of adopting the policies. In this framework, ENEA carried out an evaluation of existing policies and programs to be considered in implementing a local action plan to combat desertification in the Apulia region. The application of the environmental and socio-economic measures of the regional Rural Development Plan 2007-2013 (PSR seemed to be an effective tool to positively influence human activities such as agriculture, breeding, and forestry, with the purpose of preserving or improving soil characteristics and overall environmental conditions, and eventually resulting in a reduction of desertification processes. Therefore, we proposed that these measures should be taken into account and effectively integrated into the Local Action Plan of the Apulia region. Additionally, we considered the four priority sectors identified by the National Action Plan (PAN to combat drought and desertification as the guiding principles to carry out our analysis. These sectors were: Soil Protection, Sustainable Water Management, Reduction of the Impact of Productive Activities, and Territorial Equilibrium. We also included Climate Change, in consideration of the alarming and urgent role it has assumed. The desertification-prone province of Foggia was selected as a pilot area in where to evaluate the influences that PSR measures can directly or indirectly have on desertification-related factors, and identify and implement specific actions. The Provincial Coordination Territorial Plan (PTCP of Foggia provided the basic land units for this analysis, the

  16. Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases.

    Science.gov (United States)

    Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

    2018-03-19

    This research shows a protocol to assess the computational complexity of querying relational and non-relational (NoSQL (not only Structured Query Language)) standardized electronic health record (EHR) medical information database systems (DBMS). It uses a set of three doubling-sized databases, i.e. databases storing 5000, 10,000 and 20,000 realistic standardized EHR extracts, in three different database management systems (DBMS): relational MySQL object-relational mapping (ORM), document-based NoSQL MongoDB, and native extensible markup language (XML) NoSQL eXist. The average response times to six complexity-increasing queries were computed, and the results showed a linear behavior in the NoSQL cases. In the NoSQL field, MongoDB presents a much flatter linear slope than eXist. NoSQL systems may also be more appropriate to maintain standardized medical information systems due to the special nature of the updating policies of medical information, which should not affect the consistency and efficiency of the data stored in NoSQL databases. One limitation of this protocol is the lack of direct results of improved relational systems such as archetype relational mapping (ARM) with the same data. However, the interpolation of doubling-size database results to those presented in the literature and other published results suggests that NoSQL systems might be more appropriate in many specific scenarios and problems to be solved. For example, NoSQL may be appropriate for document-based tasks such as EHR extracts used in clinical practice, or edition and visualization, or situations where the aim is not only to query medical information, but also to restore the EHR in exactly its original form.

  17. Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases

    Science.gov (United States)

    Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

    2018-01-01

    This research shows a protocol to assess the computational complexity of querying relational and non-relational (NoSQL (not only Structured Query Language)) standardized electronic health record (EHR) medical information database systems (DBMS). It uses a set of three doubling-sized databases, i.e. databases storing 5000, 10,000 and 20,000 realistic standardized EHR extracts, in three different database management systems (DBMS): relational MySQL object-relational mapping (ORM), document-based NoSQL MongoDB, and native extensible markup language (XML) NoSQL eXist. The average response times to six complexity-increasing queries were computed, and the results showed a linear behavior in the NoSQL cases. In the NoSQL field, MongoDB presents a much flatter linear slope than eXist. NoSQL systems may also be more appropriate to maintain standardized medical information systems due to the special nature of the updating policies of medical information, which should not affect the consistency and efficiency of the data stored in NoSQL databases. One limitation of this protocol is the lack of direct results of improved relational systems such as archetype relational mapping (ARM) with the same data. However, the interpolation of doubling-size database results to those presented in the literature and other published results suggests that NoSQL systems might be more appropriate in many specific scenarios and problems to be solved. For example, NoSQL may be appropriate for document-based tasks such as EHR extracts used in clinical practice, or edition and visualization, or situations where the aim is not only to query medical information, but also to restore the EHR in exactly its original form. PMID:29608174

  18. Integrating information systems : linking global business goals to local database applications

    NARCIS (Netherlands)

    Dignum, F.P.M.; Houben, G.J.P.M.

    1999-01-01

    This paper describes a new approach to design modern information systems that offer an integrated access to the data and knowledge that is available in local applications. By integrating the local data management activities into one transparent information distribution process, modern organizations

  19. A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics.

    Directory of Open Access Journals (Sweden)

    Qiang Song

    Full Text Available DNA methylation is implicated in a surprising diversity of regulatory, evolutionary processes and diseases in eukaryotes. The introduction of whole-genome bisulfite sequencing has enabled the study of DNA methylation at a single-base resolution, revealing many new aspects of DNA methylation and highlighting the usefulness of methylome data in understanding a variety of genomic phenomena. As the number of publicly available whole-genome bisulfite sequencing studies reaches into the hundreds, reliable and convenient tools for comparing and analyzing methylomes become increasingly important. We present MethPipe, a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of annotated methylomes from the public domain. Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database.

  20. EchoBASE: an integrated post-genomic database for Escherichia coli.

    Science.gov (United States)

    Misra, Raju V; Horler, Richard S P; Reindl, Wolfgang; Goryanin, Igor I; Thomas, Gavin H

    2005-01-01

    EchoBASE (http://www.ecoli-york.org) is a relational database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. Its aim is to collate information from a wide range of sources to provide clues to the functions of the approximately 1500 gene products that have no confirmed cellular function. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. Experiments that can be held within EchoBASE include proteomics studies, microarray data, protein-protein interaction data, structural data and bioinformatics studies. EchoBASE also contains annotated information on 'orphan' enzyme activities from this microbe to aid characterization of the proteins that catalyse these elusive biochemical reactions.

  1. The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.

    Science.gov (United States)

    Harb, Omar S; Roos, David S

    2015-01-01

    Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets "big data." While such data are readily available for download and personal use and analysis from a variety of repositories, often such analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.

  2. An integrative clinical database and diagnostics platform for biomarker identification and analysis in ion mobility spectra of human exhaled air

    DEFF Research Database (Denmark)

    Schneider, Till; Hauschild, Anne-Christin; Baumbach, Jörg Ingo

    2013-01-01

    data integration and semi-automated data analysis, in particular with regard to the rapid data accumulation, emerging from the high-throughput nature of the MCC/IMS technology. Here, we present a comprehensive database application and analysis platform, which combines metabolic maps with heterogeneous...... biomedical data in a well-structured manner. The design of the database is based on a hybrid of the entity-attribute-value (EAV) model and the EAV-CR, which incorporates the concepts of classes and relationships. Additionally it offers an intuitive user interface that provides easy and quick access...... to have a clear understanding of the detailed composition of human breath. Therefore, in addition to the clinical studies, there is a need for a flexible and comprehensive centralized data repository, which is capable of gathering all kinds of related information. Moreover, there is a demand for automated...

  3. TransAtlasDB: an integrated database connecting expression data, metadata and variants

    Science.gov (United States)

    Adetunji, Modupeore O; Lamont, Susan J; Schmidt, Carl J

    2018-01-01

    Abstract High-throughput transcriptome sequencing (RNAseq) is the universally applied method for target-free transcript identification and gene expression quantification, generating huge amounts of data. The constraint of accessing such data and interpreting results can be a major impediment in postulating suitable hypothesis, thus an innovative storage solution that addresses these limitations, such as hard disk storage requirements, efficiency and reproducibility are paramount. By offering a uniform data storage and retrieval mechanism, various data can be compared and easily investigated. We present a sophisticated system, TransAtlasDB, which incorporates a hybrid architecture of both relational and NoSQL databases for fast and efficient data storage, processing and querying of large datasets from transcript expression analysis with corresponding metadata, as well as gene-associated variants (such as SNPs) and their predicted gene effects. TransAtlasDB provides the data model of accurate storage of the large amount of data derived from RNAseq analysis and also methods of interacting with the database, either via the command-line data management workflows, written in Perl, with useful functionalities that simplifies the complexity of data storage and possibly manipulation of the massive amounts of data generated from RNAseq analysis or through the web interface. The database application is currently modeled to handle analyses data from agricultural species, and will be expanded to include more species groups. Overall TransAtlasDB aims to serve as an accessible repository for the large complex results data files derived from RNAseq gene expression profiling and variant analysis. Database URL: https://modupeore.github.io/TransAtlasDB/ PMID:29688361

  4. International integral experiments databases in support of nuclear data and code validation

    International Nuclear Information System (INIS)

    Briggs, J. Blair; Gado, Janos; Hunter, Hamilton; Kodeli, Ivan; Salvatores, Massimo; Sartori, Enrico

    2002-01-01

    The OECD/NEA Nuclear Science Committee (NSC) has identified the need to establish international databases containing all the important experiments that are available for sharing among the specialists. The NSC has set up or sponsored specific activities to achieve this. The aim is to preserve them in an agreed standard format in computer accessible form, to use them for international activities involving validation of current and new calculational schemes including computer codes and nuclear data libraries, for assessing uncertainties, confidence bounds and safety margins, and to record measurement methods and techniques. The databases so far established or in preparation related to nuclear data validation cover the following areas: SINBAD - A Radiation Shielding Experiments database encompassing reactor shielding, fusion blanket neutronics, and accelerator shielding. ICSBEP - International Criticality Safety Benchmark Experiments Project Handbook, with more than 2500 critical configurations with different combination of materials and spectral indices. IRPhEP - International Reactor Physics Experimental Benchmarks Evaluation Project. The different projects are described in the following including results achieved, work in progress and planned. (author)

  5. GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis

    Directory of Open Access Journals (Sweden)

    Raquel L. Costa

    2017-07-01

    Full Text Available There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these may additionally be integrated with other biological databases, such as Protein-Protein Interactions, transcription factors and gene annotation. However, the results of these analyses remain fragmented, imposing difficulties, either for posterior inspection of results, or for meta-analysis by the incorporation of new related data. Integrating databases and tools into scientific workflows, orchestrating their execution, and managing the resulting data and its respective metadata are challenging tasks. Additionally, a great amount of effort is equally required to run in-silico experiments to structure and compose the information as needed for analysis. Different programs may need to be applied and different files are produced during the experiment cycle. In this context, the availability of a platform supporting experiment execution is paramount. We present GeNNet, an integrated transcriptome analysis platform that unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. It includes GeNNet-Wf, a scientific workflow that pre-loads biological data, pre-processes raw microarray data and conducts a series of analyses including normalization, differential expression inference, clusterization and gene set enrichment analysis. A user-friendly web interface, GeNNet-Web, allows for setting parameters, executing, and visualizing the results of GeNNet-Wf executions. To demonstrate the features of GeNNet, we performed case studies with data retrieved from GEO, particularly using a single-factor experiment in different analysis scenarios. As a result, we obtained differentially expressed genes for which biological functions were

  6. Development of an Information Database for the Integrated Airline Management System (IAMS

    Directory of Open Access Journals (Sweden)

    Bogdane Ruta

    2017-08-01

    Full Text Available In present conditions the activity of any enterprise is represented as a combination of operational processes. Each of them corresponds to relevant airline management systems. Combining two or more management systems, it is possible to obtain an integrated management system. For the effective functioning of the integrated management system, an appropriate information system should be developed. This article proposes a model of such an information system.

  7. Dietary Supplement Ingredient Database

    Science.gov (United States)

    ... and US Department of Agriculture Dietary Supplement Ingredient Database Toggle navigation Menu Home About DSID Mission Current ... values can be saved to build a small database or add to an existing database for national, ...

  8. An Integrative Database System of Agro-Ecology for the Black Soil Region of China

    Directory of Open Access Journals (Sweden)

    Cuiping Ge

    2007-12-01

    Full Text Available The comprehensive database system of the Northeast agro-ecology of black soil (CSDB_BL is user-friendly software designed to store and manage large amounts of data on agriculture. The data was collected in an efficient and systematic way by long-term experiments and observations of black land and statistics information. It is based on the ORACLE database management system and the interface is written in PB language. The database has the following main facilities:(1 runs on Windows platforms; (2 facilitates data entry from *.dbf to ORACLE or creates ORACLE tables directly; (3has a metadata facility that describes the methods used in the laboratory or in the observations; (4 data can be transferred to an expert system for simulation analysis and estimates made by Visual C++ and Visual Basic; (5 can be connected with GIS, so it is easy to analyze changes in land use ; and (6 allows metadata and data entity to be shared on the internet. The following datasets are included in CSDB_BL: long-term experiments and observations of water, soil, climate, biology, special research projects, and a natural resource survey of Hailun County in the 1980s; images from remote sensing, graphs of vectors and grids, and statistics from Northeast of China. CSDB_BL can be used in the research and evaluation of agricultural sustainability nationally, regionally, or locally. Also, it can be used as a tool to assist the government in planning for agricultural development. Expert systems connected with CSDB_BL can give farmers directions for farm planting management.

  9. A Reaction Database for Small Molecule Pharmaceutical Processes Integrated with Process Information

    DEFF Research Database (Denmark)

    Papadakis, Emmanouil; Anantpinijwatna, Amata; Woodley, John

    2017-01-01

    This article describes the development of a reaction database with the objective to collect data for multiphase reactions involved in small molecule pharmaceutical processes with a search engine to retrieve necessary data in investigations of reaction-separation schemes, such as the role of organic......; compounds participating in the reaction; use of organic solvents and their function; information for single step and multistep reactions; target products; reaction conditions and reaction data. Information for reactor scale-up together with information for the separation and other relevant information...

  10. Integrated Data Acquisition, Storage, Retrieval and Processing Using the COMPASS DataBase (CDB)

    Czech Academy of Sciences Publication Activity Database

    Urban, Jakub; Pipek, Jan; Hron, Martin; Janky, Filip; Papřok, Richard; Peterka, Matěj; Duarte, A.S.

    2014-01-01

    Roč. 89, č. 5 (2014), s. 712-716 ISSN 0920-3796. [Ninth IAEA TM on Control, Data Acquisition, and Remote Participation for Fusion Research. Hefei, 06.05.2013-10.05.2013] R&D Projects: GA ČR GP13-38121P; GA ČR GAP205/11/2470; GA MŠk(CZ) LM2011021 Institutional support: RVO:61389021 Keywords : tokamak * CODAC * database Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 1.152, year: 2014 http://dx.doi.org/10.1016/j.fusengdes.2014.03.032

  11. Integration of Narrative Processing, Data Fusion, and Database Updating Techniques in an Automated System.

    Science.gov (United States)

    1981-10-29

    are implemented, respectively, in the files "W-Update," "W-combine" and RW-Copy," listed in the appendix. The appendix begins with a typescript of an...the typescript ) and the copying process (steps 45 and 46) are shown as human actions in the typescript , but can be performed easily by a "master...for Natural Language, M. Marcus, MIT Press, 1980. I 29 APPENDIX: DATABASE UPDATING EXPERIMENT 30 CONTENTS Typescript of an experiment in Rosie

  12. Databases in welding engineering - definition and starting phase of the integrated welding engineering information system

    International Nuclear Information System (INIS)

    Barthelmess, H.; Queren, W.; Stracke, M.

    1989-01-01

    The structure and function of the Information AAssociation for Welding Engineering, newly established by the Deutscher Verband fuer Schweisstechnik, are presented. Examined are: special literature for welding techniques - value and prospects; databases accessible to the public for information on welding techniques; concept for the Information Association for Welding Engineering; the four phases to establish databasis for facts and expert systems of the Information Association for Welding Engineering; the pilot project 'MVT-Data base' (hot crack data base for data of modified varestraint-transvarestraint tests). (orig./MM) [de

  13. Integration of Hands-On Team Training into Existing Curriculum Improves Both Technical and Nontechnical Skills in Laparoscopic Cholecystectomy.

    Science.gov (United States)

    Caskey, Robert C; Owei, Lily; Rao, Raghavendra; Riddle, Elijah W; Brooks, Ari D; Dempsey, Daniel T; Morris, Jon B; Neylan, Christopher J; Williams, Noel N; Dumon, Kristoffel R

    Nontechnical skills are an essential component of surgical education and a major competency assessed by the ACGME milestones project. However, the optimal way to integrate nontechnical skills training into existing curricula and then objectively evaluate the outcome is still unknown. The aim of this study was to determine the effect laparoscopic team-based task training would have on the nontechnical skills needed for laparoscopic surgery. 9 PGY-1 residents underwent an established training curriculum for teaching the knowledge and technical skills involved in laparoscopic cholecystectomy. Initial training involved a didactic session, expert-led practice on a porcine model in a simulated operating room and laparoscopic skills practice on a virtual reality trainer. Residents then performed a laparoscopic cholecystectomy on the same porcine model as a preintervention test. Three to four months following this, residents were subjected to specific nontechnical skills training involving 2 simple team-based laparoscopic tasks. They then practiced a further 4 to 6 hours on the virtual reality trainer. A repeat postintervention laparoscopic cholecystectomy was then performed 3 to 4 months after nontechnical skills training. Both the preintervention and postintervention laparoscopic cholecystectomies were audiovisually recorded and then evaluated by 2 independent surgeons in a blinded fashion. Technical skills were assessed using objective structured assessment of technical skills (OSATS) and a technique specific rating scale (TRS) that we developed for laparoscopic cholecystectomy. Nontechnical skills were assessed using nontechnical skills for surgeons (NOTSS). Residents also completed a survey at the beginning and end of the training. Tertiary care, university based teaching institution. A total of 9 general surgery residents at the intern level. The mean OSATS score improved from 13.7 ± 1.24 to 26.7 ± 0.31 (p training. There was a strong correlation between OSATS and

  14. Data integration for European marine biodiversity research: creating a database on benthos and plankton to study large-scale patterns and long-term changes

    NARCIS (Netherlands)

    Vandepitte, L.; Vanhoorne, B.; Kraberg, A.; Anisimova, N.; Antoniadou, C.; Araújo, R.; Bartsch, I.; Beker, B.; Benedetti-Cecchi, L.; Bertocci, I.; Cochrane, S.J.; Cooper, K.; Craeymeersch, J.A.; Christou, E.; Crisp, D.J.; Dahle, S.; de Boissier, M.; De Kluijver, M.; Denisenko, S.; De Vito, D.; Duineveld, G.; Escaravage, V.L.; Fleischer, D.; Fraschetti, S.; Giangrande, A.; Heip, C.H.R.; Hummel, H.; Janas, U.; Karez, R.; Kedra, M.; Kingston, P.; Kuhlenkamp, R.; Libes, M.; Martens, P.; Mees, J.; Mieszkowska, N.; Mudrak, S.; Munda, I.; Orfanidis, S.; Orlando-Bonaca, M.; Palerud, R.; Rachor, E.; Reichert, K.; Rumohr, H.; Schiedek, D.; Schubert, P.; Sistermans, W.C.H.; Sousa Pinto, I.S.; Southward, A.J.; Terlizzi, A.; Tsiaga, E.; Van Beusekom, J.E.E.; Vanden Berghe, E.; Warzocha, J.; Wasmund, N.; Weslawski, J.M.; Widdicombe, C.; Wlodarska-Kowalczuk, M.; Zettler, M.L.

    2010-01-01

    The general aim of setting up a central database on benthos and plankton was to integrate long-, medium- and short-term datasets on marine biodiversity. Such a database makes it possible to analyse species assemblages and their changes on spatial and temporal scales across Europe. Data collation

  15. An integrated data-analysis and database system for AMS {sup 14}C

    Energy Technology Data Exchange (ETDEWEB)

    Kjeldsen, Henrik, E-mail: kjeldsen@phys.au.d [AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Aarhus (Denmark); Olsen, Jesper [Department of Earth Sciences, Aarhus University, Aarhus (Denmark); Heinemeier, Jan [AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Aarhus (Denmark)

    2010-04-15

    AMSdata is the name of a combined database and data-analysis system for AMS {sup 14}C and stable-isotope work that has been developed at Aarhus University. The system (1) contains routines for data analysis of AMS and MS data, (2) allows a flexible and accurate description of sample extraction and pretreatment, also when samples are split into several fractions, and (3) keeps track of all measured, calculated and attributed data. The structure of the database is flexible and allows an unlimited number of measurement and pretreatment procedures. The AMS {sup 14}C data analysis routine is fairly advanced and flexible, and it can be easily optimized for different kinds of measuring processes. Technically, the system is based on a Microsoft SQL server and includes stored SQL procedures for the data analysis. Microsoft Office Access is used for the (graphical) user interface, and in addition Excel, Word and Origin are exploited for input and output of data, e.g. for plotting data during data analysis.

  16. An integrated data-analysis and database system for AMS 14C

    International Nuclear Information System (INIS)

    Kjeldsen, Henrik; Olsen, Jesper; Heinemeier, Jan

    2010-01-01

    AMSdata is the name of a combined database and data-analysis system for AMS 14 C and stable-isotope work that has been developed at Aarhus University. The system (1) contains routines for data analysis of AMS and MS data, (2) allows a flexible and accurate description of sample extraction and pretreatment, also when samples are split into several fractions, and (3) keeps track of all measured, calculated and attributed data. The structure of the database is flexible and allows an unlimited number of measurement and pretreatment procedures. The AMS 14 C data analysis routine is fairly advanced and flexible, and it can be easily optimized for different kinds of measuring processes. Technically, the system is based on a Microsoft SQL server and includes stored SQL procedures for the data analysis. Microsoft Office Access is used for the (graphical) user interface, and in addition Excel, Word and Origin are exploited for input and output of data, e.g. for plotting data during data analysis.

  17. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome

    Science.gov (United States)

    Schoof, Heiko; Zaccaria, Paolo; Gundlach, Heidrun; Lemcke, Kai; Rudd, Stephen; Kolesov, Grigory; Arnold, Roland; Mewes, H. W.; Mayer, Klaus F. X.

    2002-01-01

    Arabidopsis thaliana is the first plant for which the complete genome has been sequenced and published. Annotation of complex eukaryotic genomes requires more than the assignment of genetic elements to the sequence. Besides completing the list of genes, we need to discover their cellular roles, their regulation and their interactions in order to understand the workings of the whole plant. The MIPS Arabidopsis thaliana Database (MAtDB; http://mips.gsf.de/proj/thal/db) started out as a repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project and the Arabidopsis Genome Initiative. Our aim is to transform MAtDB into an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities and by creating a comprehensive resource for Arabidopsis as a reference model for other species, including crop plants. PMID:11752263

  18. Disciplining Change, Displacing Frictions. Two Structural Dimensions of Digital Circulation Across Land Registry Database Integration

    NARCIS (Netherlands)

    Pelizza, Annalisa

    2016-01-01

    Data acquire meaning through circulation. Yet most approaches to high-quality data aim to flatten this stratification of meanings. In government, data quality is achieved through integrated systems of authentic registers that reduce multiple trajectories to a single, official one. These systems can

  19. Report on Integration of Existing Grid Models for N-R HES Interaction Focused on Balancing Authorities for Sub-hour Penalties and Opportunities

    International Nuclear Information System (INIS)

    McJunkin, Timothy; Epiney, Aaron; Rabiti, Cristian

    2017-01-01

    This report provides a summary of the effort in the Nuclear-Renewable Hybrid Energy System (N-R HES) project on the level 4 milestone to consider integration of existing grid models into the factors for optimization on shorter time intervals than the existing electric grid models with the Risk Analysis Virtual Environment (RAVEN) and Modelica [1] optimizations and economic analysis that are the focus of the project to date.

  20. Report on Integration of Existing Grid Models for N-R HES Interaction Focused on Balancing Authorities for Sub-hour Penalties and Opportunities

    Energy Technology Data Exchange (ETDEWEB)

    McJunkin, Timothy [Idaho National Lab. (INL), Idaho Falls, ID (United States); Epiney, Aaron [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2017-06-01

    This report provides a summary of the effort in the Nuclear-Renewable Hybrid Energy System (N-R HES) project on the level 4 milestone to consider integration of existing grid models into the factors for optimization on shorter time intervals than the existing electric grid models with the Risk Analysis Virtual Environment (RAVEN) and Modelica [1] optimizations and economic analysis that are the focus of the project to date.

  1. Database Security for an Integrated Solution to Automate Sales Processes in Banking

    OpenAIRE

    Alexandra Maria Ioana FLOREA

    2013-01-01

    In order to maintain a competitive edge in a very active banking market the implementation of a web-based solution to standardize, optimize and manage the flow of sales / pre-sales and generating new leads is requested by a company. This article presents the realization of a development framework for software interoperability in the banking financial institutions and an integrated solution for achieving sales process automation in banking. The paper focuses on presenting the requirements for ...

  2. Blockchain-based database to ensure data integrity in cloud computing environments

    OpenAIRE

    Gaetani, Edoardo; Aniello, Leonardo; Baldoni, Roberto; Lombardi, Federico; Margheri, Andrea; Sassone, Vladimiro

    2017-01-01

    Data is nowadays an invaluable resource, indeed it guides all business decisions in most of the computer-aided human activities. Threats to data integrity are thus of paramount relevance, as tampering with data may maliciously affect crucial business decisions. This issue is especially true in cloud computing environments, where data owners cannot control fundamental data aspects, like the physical storage of data and the control of its accesses. Blockchain has recently emerged as a fascinati...

  3. BEopt-CA (Ex): A Tool for Optimal Integration of EE, DR and PV in Existing California Homes

    Energy Technology Data Exchange (ETDEWEB)

    Christensen, C.; Horowitz, S.; Maguire, J.; Tabares-Velasco, P.; Springer, D.; Coates, P.; Bell, C.; Price, S.; Sreedharan, P.; Pickrell, K.

    2014-04-01

    Opportunities for combining energy efficiency, demand response, and energy storage with PV are often missed, because the required knowledge and expertise for these different technologies exist in separate organizations or individuals. Furthermore, there is a lack of quantitative tools to optimize energy efficiency, demand response and energy storage with PV, especially for existing buildings. As technology costs evolve (e.g., the ongoing reduction in the cost of PV), design strategies need to be adjusted accordingly based on quantitative analysis.

  4. An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air

    Directory of Open Access Journals (Sweden)

    Schneider Till

    2013-06-01

    Full Text Available Over the last decade the evaluation of odors and vapors in human breath has gained more and more attention, particularly in the diagnostics of pulmonary diseases. Ion mobility spectrometry coupled with multi-capillary columns (MCC/IMS, is a well known technology for detecting volatile organic compounds (VOCs in air. It is a comparatively inexpensive, non-invasive, high-throughput method, which is able to handle the moisture that comes with human exhaled air, and allows for characterizing of VOCs in very low concentrations. To identify discriminating compounds as biomarkers, it is necessary to have a clear understanding of the detailed composition of human breath. Therefore, in addition to the clinical studies, there is a need for a flexible and comprehensive centralized data repository, which is capable of gathering all kinds of related information. Moreover, there is a demand for automated data integration and semi-automated data analysis, in particular with regard to the rapid data accumulation, emerging from the high-throughput nature of the MCC/IMS technology. Here, we present a comprehensive database application and analysis platform, which combines metabolic maps with heterogeneous biomedical data in a well-structured manner. The design of the database is based on a hybrid of the entity-attribute- value (EAV model and the EAV-CR, which incorporates the concepts of classes and relationships. Additionally it offers an intuitive user interface that provides easy and quick access to the platform’s functionality: automated data integration and integrity validation, versioning and roll-back strategy, data retrieval as well as semi-automatic data mining and machine learning capabilities. The platform will support MCC/IMS-based biomarker identification and validation. The software, schemata, data sets and further information is publicly available at http://imsdb.mpi-inf.mpg.de.

  5. IMPACT web portal: oncology database integrating molecular profiles with actionable therapeutics.

    Science.gov (United States)

    Hintzsche, Jennifer D; Yoo, Minjae; Kim, Jihye; Amato, Carol M; Robinson, William A; Tan, Aik Choon

    2018-04-20

    With the advancement of next generation sequencing technology, researchers are now able to identify important variants and structural changes in DNA and RNA in cancer patient samples. With this information, we can now correlate specific variants and/or structural changes with actionable therapeutics known to inhibit these variants. We introduce the creation of the IMPACT Web Portal, a new online resource that connects molecular profiles of tumors to approved drugs, investigational therapeutics and pharmacogenetics associated drugs. IMPACT Web Portal contains a total of 776 drugs connected to 1326 target genes and 435 target variants, fusion, and copy number alterations. The online IMPACT Web Portal allows users to search for various genetic alterations and connects them to three levels of actionable therapeutics. The results are categorized into 3 levels: Level 1 contains approved drugs separated into two groups; Level 1A contains approved drugs with variant specific information while Level 1B contains approved drugs with gene level information. Level 2 contains drugs currently in oncology clinical trials. Level 3 provides pharmacogenetic associations between approved drugs and genes. IMPACT Web Portal allows for sequencing data to be linked to actionable therapeutics for translational and drug repurposing research. The IMPACT Web Portal online resource allows users to query genes and variants to approved and investigational drugs. We envision that this resource will be a valuable database for personalized medicine and drug repurposing. IMPACT Web Portal is freely available for non-commercial use at http://tanlab.ucdenver.edu/IMPACT .

  6. Database Security for an Integrated Solution to Automate Sales Processes in Banking

    Directory of Open Access Journals (Sweden)

    Alexandra Maria Ioana FLOREA

    2013-05-01

    Full Text Available In order to maintain a competitive edge in a very active banking market the implementation of a web-based solution to standardize, optimize and manage the flow of sales / pre-sales and generating new leads is requested by a company. This article presents the realization of a development framework for software interoperability in the banking financial institutions and an integrated solution for achieving sales process automation in banking. The paper focuses on presenting the requirements for security and confidentiality of stored data and also on presenting the identified techniques and procedures to implement these requirements.

  7. The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

    Science.gov (United States)

    Cooper, Laurel; Meier, Austin; Laporte, Marie-Angélique; Elser, Justin L; Mungall, Chris; Sinn, Brandon T; Cavaliere, Dario; Carbon, Seth; Dunn, Nathan A; Smith, Barry; Qu, Botong; Preece, Justin; Zhang, Eugene; Todorovic, Sinisa; Gkoutos, Georgios; Doonan, John H; Stevenson, Dennis W; Arnaud, Elizabeth

    2018-01-01

    Abstract The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement. All the Planteome ontologies are publicly available and are maintained at the Planteome GitHub site (https://github.com/Planteome) for sharing, tracking revisions and new requests. The annotated data are freely accessible from the ontology browser (http://browser.planteome.org/amigo) and our data repository. PMID:29186578

  8. The Effectiveness of Business Codes: A Critical Examination of Existing Studies and the Development of an Integrated Research Model

    OpenAIRE

    Kaptein, S.P.; Schwartz, M.S.

    2007-01-01

    textabstractBusiness codes are a widely used management instrument. Research into the effectiveness of business codes has, however, produced conflicting results. The main reasons for the divergent findings are: varying definitions of key terms; deficiencies in the empirical data and methodologies used; and a lack of theory. In this paper, we propose an integrated research model and suggest directions for future research.

  9. On the existence and uniqueness of minima and maxima on spheres of the integral functional of the calculus of variations

    Science.gov (United States)

    Ricceri, Biagio

    2006-12-01

    Given a bounded domain [Omega][subset of]Rn, we prove that if is a C1 function whose gradient is Lipschitzian in Rn+1 and non-zero at 0, then, for each r>0 small enough, the restriction of the integral functional to the sphere has a unique global minimum and a unique global maximum.

  10. On the existence and uniqueness of minima and maxima on spheres of the integral functional of the calculus of variations

    OpenAIRE

    Ricceri, Biagio

    2005-01-01

    We deal with the integral functional of the calculus of variations assuming that the gradient of the integrand is Lipschitzian. We then prove that if this gradient does not vanish at zero, then the functional has a unique minimum and a unique maximum on each sphere, centered at zero, with radius small enough.

  11. Using reefcheck monitoring database to develop the coral reef index of biological integrity

    DEFF Research Database (Denmark)

    Nguyen, Hai Yen T.; Pedersen, Ole; Ikejima, Kou

    2009-01-01

    The coral reef indices of biological integrity was constituted based on the reef check monitoring data. Seventy six minimally disturbed sites and 72 maximallv disturbed sites in shallow water and 39 minimally disturbed sites and 37 maximally disturbed sites in deep water were classified based...... on the high-end and low-end percentages and ratios of hard coral, dead coral and fieshy algae. A total of 52 candidate metrics was identified and compiled, Eight and four metrics were finally selected to constitute the shallow and deep water coral reef indices respectively. The rating curve was applied.......05) and coral damaged by other factors -0.283 (pcoral reef indices were sensitive responses to stressors and can be capable to use as the coral reef biological monitoring tool....

  12. Development and Exploration of a Regional Stormwater BMP Performance Database to Parameterize an Integrated Decision Support Tool (i-DST)

    Science.gov (United States)

    Bell, C.; Li, Y.; Lopez, E.; Hogue, T. S.

    2017-12-01

    Decision support tools that quantitatively estimate the cost and performance of infrastructure alternatives are valuable for urban planners. Such a tool is needed to aid in planning stormwater projects to meet diverse goals such as the regulation of stormwater runoff and its pollutants, minimization of economic costs, and maximization of environmental and social benefits in the communities served by the infrastructure. This work gives a brief overview of an integrated decision support tool, called i-DST, that is currently being developed to serve this need. This presentation focuses on the development of a default database for the i-DST that parameterizes water quality treatment efficiency of stormwater best management practices (BMPs) by region. Parameterizing the i-DST by region will allow the tool to perform accurate simulations in all parts of the United States. A national dataset of BMP performance is analyzed to determine which of a series of candidate regionalizations explains the most variance in the national dataset. The data used in the regionalization analysis comes from the International Stormwater BMP Database and data gleaned from an ongoing systematic review of peer-reviewed and gray literature. In addition to identifying a regionalization scheme for water quality performance parameters in the i-DST, our review process will also provide example methods and protocols for systematic reviews in the field of Earth Science.

  13. [Research and development of medical case database: a novel medical case information system integrating with biospecimen management].

    Science.gov (United States)

    Pan, Shiyang; Mu, Yuan; Wang, Hong; Wang, Tong; Huang, Peijun; Ma, Jianfeng; Jiang, Li; Zhang, Jie; Gu, Bing; Yi, Lujiang

    2010-04-01

    To meet the needs of management of medical case information and biospecimen simultaneously, we developed a novel medical case information system integrating with biospecimen management. The database established by MS SQL Server 2000 covered, basic information, clinical diagnosis, imaging diagnosis, pathological diagnosis and clinical treatment of patient; physicochemical property, inventory management and laboratory analysis of biospecimen; users log and data maintenance. The client application developed by Visual C++ 6.0 was used to implement medical case and biospecimen management, which was based on Client/Server model. This system can perform input, browse, inquest, summary of case and related biospecimen information, and can automatically synthesize case-records based on the database. Management of not only a long-term follow-up on individual, but also of grouped cases organized according to the aim of research can be achieved by the system. This system can improve the efficiency and quality of clinical researches while biospecimens are used coordinately. It realizes synthesized and dynamic management of medical case and biospecimen, which may be considered as a new management platform.

  14. Database Description - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Arabidopsis Phenome Database Database Description General information of database Database n... BioResource Center Hiroshi Masuya Database classification Plant databases - Arabidopsis thaliana Organism T...axonomy Name: Arabidopsis thaliana Taxonomy ID: 3702 Database description The Arabidopsis thaliana phenome i...heir effective application. We developed the new Arabidopsis Phenome Database integrating two novel database...seful materials for their experimental research. The other, the “Database of Curated Plant Phenome” focusing

  15. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

    Directory of Open Access Journals (Sweden)

    Baseler Michael W

    2007-11-01

    Full Text Available Abstract Background Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.

  16. Existence and Analytic Approximation of Solutions of Duffing Type Nonlinear Integro-Differential Equation with Integral Boundary Conditions

    Directory of Open Access Journals (Sweden)

    Alsaedi Ahmed

    2009-01-01

    Full Text Available A generalized quasilinearization technique is developed to obtain a sequence of approximate solutions converging monotonically and quadratically to a unique solution of a boundary value problem involving Duffing type nonlinear integro-differential equation with integral boundary conditions. The convergence of order for the sequence of iterates is also established. It is found that the work presented in this paper not only produces new results but also yields several old results in certain limits.

  17. Waterborne disease outbreak detection: an integrated approach using health administrative databases.

    Science.gov (United States)

    Coly, S; Vincent, N; Vaissiere, E; Charras-Garrido, M; Gallay, A; Ducrot, C; Mouly, D

    2017-08-01

    Hundreds of waterborne disease outbreaks (WBDO) of acute gastroenteritis (AGI) due to contaminated tap water are reported in developed countries each year. Such outbreaks are probably under-detected. The aim of our study was to develop an integrated approach to detect and study clusters of AGI in geographical areas with homogeneous exposure to drinking water. Data for the number of AGI cases are available at the municipality level while exposure to tap water depends on drinking water networks (DWN). These two geographical units do not systematically overlap. This study proposed to develop an algorithm which would match the most relevant grouping of municipalities with a specific DWN, in order that tap water exposure can be taken into account when investigating future disease outbreaks. A space-time detection method was applied to the grouping of municipalities. Seven hundred and fourteen new geographical areas (groupings of municipalities) were obtained compared with the 1,310 municipalities and the 1,706 DWN. Eleven potential WBDO were identified in these groupings of municipalities. For ten of them, additional environmental investigations identified at least one event that could have caused microbiological contamination of DWN in the days previous to the occurrence of a reported WBDO.

  18. Multisource Data-Based Integrated Agricultural Drought Monitoring in the Huai River Basin, China

    Science.gov (United States)

    Sun, Peng; Zhang, Qiang; Wen, Qingzhi; Singh, Vijay P.; Shi, Peijun

    2017-10-01

    Drought monitoring is critical for early warning of drought hazard. This study attempted to develop an integrated remote sensing drought monitoring index (IRSDI), based on meteorological data for 2003-2013 from 40 meteorological stations and soil moisture data from 16 observatory stations, as well as Moderate Resolution Imaging Spectroradiometer data using a linear trend detection method, and standardized precipitation evapotranspiration index. The objective was to investigate drought conditions across the Huai River basin in both space and time. Results indicate that (1) the proposed IRSDI monitors and describes drought conditions across the Huai River basin reasonably well in both space and time; (2) frequency of drought and severe drought are observed during April-May and July-September. The northeastern and eastern parts of Huai River basin are dominated by frequent droughts and intensified drought events. These regions are dominated by dry croplands, grasslands, and highly dense population and are hence more sensitive to drought hazards; (3) intensified droughts are detected during almost all months except January, August, October, and December. Besides, significant intensification of droughts is discerned mainly in eastern and western Huai River basin. The duration and regions dominated by intensified drought events would be a challenge for water resources management in view of agricultural and other activities in these regions in a changing climate.

  19. Existing right-of-way plats database.

    Science.gov (United States)

    2010-02-01

    The Maryland State Highway Administrations Office of Real Estate processes a high volume of plat information and research : requests on a daily basis. This is a lengthy process which is completed manually. The Office of Real Estate intends to impr...

  20. Database Description - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name RMOS Alternative nam...arch Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice Microarray Data and other Gene Expression Database...s Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description The Ric...19&lang=en Whole data download - Referenced database Rice Expression Database (RED) Rice full-length cDNA Database... (KOME) Rice Genome Integrated Map Database (INE) Rice Mutant Panel Database (Tos17) Rice Genome Annotation Database

  1. Integration of an Evidence Base into a Probabilistic Risk Assessment Model. The Integrated Medical Model Database: An Organized Evidence Base for Assessing In-Flight Crew Health Risk and System Design

    Science.gov (United States)

    Saile, Lynn; Lopez, Vilma; Bickham, Grandin; FreiredeCarvalho, Mary; Kerstman, Eric; Byrne, Vicky; Butler, Douglas; Myers, Jerry; Walton, Marlei

    2011-01-01

    This slide presentation reviews the Integrated Medical Model (IMM) database, which is an organized evidence base for assessing in-flight crew health risk. The database is a relational database accessible to many people. The database quantifies the model inputs by a ranking based on the highest value of the data as Level of Evidence (LOE) and the quality of evidence (QOE) score that provides an assessment of the evidence base for each medical condition. The IMM evidence base has already been able to provide invaluable information for designers, and for other uses.

  2. Adding New Features to New and Existing Remote Experiments through their Integration in WebLab-Deusto

    Directory of Open Access Journals (Sweden)

    Diego López-de-Ipiña

    2011-10-01

    Full Text Available During the last decade, efforts have been made in the development and publishing of remote experiments for educational purposes. In order to reduce the duplicity of work and to improve the common requirements that are shared by different remote laboratories, remote experiment management platforms have been developed, such as MIT iLabs, LabShare Sahara or WebLab-Deusto. In this paper, we describe how the development of experiments is handled in WebLab-Deusto, supporting both managed (developed used the APIs provided by WebLab-Deusto and unmanaged experiments (using Virtual Machines or LabVIEW, and comparing both approaches. It also shows the results of integrating remote experiments under this system, with the use case of VISIR, the electronics remote laboratory developed in BTH.

  3. Integrating radiation protection criteria for radioactive waste management into remediation procedures in existing exposure situations after a nuclear accident.

    Science.gov (United States)

    Sugiyama, Daisuke; Kimura, Hideo; Tachikawa, Hirokazu; Iimoto, Takeshi; Kawata, Yosuke; Ogino, Haruyuki; Okoshi, Minoru

    2018-03-01

    Experience after the accident at the Fukushima Daiichi nuclear power station has shown that there is a need to establish radiation protection criteria for radioactive waste management consistent with the criteria adopted for the remediation of existing exposure situations. A stepwise approach to setting such criteria is proposed. Initially, a reference level for the annual effective dose from waste management activities in the range 1-10 mSv should be set, with the reference level being less than the reference level for the ambient dose. Subsequently, the reference level for the annual effective dose from waste management activities should be reduced in one or more steps to achieve a final target value of 1 mSv. The dose criteria at each stage should be determined with relevant stakeholder involvement. Illustrative case studies show how this stepwise approach might be applied in practice.

  4. Operational, cost, and technical study of large windpower systems integrated with an existing electric utility. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Ligon, C.; Kirby, G.; Jordan, D.; Lawrence, J.H.; Wiesner, W.; Kosovec, A.; Swanson, R.K.; Smith, R.T.; Johnson, C.C.; Hodson, H.O.

    1976-04-01

    Detailed wind energy assessment from the available wind records, and evaluation of the application of wind energy systems to an existing electric utility were performed in an area known as the Texas Panhandle, on the Great Plains. The study area includes parts of Texas, eastern New Mexico, the Oklahoma Panhandle and southern Kansas. The region is shown to have uniformly distributed winds of relatively high velocity, with average wind power density of 0.53 kW/m/sup 2/ at 30 m height at Amarillo, Texas, a representative location. The annual period of calm is extremely low. Three separate compressed air storage systems with good potential were analyzed in detail, and two potential pumped-hydro facilities were identified and given preliminary consideration. Aquifer storage of compressed air is a promising possibility in the region.

  5. A knowledge transfer scheme to bridge the gap between science and practice: an integration of existing research frameworks into a tool for practice.

    Science.gov (United States)

    Verhagen, Evert; Voogt, Nelly; Bruinsma, Anja; Finch, Caroline F

    2014-04-01

    Evidence of effectiveness does not equal successful implementation. To progress the field, practical tools are needed to bridge the gap between research and practice and to truly unite effectiveness and implementation evidence. This paper describes the Knowledge Transfer Scheme integrating existing implementation research frameworks into a tool which has been developed specifically to bridge the gap between knowledge derived from research on the one side and evidence-based usable information and tools for practice on the other.

  6. MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

    Directory of Open Access Journals (Sweden)

    Kuczmarski Thomas A

    2006-10-01

    Full Text Available Abstract Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. Description MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. Conclusion MannDB comprises a large number of genomes and comprehensive protein

  7. A development and integration of the concentration database for relative method, k0 method and absolute method in instrumental neutron activation analysis using Microsoft Access

    International Nuclear Information System (INIS)

    Hoh Siew Sin

    2012-01-01

    Instrumental Neutron Activation Analysis (INAA) is offen used to determine and calculate the concentration of an element in the sample by the National University of Malaysia, especially students of Nuclear Science Program. The lack of a database service leads consumers to take longer time to calculate the concentration of an element in the sample. This is because we are more dependent on software that is developed by foreign researchers which are costly. To overcome this problem, a study has been carried out to build an INAA database software. The objective of this study is to build a database software that help the users of INAA in Relative Method and Absolute Method for calculating the element concentration in the sample using Microsoft Excel 2010 and Microsoft Access 2010. The study also integrates k 0 data, k 0 Concent and k 0 -Westcott to execute and complete the system. After the integration, a study was conducted to test the effectiveness of the database software by comparing the concentrations between the experiments and in the database. Triple Bare Monitor Zr-Au and Cr-Mo-Au were used in Abs-INAA as monitor to determine the thermal to epithermal neutron flux ratio (f). Calculations involved in determining the concentration are the net peak area (N p ), the measurement time (t m ), the irradiation time (t irr ), k-factor (k), thermal to epithermal neutron flux ratio (f), the parameters of the neutron flux distribution epithermal (α) and detection efficiency (ε p ). For Com-INAA databases, reference material IAEA-375 Soil was used to calculate the concentration of elements in the sample. CRM, SRM are also used in this database. After the INAA database integration, a verification process was to examine the effectiveness of the Abs-INAA was carried out by comparing the sample concentration between the in database and the experiment. The result of the experimental concentration value of INAA database software performed with high accuracy and precision. ICC

  8. MINDMAP: establishing an integrated database infrastructure for research in ageing, mental well-being, and the urban environment.

    Science.gov (United States)

    Beenackers, Mariëlle A; Doiron, Dany; Fortier, Isabel; Noordzij, J Mark; Reinhard, Erica; Courtin, Emilie; Bobak, Martin; Chaix, Basile; Costa, Giuseppe; Dapp, Ulrike; Diez Roux, Ana V; Huisman, Martijn; Grundy, Emily M; Krokstad, Steinar; Martikainen, Pekka; Raina, Parminder; Avendano, Mauricio; van Lenthe, Frank J

    2018-01-19

    Urbanization and ageing have important implications for public mental health and well-being. Cities pose major challenges for older citizens, but also offer opportunities to develop, test, and implement policies, services, infrastructure, and interventions that promote mental well-being. The MINDMAP project aims to identify the opportunities and challenges posed by urban environmental characteristics for the promotion and management of mental well-being and cognitive function of older individuals. MINDMAP aims to achieve its research objectives by bringing together longitudinal studies from 11 countries covering over 35 cities linked to databases of area-level environmental exposures and social and urban policy indicators. The infrastructure supporting integration of this data will allow multiple MINDMAP investigators to safely and remotely co-analyse individual-level and area-level data. Individual-level data is derived from baseline and follow-up measurements of ten participating cohort studies and provides information on mental well-being outcomes, sociodemographic variables, health behaviour characteristics, social factors, measures of frailty, physical function indicators, and chronic conditions, as well as blood derived clinical biochemistry-based biomarkers and genetic biomarkers. Area-level information on physical environment characteristics (e.g. green spaces, transportation), socioeconomic and sociodemographic characteristics (e.g. neighbourhood income, residential segregation, residential density), and social environment characteristics (e.g. social cohesion, criminality) and national and urban social policies is derived from publically available sources such as geoportals and administrative databases. The linkage, harmonization, and analysis of data from different sources are being carried out using piloted tools to optimize the validity of the research results and transparency of the methodology. MINDMAP is a novel research collaboration that is

  9. TriMEDB: A database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae

    Directory of Open Access Journals (Sweden)

    Yoshida Takuhiro

    2008-06-01

    Full Text Available Abstract Background The recent rapid accumulation of sequence resources of various crop species ensures an improvement in the genetics approach, including quantitative trait loci (QTL analysis as well as the holistic population analysis and association mapping of natural variations. Because the tribe Triticeae includes important cereals such as wheat and barley, integration of information on the genetic markers in these crops should effectively accelerate map-based genetic studies on Triticeae species and lead to the discovery of key loci involved in plant productivity, which can contribute to sustainable food production. Therefore, informatics applications and a semantic knowledgebase of genome-wide markers are required for the integration of information on and further development of genetic markers in wheat and barley in order to advance conventional marker-assisted genetic analyses and population genomics of Triticeae species. Description The Triticeae mapped expressed sequence tag (EST database (TriMEDB provides information, along with various annotations, regarding mapped cDNA markers that are related to barley and their homologues in wheat. The current version of TriMEDB provides map-location data for barley and wheat ESTs that were retrieved from 3 published barley linkage maps (the barley single nucleotide polymorphism database of the Scottish Crop Research Institute, the barley transcript map of Leibniz Institute of Plant Genetics and Crop Plant Research, and HarvEST barley ver. 1.63 and 1 diploid wheat map. These data were imported to CMap to allow the visualization of the map positions of the ESTs and interrelationships of these ESTs with public gene models and representative cDNA sequences. The retrieved cDNA sequences corresponding to each EST marker were assigned to the rice genome to predict an exon-intron structure. Furthermore, to generate a unique set of EST markers in Triticeae plants among the public domain, 3472 markers were

  10. Applied immuno-epidemiological research: an approach for integrating existing knowledge into the statistical analysis of multiple immune markers.

    Science.gov (United States)

    Genser, Bernd; Fischer, Joachim E; Figueiredo, Camila A; Alcântara-Neves, Neuza; Barreto, Mauricio L; Cooper, Philip J; Amorim, Leila D; Saemann, Marcus D; Weichhart, Thomas; Rodrigues, Laura C

    2016-05-20

    Immunologists often measure several correlated immunological markers, such as concentrations of different cytokines produced by different immune cells and/or measured under different conditions, to draw insights from complex immunological mechanisms. Although there have been recent methodological efforts to improve the statistical analysis of immunological data, a framework is still needed for the simultaneous analysis of multiple, often correlated, immune markers. This framework would allow the immunologists' hypotheses about the underlying biological mechanisms to be integrated. We present an analytical approach for statistical analysis of correlated immune markers, such as those commonly collected in modern immuno-epidemiological studies. We demonstrate i) how to deal with interdependencies among multiple measurements of the same immune marker, ii) how to analyse association patterns among different markers, iii) how to aggregate different measures and/or markers to immunological summary scores, iv) how to model the inter-relationships among these scores, and v) how to use these scores in epidemiological association analyses. We illustrate the application of our approach to multiple cytokine measurements from 818 children enrolled in a large immuno-epidemiological study (SCAALA Salvador), which aimed to quantify the major immunological mechanisms underlying atopic diseases or asthma. We demonstrate how to aggregate systematically the information captured in multiple cytokine measurements to immunological summary scores aimed at reflecting the presumed underlying immunological mechanisms (Th1/Th2 balance and immune regulatory network). We show how these aggregated immune scores can be used as predictors in regression models with outcomes of immunological studies (e.g. specific IgE) and compare the results to those obtained by a traditional multivariate regression approach. The proposed analytical approach may be especially useful to quantify complex immune

  11. Building a comprehensive mill-level database for the Industrial Sectors Integrated Solutions (ISIS) model of the U.S. pulp and paper sector.

    Science.gov (United States)

    Modak, Nabanita; Spence, Kelley; Sood, Saloni; Rosati, Jacky Ann

    2015-01-01

    Air emissions from the U.S. pulp and paper sector have been federally regulated since 1978; however, regulations are periodically reviewed and revised to improve efficiency and effectiveness of existing emission standards. The Industrial Sectors Integrated Solutions (ISIS) model for the pulp and paper sector is currently under development at the U.S. Environmental Protection Agency (EPA), and can be utilized to facilitate multi-pollutant, sector-based analyses that are performed in conjunction with regulatory development. The model utilizes a multi-sector, multi-product dynamic linear modeling framework that evaluates the economic impact of emission reduction strategies for multiple air pollutants. The ISIS model considers facility-level economic, environmental, and technical parameters, as well as sector-level market data, to estimate the impacts of environmental regulations on the pulp and paper industry. Specifically, the model can be used to estimate U.S. and global market impacts of new or more stringent air regulations, such as impacts on product price, exports and imports, market demands, capital investment, and mill closures. One major challenge to developing a representative model is the need for an extensive amount of data. This article discusses the collection and processing of data for use in the model, as well as the methods used for building the ISIS pulp and paper database that facilitates the required analyses to support the air quality management of the pulp and paper sector.

  12. Building a Comprehensive Mill-Level Database for the Industrial Sectors Integrated Solutions (ISIS) Model of the U.S. Pulp and Paper Sector

    Science.gov (United States)

    Modak, Nabanita; Spence, Kelley; Sood, Saloni; Rosati, Jacky Ann

    2015-01-01

    Air emissions from the U.S. pulp and paper sector have been federally regulated since 1978; however, regulations are periodically reviewed and revised to improve efficiency and effectiveness of existing emission standards. The Industrial Sectors Integrated Solutions (ISIS) model for the pulp and paper sector is currently under development at the U.S. Environmental Protection Agency (EPA), and can be utilized to facilitate multi-pollutant, sector-based analyses that are performed in conjunction with regulatory development. The model utilizes a multi-sector, multi-product dynamic linear modeling framework that evaluates the economic impact of emission reduction strategies for multiple air pollutants. The ISIS model considers facility-level economic, environmental, and technical parameters, as well as sector-level market data, to estimate the impacts of environmental regulations on the pulp and paper industry. Specifically, the model can be used to estimate U.S. and global market impacts of new or more stringent air regulations, such as impacts on product price, exports and imports, market demands, capital investment, and mill closures. One major challenge to developing a representative model is the need for an extensive amount of data. This article discusses the collection and processing of data for use in the model, as well as the methods used for building the ISIS pulp and paper database that facilitates the required analyses to support the air quality management of the pulp and paper sector. PMID:25806516

  13. Project Independence: Construction of an Integrated Biorefinery for Production of Renewable Biofuels at an Existing Pulp and Paper Mill

    Energy Technology Data Exchange (ETDEWEB)

    Freeman, Douglas

    2012-06-01

    Project Independence proposed to construct a demonstration biomass-to-liquids (BTL) biorefinery in Wisconsin Rapids, isconsin. The biorefinery was to be co-located at the existing pulp and paper mill, NewPage Wisconsin System Incorporated’s Wisconsin Rapids Mill, and when in full operation would both generate renewable energy for Wisconsin Rapids Mill and produce liquid fuels from abundant and renewable lignocellulosic biomass. The biorefinery would serve to validate the thermochemical pathway and economic models for BTL production using forest residuals and wood waste, providing a basis for proliferating BTL conversion technologies throughout the United States. It was a project goal to create a compelling new business model for the pulp and paper industry, and support the nation’s goal for increasing renewable fuels production and reducing its dependence on foreign oil. NewPage Corporation planned to replicate this facility at other NewPage Corporation mills after this first demonstration scale plant was operational and had proven technical and economic feasibility. An overview of the process begins with biomass being harvested, sized, conditioned and fed into a ThermoChem Recovery International (TRI) steam reformer where it is converted to high quality synthetic gas (syngas). The syngas is then cleaned, compressed, scrubbed, polished and fed into the Fischer-Tropsch (F-T) catalytic reactors where the gas is converted into two, sulfur-free, clean crude products which will be marketed as revenue generating streams. Additionally, the Fischer-Tropsch products could be upgraded for use in automotive, aviation and chemical industries as valuable products, if desired. As the Project Independence project set out to prove forest products could be used to commercially produce biofuels, they planned to address and mitigate issues as they arose. In the early days of the Project Independence project, the plant was sized to process 500 dry tons of biomass per day but would

  14. Proteomic biomarkers for ovarian cancer risk in women with polycystic ovary syndrome: a systematic review and biomarker database integration.

    Science.gov (United States)

    Galazis, Nicolas; Olaleye, Olalekan; Haoula, Zeina; Layfield, Robert; Atiomo, William

    2012-12-01

    To review and identify possible biomarkers for ovarian cancer (OC) in women with polycystic ovary syndrome (PCOS). Systematic literature searches of MEDLINE, EMBASE, and Cochrane using the search terms "proteomics," "proteomic," and "ovarian cancer" or "ovarian carcinoma." Proteomic biomarkers for OC were then integrated with an updated previously published database of all proteomic biomarkers identified to date in patients with PCOS. Academic department of obstetrics and gynecology in the United Kingdom. A total of 180 women identified in the six studies. Tissue samples from women with OC vs. tissue samples from women without OC. Proteomic biomarkers, proteomic technique used, and methodologic quality score. A panel of six biomarkers was overexpressed both in women with OC and in women with PCOS. These biomarkers include calreticulin, fibrinogen-γ, superoxide dismutase, vimentin, malate dehydrogenase, and lamin B2. These biomarkers could help improve our understanding of the links between PCOS and OC and could potentially be used to identify subgroups of women with PCOS at increased risk of OC. More studies are required to further evaluate the role these biomarkers play in women with PCOS and OC. Copyright © 2012 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  15. The ESID Online Database network.

    Science.gov (United States)

    Guzman, D; Veit, D; Knerr, V; Kindle, G; Gathmann, B; Eades-Perner, A M; Grimbacher, B

    2007-03-01

    Primary immunodeficiencies (PIDs) belong to the group of rare diseases. The European Society for Immunodeficiencies (ESID), is establishing an innovative European patient and research database network for continuous long-term documentation of patients, in order to improve the diagnosis, classification, prognosis and therapy of PIDs. The ESID Online Database is a web-based system aimed at data storage, data entry, reporting and the import of pre-existing data sources in an enterprise business-to-business integration (B2B). The online database is based on Java 2 Enterprise System (J2EE) with high-standard security features, which comply with data protection laws and the demands of a modern research platform. The ESID Online Database is accessible via the official website (http://www.esid.org/). Supplementary data are available at Bioinformatics online.

  16. Reconstruction of the Leudelange refuse incineration plant with integration of existing plant parts; Erneuerung der MVA Leudelange unter Integration vorhandener Anlagenteile

    Energy Technology Data Exchange (ETDEWEB)

    Buechner, Harm-Peter; Jolas, Uwe [EEW Energy from Waste GmbH, Helmstedt (Germany)

    2013-10-01

    SIDOR, a special purpose association for waste management in Luxembourg, manages the waste disposal of around two-thirds of Luxembourg's entire population. E.ON Energy from Waste (EEW) participated in SIDOR's tender process for both constructing as well as operating a new incineration line with an overall capacity of 150,000 t/a, which was accepted by SIDOR in October 2006. The new incineration line with an overall gross heat output of 67 MWth replaced the existing lines after completion. (orig.)

  17. KALIMER database development

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Kwan Seong; Lee, Yong Bum; Jeong, Hae Yong; Ha, Kwi Seok

    2003-03-01

    KALIMER database is an advanced database to utilize the integration management for liquid metal reactor design technology development using Web applications. KALIMER design database is composed of results database, Inter-Office Communication (IOC), 3D CAD database, and reserved documents database. Results database is a research results database during all phase for liquid metal reactor design technology development of mid-term and long-term nuclear R and D. IOC is a linkage control system inter sub project to share and integrate the research results for KALIMER. 3D CAD database is a schematic overview for KALIMER design structure. And reserved documents database is developed to manage several documents and reports since project accomplishment.

  18. KALIMER database development

    International Nuclear Information System (INIS)

    Jeong, Kwan Seong; Lee, Yong Bum; Jeong, Hae Yong; Ha, Kwi Seok

    2003-03-01

    KALIMER database is an advanced database to utilize the integration management for liquid metal reactor design technology development using Web applications. KALIMER design database is composed of results database, Inter-Office Communication (IOC), 3D CAD database, and reserved documents database. Results database is a research results database during all phase for liquid metal reactor design technology development of mid-term and long-term nuclear R and D. IOC is a linkage control system inter sub project to share and integrate the research results for KALIMER. 3D CAD database is a schematic overview for KALIMER design structure. And reserved documents database is developed to manage several documents and reports since project accomplishment

  19. Can existing mobile apps support healthier food purchasing behaviour? Content analysis of nutrition content, behaviour change theory and user quality integration.

    Science.gov (United States)

    Flaherty, Sarah-Jane; McCarthy, Mary; Collins, Alan; McAuliffe, Fionnuala

    2018-02-01

    To assess the quality of nutrition content and the integration of user quality components and behaviour change theory relevant to food purchasing behaviour in a sample of existing mobile apps. Descriptive comparative analysis of eleven mobile apps comprising an assessment of their alignment with existing evidence on nutrition, behaviour change and user quality, and their potential ability to support healthier food purchasing behaviour. Mobile apps freely available for public use in GoogePlay were assessed and scored according to agreed criteria to assess nutrition content quality and integration of behaviour change theory and user quality components. A sample of eleven mobile apps that met predefined inclusion criteria to ensure relevance and good quality. The quality of the nutrition content varied. Improvements to the accuracy and appropriateness of nutrition content are needed to ensure mobile apps support a healthy behaviour change process and are accessible to a wider population. There appears to be a narrow focus towards behaviour change with an overemphasis on behavioural outcomes and a small number of behaviour change techniques, which may limit effectiveness. A significant effort from the user was required to use the mobile apps appropriately which may negatively influence user acceptability and subsequent utilisation. Existing mobile apps may offer a potentially effective approach to supporting healthier food purchasing behaviour but improvements in mobile app design are required to maximise their potential effectiveness. Engagement of mobile app users and nutrition professionals is recommended to support effective design.

  20. An Interoperable Cartographic Database

    OpenAIRE

    Slobodanka Ključanin; Zdravko Galić

    2007-01-01

    The concept of producing a prototype of interoperable cartographic database is explored in this paper, including the possibilities of integration of different geospatial data into the database management system and their visualization on the Internet. The implementation includes vectorization of the concept of a single map page, creation of the cartographic database in an object-relation database, spatial analysis, definition and visualization of the database content in the form of a map on t...

  1. Experiment Databases

    Science.gov (United States)

    Vanschoren, Joaquin; Blockeel, Hendrik

    Next to running machine learning algorithms based on inductive queries, much can be learned by immediately querying the combined results of many prior studies. Indeed, all around the globe, thousands of machine learning experiments are being executed on a daily basis, generating a constant stream of empirical information on machine learning techniques. While the information contained in these experiments might have many uses beyond their original intent, results are typically described very concisely in papers and discarded afterwards. If we properly store and organize these results in central databases, they can be immediately reused for further analysis, thus boosting future research. In this chapter, we propose the use of experiment databases: databases designed to collect all the necessary details of these experiments, and to intelligently organize them in online repositories to enable fast and thorough analysis of a myriad of collected results. They constitute an additional, queriable source of empirical meta-data based on principled descriptions of algorithm executions, without reimplementing the algorithms in an inductive database. As such, they engender a very dynamic, collaborative approach to experimentation, in which experiments can be freely shared, linked together, and immediately reused by researchers all over the world. They can be set up for personal use, to share results within a lab or to create open, community-wide repositories. Here, we provide a high-level overview of their design, and use an existing experiment database to answer various interesting research questions about machine learning algorithms and to verify a number of recent studies.

  2. Interactive Electronic Decision Trees for the Integrated Primary Care Management of Febrile Children in Low Resource Settings - Review of existing tools.

    Science.gov (United States)

    Keitel, Kristina; D'Acremont, Valérie

    2018-04-20

    The lack of effective, integrated diagnostic tools pose a major challenge to the primary care management of febrile childhood illnesses. These limitations are especially evident in low-resource settings and are often inappropriately compensated by antimicrobial over-prescription. Interactive electronic decision trees (IEDTs) have the potential to close these gaps: guiding antibiotic use and better identifying serious disease. This narrative review summarizes existing IEDTs, to provide an overview of their degree of validation, as well as to identify gaps in current knowledge and prospects for future innovation. Structured literature review in PubMed and Embase complemented by google search and contact with developers. Six integrated IEDTs were identified: three (eIMCI, REC, and Bangladesh digital IMCI) based on Integrated Management of Childhood Illnesses (IMCI); four (SL eCCM, MEDSINC, e-iCCM, and D-Tree eCCM) on Integrated Community Case Management (iCCM); two (ALMANACH, MSFeCARE) with a modified IMCI content; and one (ePOCT) that integrates novel content with biomarker testing. The types of publications and evaluation studies varied greatly: the content and evidence-base was published for two (ALMANACH and ePOCT), ALMANACH and ePOCT were validated in efficacy studies. Other types of evaluations, such as compliance, acceptability were available for D-Tree eCCM, eIMCI, ALMANACH. Several evaluations are still ongoing. Future prospects include conducting effectiveness and impact studies using data gathered through larger studies to adapt the medical content to local epidemiology, improving the software and sensors, and Assessing factors that influence compliance and scale-up. IEDTs are valuable tools that have the potential to improve management of febrile children in primary care and increase the rational use of diagnostics and antimicrobials. Next steps in the evidence pathway should be larger effectiveness and impact studies (including cost analysis) and

  3. Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories.

    Science.gov (United States)

    Kuhn, Stefan; Schlörer, Nils E

    2015-08-01

    nmrshiftdb2 supports with its laboratory information management system the integration of an electronic lab administration and management into academic NMR facilities. Also, it offers the setup of a local database, while full access to nmrshiftdb2's World Wide Web database is granted. This freely available system allows on the one hand the submission of orders for measurement, transfers recorded data automatically or manually, and enables download of spectra via web interface, as well as the integrated access to prediction, search, and assignment tools of the NMR database for lab users. On the other hand, for the staff and lab administration, flow of all orders can be supervised; administrative tools also include user and hardware management, a statistic functionality for accounting purposes, and a 'QuickCheck' function for assignment control, to facilitate quality control of assignments submitted to the (local) database. Laboratory information management system and database are based on a web interface as front end and are therefore independent of the operating system in use. Copyright © 2015 John Wiley & Sons, Ltd.

  4. Optimising design and cost-effective implementation of future pan-African dietary studies: a review of existing economic integration and nutritional indicators for scenario-based profiling and clustering of countries.

    Science.gov (United States)

    Aglago, Elom K; Landais, Edwige; Zotor, Francis; Nicolas, Genevieve; Gunter, Marc J; Amuna, Paul; Slimani, Nadia

    2018-02-01

    Most of the African countries are undergoing a complex nutrition and epidemiologic transition associated with a rapid increase in the prevalence of diverse non-communicable diseases. Despite this alarming situation, the still limited and fragmented resources available in Africa impede the implementation of effective action plans to tackle the current and projected diet-disease burden. In order to address these common needs and challenges, the African Union is increasingly supporting continental approaches and strategies as reflected in the launching of the Agenda 2063 and the African regional nutrition strategy 2015-2025, among others. To assure the successful implementation of pan-African nutritional and health initiatives, cost-effective approaches considering similarities/disparities in economy, regional integration, development and nutritional aspects between countries are needed. In the absence of pre-existing models, we reviewed regional economic integration and nutritional indicators (n 13) available in international organisations databases or governmental agencies websites, for fifty-two African countries. These indicators were used to map the countries according to common languages (e.g. Arabic, English, French, Portuguese), development status (e.g. human development index), malnutrition status (e.g. obesity) and diet (e.g. staples predominantly based on either cereals or tubers). The review of the indicators showed that there exist similarities between African countries that can be exploited to benefit the continent with cross-national experiences in order to avoid duplication of efforts in the implementation of future pan-African health studies. In addition, including present and future nutrition surveillance programmes in Africa into national statistical systems might be cost-effective and sustainable in the longer term.

  5. Integrability conditions for the existence of a Lagrangian in Newtonian mechanics and field theory. Annual progress report, March 1, 1978-May 31, 1979

    International Nuclear Information System (INIS)

    Sternberg, S.; Santilli, R.M.

    1979-01-01

    Studies of general covariance and its application to particle motion and continuum mechanics were continued. Also developed was a new method in microlocal analysis which has applications to integral geometry, geometrical quantization and the fine structure of certain types of spectra. The classical aspect of a program was studied by a comprehensive analysis of the integrability conditions for the existence of a Lagrangian or, independently, of a Hamiltonian for the representation of given Newtonian systems with forces nonderivable from a potential, as well as the methods for the computation of these functions from the equations of motion. The study of a classical, complementary, methodological approach to the same class of systems was also initiated. It consists of the representation of systems with forces nonderivable from a potential via a generalization of Hamilton's equations posessing a Lie-admissible algebraic structure. The problem of the quantization of forces nonderivable from a potential was then studied via the use of these complementary methods. The use of the integrability conditions for the existence of a Hamiltonian representation (the inverse problem) yielded, under certain restrictions, the conventional Heisenberg's equations, but expressed in terms of a generalized Hamiltonian structure. The use of the Lie-admissible formulations yielded a generalization of Heisenberg's equations possessing a generalized (Lie-admissible) algebraic structure, but expressed in terms of a conventional Hamiltonian structure. These preliminary studies were then applied to the investigation of the old idea that the strong interactions are of the type considered, local and nonderivable from a potential, as an approximation of expected nonlocal settings. The experimental verification of Pauli's exclusion principle and other basic physical laws for the nuclear and the hadronic structure was proposed. A list of publications is included

  6. Distributed Database Access in the LHC Computing Grid with CORAL

    CERN Document Server

    Molnár, Z; Düllmann, D; Giacomo, G; Kalkhof, A; Valassi, A; CERN. Geneva. IT Department

    2009-01-01

    The CORAL package is the LCG Persistency Framework foundation for accessing relational databases. From the start CORAL has been designed to facilitate the deployment of the LHC experiment database applications in a distributed computing environment. In particular we cover - improvements to database service scalability by client connection management - platform-independent, multi-tier scalable database access by connection multiplexing, caching - a secure authentication and authorisation scheme integrated with existing grid services. We will summarize the deployment experience from several experiment productions using the distributed database infrastructure, which is now available in LCG. Finally, we present perspectives for future developments in this area.

  7. Tight-coupling of groundwater flow and transport modelling engines with spatial databases and GIS technology: a new approach integrating Feflow and ArcGIS

    Directory of Open Access Journals (Sweden)

    Ezio Crestaz

    2012-09-01

    Full Text Available Implementation of groundwater flow and transport numerical models is generally a challenge, time-consuming and financially-demanding task, in charge to specialized modelers and consulting firms. At a later stage, within clearly stated limits of applicability, these models are often expected to be made available to less knowledgeable personnel to support/design and running of predictive simulations within more familiar environments than specialized simulation systems. GIS systems coupled with spatial databases appear to be ideal candidates to address problem above, due to their much wider diffusion and expertise availability. Current paper discusses the issue from a tight-coupling architecture perspective, aimed at integration of spatial databases, GIS and numerical simulation engines, addressing both observed and computed data management, retrieval and spatio-temporal analysis issues. Observed data can be migrated to the central database repository and then used to set up transient simulation conditions in the background, at run time, while limiting additional complexity and integrity failure risks as data duplication during data transfer through proprietary file formats. Similarly, simulation scenarios can be set up in a familiar GIS system and stored to spatial database for later reference. As numerical engine is tightly coupled with the GIS, simulations can be run within the environment and results themselves saved to the database. Further tasks, as spatio-temporal analysis (i.e. for postcalibration auditing scopes, cartography production and geovisualization, can then be addressed using traditional GIS tools. Benefits of such an approach include more effective data management practices, integration and availability of modeling facilities in a familiar environment, streamlining spatial analysis processes and geovisualization requirements for the non-modelers community. Major drawbacks include limited 3D and time-dependent support in

  8. SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803

    OpenAIRE

    Kim, Woo-Yeon; Kang, Sungsoo; Kim, Byoung-Chul; Oh, Jeehyun; Cho, Seongwoong; Bhak, Jong; Choi, Jong-Soon

    2008-01-01

    Background Cyanobacteria are model organisms for studying photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Despite many studies on cyanobacteria, there is no web-based database of their regulatory and signaling protein-protein interaction networks to date. Description We report a database and website SynechoNET that provides predicted protein-protein interactions. SynechoNET shows cyanobacterial domain-domain interactio...

  9. Utilization of a Clinical Trial Management System for the Whole Clinical Trial Process as an Integrated Database: System Development.

    Science.gov (United States)

    Park, Yu Rang; Yoon, Young Jo; Koo, HaYeong; Yoo, Soyoung; Choi, Chang-Min; Beck, Sung-Ho; Kim, Tae Won

    2018-04-24

    Clinical trials pose potential risks in both communications and management due to the various stakeholders involved when performing clinical trials. The academic medical center has a responsibility and obligation to conduct and manage clinical trials while maintaining a sufficiently high level of quality, therefore it is necessary to build an information technology system to support standardized clinical trial processes and comply with relevant regulations. The objective of the study was to address the challenges identified while performing clinical trials at an academic medical center, Asan Medical Center (AMC) in Korea, by developing and utilizing a clinical trial management system (CTMS) that complies with standardized processes from multiple departments or units, controlled vocabularies, security, and privacy regulations. This study describes the methods, considerations, and recommendations for the development and utilization of the CTMS as a consolidated research database in an academic medical center. A task force was formed to define and standardize the clinical trial performance process at the site level. On the basis of the agreed standardized process, the CTMS was designed and developed as an all-in-one system complying with privacy and security regulations. In this study, the processes and standard mapped vocabularies of a clinical trial were established at the academic medical center. On the basis of these processes and vocabularies, a CTMS was built which interfaces with the existing trial systems such as the electronic institutional review board health information system, enterprise resource planning, and the barcode system. To protect patient data, the CTMS implements data governance and access rules, and excludes 21 personal health identifiers according to the Health Insurance Portability and Accountability Act (HIPAA) privacy rule and Korean privacy laws. Since December 2014, the CTMS has been successfully implemented and used by 881 internal and

  10. Solutions for medical databases optimal exploitation.

    Science.gov (United States)

    Branescu, I; Purcarea, V L; Dobrescu, R

    2014-03-15

    The paper discusses the methods to apply OLAP techniques for multidimensional databases that leverage the existing, performance-enhancing technique, known as practical pre-aggregation, by making this technique relevant to a much wider range of medical applications, as a logistic support to the data warehousing techniques. The transformations have practically low computational complexity and they may be implemented using standard relational database technology. The paper also describes how to integrate the transformed hierarchies in current OLAP systems, transparently to the user and proposes a flexible, "multimodel" federated system for extending OLAP querying to external object databases.

  11. EXTRAPOLATING THE SUITABILITY OF SOILS AS NATURAL REACTORS USING AN EXISTING SOIL MAP: APPLICATION OF PEDOTRANSFER FUNCTIONS, SPATIAL INTEGRATION AND VALIDATION PROCEDURES

    Directory of Open Access Journals (Sweden)

    Yameli Guadalupe Aguilar Duarte

    2011-04-01

    Full Text Available The aim of this study was the spatial identification of the suitability of soils as reactors in the treatment of swine wastewater in the Mexican state of Yucatan, as well as the development of a map with validation procedures. Pedotransfer functions were applied to the existing soils database. A methodological approach was adopted that allowed the spatialization of pedotransfer function data points. A map of the suitability of soil associations as reactors was produced, as well as a map of the level of accuracy of the associations using numerical classification technique, such as discriminant analysis. Soils with the highest suitability indices were found to be Vertisols, Stagnosols, Nitisols and Luvisols. Some 83.9% of the area of Yucatan is marginally suitable for the reception of swine wastewater, 6.5% is moderately suitable, while 6% is suitable. The percentages of the spatial accuracy of the pedotransfer functions range from 62% to 95% with an overall value of 71.5%. The methodological approach proved to be practical, accurate and inexpensive.

  12. Written records of historical tsunamis in the northeastern South China Sea – challenges associated with developing a new integrated database

    Directory of Open Access Journals (Sweden)

    A. Y. A. Lau

    2010-09-01

    Full Text Available Comprehensive analysis of 15 previously published regional databases incorporating more than 100 sources leads to a newly revised historical tsunami database for the northeastern (NE region of the South China Sea (SCS including Taiwan. The validity of each reported historical tsunami event listed in our database is assessed by comparing and contrasting the information and descriptions provided in the other databases. All earlier databases suffer from errors associated with inaccuracies in translation between different languages, calendars and location names. The new database contains 205 records of "events" reported to have occurred between AD 1076 and 2009. We identify and investigate 58 recorded tsunami events in the region. The validity of each event is based on the consistency and accuracy of the reports along with the relative number of individual records for that event. Of the 58 events, 23 are regarded as "valid" (confirmed events, three are "probable" events and six are "possible". Eighteen events are considered "doubtful" and eight events "invalid". The most destructive tsunami of the 23 valid events occurred in 1867 and affected Keelung, northern Taiwan, killing at least 100 people. Inaccuracies in the historical record aside, this new database highlights the occurrence and geographical extent of several large tsunamis in the NE SCS region and allows an elementary statistical analysis of annual recurrence intervals. Based on historical records from 1951–2009 the probability of a tsunami (from any source affecting the region in any given year is relatively high (33.4%. However, the likelihood of a tsunami that has a wave height >1 m, and/or causes fatalities and damage to infrastructure occurring in the region in any given year is low (1–2%. This work indicates the need for further research using coastal stratigraphy and inundation modeling to help validate some of the historical accounts of tsunamis as well as adequately evaluate

  13. Successful introduction of an underutilized elderly pneumococcal vaccine in a national immunization program by integrating the pre-existing public health infrastructure.

    Science.gov (United States)

    Yang, Tae Un; Kim, Eunsung; Park, Young-Joon; Kim, Dongwook; Kwon, Yoon Hyung; Shin, Jae Kyong; Park, Ok

    2016-03-18

    Although pneumococcal vaccines had been recommended for the elderly population in South Korea for a considerable period of time, the coverage has been well below the optimal level. To increase the vaccination rate with integrating the pre-existing public health infrastructure and governmental funding, the Korean government introduced an elderly pneumococcal vaccination into the national immunization program with a 23-valent pneumococcal polysaccharide vaccine in May 2013. The aim of this study was to assess the performance of the program in increasing the vaccine coverage rate and maintaining stable vaccine supply and safe vaccination during the 20 months of the program. We qualitatively and quantitatively analyzed the process of introducing and the outcomes of the program in terms of the systematic organization, efficiency, and stability at the national level. A staggered introduction during the first year utilizing the public sector, with a target coverage of 60%, was implemented based on the public demand for an elderly pneumococcal vaccination, vaccine supply capacity, vaccine delivery capacity, safety, and sustainability. During the 20-month program period, the pneumococcal vaccine coverage rate among the population aged ≥65 years increased from 5.0% to 57.3% without a noticeable vaccine shortage or safety issues. A web-based integrated immunization information system, which includes the immunization registry, vaccine supply chain management, and surveillance of adverse events following immunization, reduced programmatic errors and harmonized the overall performance of the program. Introduction of an elderly pneumococcal vaccination in the national immunization program based on strong government commitment, meticulous preparation, financial support, and the pre-existing public health infrastructure resulted in an efficient, stable, and sustainable increase in vaccination coverage. Copyright © 2016. Published by Elsevier Ltd.

  14. An integrated database on ticks and tick-borne zoonoses in the tropics and subtropics with special reference to developing and emerging countries.

    Science.gov (United States)

    Vesco, Umberto; Knap, Nataša; Labruna, Marcelo B; Avšič-Županc, Tatjana; Estrada-Peña, Agustín; Guglielmone, Alberto A; Bechara, Gervasio H; Gueye, Arona; Lakos, Andras; Grindatto, Anna; Conte, Valeria; De Meneghi, Daniele

    2011-05-01

    Tick-borne zoonoses (TBZ) are emerging diseases worldwide. A large amount of information (e.g. case reports, results of epidemiological surveillance, etc.) is dispersed through various reference sources (ISI and non-ISI journals, conference proceedings, technical reports, etc.). An integrated database-derived from the ICTTD-3 project ( http://www.icttd.nl )-was developed in order to gather TBZ records in the (sub-)tropics, collected both by the authors and collaborators worldwide. A dedicated website ( http://www.tickbornezoonoses.org ) was created to promote collaboration and circulate information. Data collected are made freely available to researchers for analysis by spatial methods, integrating mapped ecological factors for predicting TBZ risk. The authors present the assembly process of the TBZ database: the compilation of an updated list of TBZ relevant for (sub-)tropics, the database design and its structure, the method of bibliographic search, the assessment of spatial precision of geo-referenced records. At the time of writing, 725 records extracted from 337 publications related to 59 countries in the (sub-)tropics, have been entered in the database. TBZ distribution maps were also produced. Imported cases have been also accounted for. The most important datasets with geo-referenced records were those on Spotted Fever Group rickettsiosis in Latin-America and Crimean-Congo Haemorrhagic Fever in Africa. The authors stress the need for international collaboration in data collection to update and improve the database. Supervision of data entered remains always necessary. Means to foster collaboration are discussed. The paper is also intended to describe the challenges encountered to assemble spatial data from various sources and to help develop similar data collections.

  15. BioWarehouse: a bioinformatics database warehouse toolkit

    Directory of Open Access Journals (Sweden)

    Stringer-Calvert David WJ

    2006-03-01

    Full Text Available Abstract Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the

  16. BioWarehouse: a bioinformatics database warehouse toolkit.

    Science.gov (United States)

    Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

    2006-03-23

    This article addresses the problem of interoperation of heterogeneous bioinformatics databases. We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

  17. The Development of PIPA: An Integrated and Automated Pipeline for Genome-Wide Protein Function Annotation

    National Research Council Canada - National Science Library

    Yu, Chenggang; Zavaljevski, Nela; Desai, Valmik; Johnson, Seth; Stevens, Fred J; Reifman, Jaques

    2008-01-01

    .... With the existence of many programs and databases for inferring different protein functions, a pipeline that properly integrates these resources will benefit from the advantages of each method...

  18. Scaling up health knowledge at European level requires sharing integrated data: an approach for collection of database specification

    Directory of Open Access Journals (Sweden)

    Menditto E

    2016-06-01

    Full Text Available Enrica Menditto,1 Angela Bolufer De Gea,2 Caitriona Cahir,3,4 Alessandra Marengoni,5 Salvatore Riegler,1 Giuseppe Fico,6 Elisio Costa,7 Alessandro Monaco,8 Sergio Pecorelli,5 Luca Pani,8 Alexandra Prados-Torres9 1School of Pharmacy, CIRFF/Center of Pharmacoeconomics, University of Naples Federico II, Naples, Italy; 2Directorate-General for Health and Food Safety, European Commission, Brussels, Belgium; 3Division of Population Health Sciences, Royal College of Surgeons in Ireland, 4Department of Pharmacology and Therapeutics, St James’s Hospital, Dublin, Ireland; 5Department of Clinical and Experimental Science, University of Brescia, Brescia; 6Life Supporting Technologies, Photonics Technology and Bioengineering Department, School of Telecomunications Engineering, Polytechnic University of Madrid, Madrid, Spain; 7Faculty of Pharmacy, University of Porto, Porto, Portugal; 8Italian Medicines Agency – AIFA, Rome, Italy; 9EpiChron Research Group on Chronic Diseases, Aragón Health Sciences Institute (IACS, IIS Aragón REDISSEC ISCIII, Miguel Servet University Hospital, University of Zaragoza, Zaragoza, Spain Abstract: Computerized health care databases have been widely described as an excellent opportunity for research. The availability of “big data” has brought about a wave of innovation in projects when conducting health services research. Most of the available secondary data sources are restricted to the geographical scope of a given country and present heterogeneous structure and content. Under the umbrella of the European Innovation Partnership on Active and Healthy Ageing, collaborative work conducted by the partners of the group on “adherence to prescription and medical plans” identified the use of observational and large-population databases to monitor medication-taking behavior in the elderly. This article describes the methodology used to gather the information from available databases among the Adherence Action Group partners

  19. Study of developing a database of energy statistics

    Energy Technology Data Exchange (ETDEWEB)

    Park, T.S. [Korea Energy Economics Institute, Euiwang (Korea, Republic of)

    1997-08-01

    An integrated energy database should be prepared in advance for managing energy statistics comprehensively. However, since much manpower and budget is required for developing an integrated energy database, it is difficult to establish a database within a short period of time. Therefore, this study sets the purpose in drawing methods to analyze existing statistical data lists and to consolidate insufficient data as first stage work for the energy database, and at the same time, in analyzing general concepts and the data structure of the database. I also studied the data content and items of energy databases in operation in international energy-related organizations such as IEA, APEC, Japan, and the USA as overseas cases as well as domestic conditions in energy databases, and the hardware operating systems of Japanese databases. I analyzed the making-out system of Korean energy databases, discussed the KEDB system which is representative of total energy databases, and present design concepts for new energy databases. In addition, I present the establishment directions and their contents of future Korean energy databases, data contents that should be collected by supply and demand statistics, and the establishment of data collection organization, etc. by analyzing the Korean energy statistical data and comparing them with the system of OECD/IEA. 26 refs., 15 figs., 11 tabs.

  20. An Interoperable Cartographic Database

    Directory of Open Access Journals (Sweden)

    Slobodanka Ključanin

    2007-05-01

    Full Text Available The concept of producing a prototype of interoperable cartographic database is explored in this paper, including the possibilities of integration of different geospatial data into the database management system and their visualization on the Internet. The implementation includes vectorization of the concept of a single map page, creation of the cartographic database in an object-relation database, spatial analysis, definition and visualization of the database content in the form of a map on the Internet. 

  1. Event driven software package for the database of Integrated Coastal and Marine Area Management (ICMAM) (Developed in 'C')

    Digital Repository Service at National Institute of Oceanography (India)

    Sadhuram, Y.; Murty, T.V.R.; Chandramouli, P.; Murthy, K.S.R.

    National Institute of Oceanography (NIO, RC, Visakhapatnam, India) had taken up the Integrated Coastal and Marine Area Management (ICMAM) project funded by Department of Ocean Development (DOD), New Delhi, India. The main objective of this project...

  2. Upgrade of laser and electron beam welding database

    CERN Document Server

    Furman, Magdalena

    2014-01-01

    The main purpose of this project was to fix existing issues and update the existing database holding parameters of laser-beam and electron-beam welding machines. Moreover, the database had to be extended to hold the data for the new machines that arrived recently at the workshop. As a solution - the database had to be migrated to Oracle framework, the new user interface (using APEX) had to be designed and implemented with the integration with the CERN web services (EDMS, Phonebook, JMT, CDD and EDH).

  3. Integrated remote sensing and visualization (IRSV) system for transportation infrastructure operations and management, phase two, volume 4 : web-based bridge information database--visualization analytics and distributed sensing.

    Science.gov (United States)

    2012-03-01

    This report introduces the design and implementation of a Web-based bridge information visual analytics system. This : project integrates Internet, multiple databases, remote sensing, and other visualization technologies. The result : combines a GIS ...

  4. TcruziDB, an Integrated Database, and the WWW Information Server for the Trypanosoma cruzi Genome Project

    Directory of Open Access Journals (Sweden)

    Degrave Wim

    1997-01-01

    Full Text Available Data analysis, presentation and distribution is of utmost importance to a genome project. A public domain software, ACeDB, has been chosen as the common basis for parasite genome databases, and a first release of TcruziDB, the Trypanosoma cruzi genome database, is available by ftp from ftp://iris.dbbm.fiocruz.br/pub/genomedb/TcruziDB as well as versions of the software for different operating systems (ftp://iris.dbbm.fiocruz.br/pub/unixsoft/. Moreover, data originated from the project are available from the WWW server at http://www.dbbm.fiocruz.br. It contains biological and parasitological data on CL Brener, its karyotype, all available T. cruzi sequences from Genbank, data on the EST-sequencing project and on available libraries, a T. cruzi codon table and a listing of activities and participating groups in the genome project, as well as meeting reports. T. cruzi discussion lists (tcruzi-l@iris.dbbm.fiocruz.br and tcgenics@iris.dbbm.fiocruz.br are being maintained for communication and to promote collaboration in the genome project

  5. CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803.

    Science.gov (United States)

    Hernandez-Prieto, Miguel A; Futschik, Matthias E

    2012-01-01

    Synechocystis sp. PCC6803 is one of the best studied cyanobacteria and an important model organism for our understanding of photosynthesis. The early availability of its complete genome sequence initiated numerous transcriptome studies, which have generated a wealth of expression data. Analysis of the accumulated data can be a powerful tool to study transcription in a comprehensive manner and to reveal underlying regulatory mechanisms, as well as to annotate genes whose functions are yet unknown. However, use of divergent microarray platforms, as well as distributed data storage make meta-analyses of Synechocystis expression data highly challenging, especially for researchers with limited bioinformatic expertise and resources. To facilitate utilisation of the accumulated expression data for a wider research community, we have developed CyanoEXpress, a web database for interactive exploration and visualisation of transcriptional response patterns in Synechocystis. CyanoEXpress currently comprises expression data for 3073 genes and 178 environmental and genetic perturbations obtained in 31 independent studies. At present, CyanoEXpress constitutes the most comprehensive collection of expression data available for Synechocystis and can be freely accessed. The database is available for free at http://cyanoexpress.sysbiolab.eu.

  6. Stackfile Database

    Science.gov (United States)

    deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

    2013-01-01

    This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

  7. Diffuse nitrogen loss simulation and impact assessment of stereoscopic agriculture pattern by integrated water system model and consideration of multiple existence forms

    Science.gov (United States)

    Zhang, Yongyong; Gao, Yang; Yu, Qiang

    2017-09-01

    Agricultural nitrogen loss becomes an increasingly important source of water quality deterioration and eutrophication, even threatens water safety for humanity. Nitrogen dynamic mechanism is still too complicated to be well captured at watershed scale due to its multiple existence forms and instability, disturbance of agricultural management practices. Stereoscopic agriculture is a novel agricultural planting pattern to efficiently use local natural resources (e.g., water, land, sunshine, heat and fertilizer). It is widely promoted as a high yield system and can obtain considerable economic benefits, particularly in China. However, its environmental quality implication is not clear. In our study, Qianyanzhou station is famous for its stereoscopic agriculture pattern of Southern China, and an experimental watershed was selected as our study area. Regional characteristics of runoff and nitrogen losses were simulated by an integrated water system model (HEQM) with multi-objective calibration, and multiple agriculture practices were assessed to find the effective approach for the reduction of diffuse nitrogen losses. Results showed that daily variations of runoff and nitrogen forms were well reproduced throughout watershed, i.e., satisfactory performances for ammonium and nitrate nitrogen (NH4-N and NO3-N) loads, good performances for runoff and organic nitrogen (ON) load, and very good performance for total nitrogen (TN) load. The average loss coefficient was 62.74 kg/ha for NH4-N, 0.98 kg/ha for NO3-N, 0.0004 kg/ha for ON and 63.80 kg/ha for TN. The dominating form of nitrogen losses was NH4-N due to the applied fertilizers, and the most dramatic zones aggregated in the middle and downstream regions covered by paddy and orange orchard. In order to control diffuse nitrogen losses, the most effective practices for Qianyanzhou stereoscopic agriculture pattern were to reduce farmland planting scale in the valley by afforestation, particularly for orchard in the

  8. Lebesgue Sets Immeasurable Existence

    Directory of Open Access Journals (Sweden)

    Diana Marginean Petrovai

    2012-12-01

    Full Text Available It is well known that the notion of measure and integral were released early enough in close connection with practical problems of measuring of geometric figures. Notion of measure was outlined in the early 20th century through H. Lebesgue’s research, founder of the modern theory of measure and integral. It was developed concurrently a technique of integration of functions. Gradually it was formed a specific area todaycalled the measure and integral theory. Essential contributions to building this theory was made by a large number of mathematicians: C. Carathodory, J. Radon, O. Nikodym, S. Bochner, J. Pettis, P. Halmos and many others. In the following we present several abstract sets, classes of sets. There exists the sets which are not Lebesgue measurable and the sets which are Lebesgue measurable but are not Borel measurable. Hence B ⊂ L ⊂ P(X.

  9. Interconnecting heterogeneous database management systems

    Science.gov (United States)

    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.

  10. Study on safety of a nuclear ship having an integral marine water reactor. Intelligent information database program concerned with thermal-hydraulic characteristics

    International Nuclear Information System (INIS)

    Inasaka, Fujio; Nariai, Hideki; Kobayashi, Michiyuki; Murata, Hiroyuki; Aya, Izuo

    2001-01-01

    As a high economical marine reactor with sufficient safety functions, an integrated type marine water reactor has been considered most promising. At the National Maritime Research Institute, a series of the experimental studies on the thermal-hydraulic characteristics of an integrated/passive-safety type marine water reactor such as the flow boiling of a helical-coil type steam generator, natural circulation of primary water under a ship rolling motion and flashing-condensation oscillation phenomena in pool water has been conducted. This current study aims at making use of the safety analysis or evaluation of a future marine water reactor by developing an intelligent information database program concerned with the thermal-hydraulic characteristics of an integral/passive-safety reactor on the basis of the above-mentioned valuable experimental knowledge. Since the program was created as a Windows application using the Visual Basic, it is available to the public and can be easily installed in the operating system. Main functions of the program are as follows: (1) steady state flow boiling analysis and determination of stability limit for any helical-coil type once-through steam generator design. (2) analysis and comparison with the flow boiling data, (3) reference and graphic display of the experimental data, (4) indication of the knowledge information such as analysis method and results of the study. The program will be useful for the design of not only the future integrated type marine water reactor but also the small sized water reactor. (author)

  11. Relational databases

    CERN Document Server

    Bell, D A

    1986-01-01

    Relational Databases explores the major advances in relational databases and provides a balanced analysis of the state of the art in relational databases. Topics covered include capture and analysis of data placement requirements; distributed relational database systems; data dependency manipulation in database schemata; and relational database support for computer graphics and computer aided design. This book is divided into three sections and begins with an overview of the theory and practice of distributed systems, using the example of INGRES from Relational Technology as illustration. The

  12. INTEGRATION OF DATABASE INTO BUSINESS PROCESS TO SUPPORT IMPLEMENTATION OF CUSTOMER RELATIONSHIP MANAGEMENT: CASE STUDY IN PT TDI

    Directory of Open Access Journals (Sweden)

    Tanty Octavia

    2013-05-01

    Full Text Available Information now is an important element to every growing industry in the world. Inorder to keep up with other competitors, endless improvements in optimizing overall efficiency areneeded. There still exist barriers that separate departments in PT. XYZ and cause limitation to theinformation sharing in the system. Open-Source Manufacturing Execution System (MES presentsas an IT-based application that offers wide variety of customization to eliminate stovepipes bysharing information between departments. Benchmarking is used to choose the best Open-SourceMES Application; and Dynamic System Development Method (DSDM is adopted as this workguideline. As a result, recommendations of the chosen Open-Source MES Application arerepresented.

  13. KALIMER database development (database configuration and design methodology)

    International Nuclear Information System (INIS)

    Jeong, Kwan Seong; Kwon, Young Min; Lee, Young Bum; Chang, Won Pyo; Hahn, Do Hee

    2001-10-01

    KALIMER Database is an advanced database to utilize the integration management for Liquid Metal Reactor Design Technology Development using Web Applicatins. KALIMER Design database consists of Results Database, Inter-Office Communication (IOC), and 3D CAD database, Team Cooperation system, and Reserved Documents, Results Database is a research results database during phase II for Liquid Metal Reactor Design Technology Develpment of mid-term and long-term nuclear R and D. IOC is a linkage control system inter sub project to share and integrate the research results for KALIMER. 3D CAD Database is s schematic design overview for KALIMER. Team Cooperation System is to inform team member of research cooperation and meetings. Finally, KALIMER Reserved Documents is developed to manage collected data and several documents since project accomplishment. This report describes the features of Hardware and Software and the Database Design Methodology for KALIMER

  14. The economic impact of GERD and PUD: examination of direct and indirect costs using a large integrated employer claims database.

    Science.gov (United States)

    Joish, Vijay N; Donaldson, Gary; Stockdale, William; Oderda, Gary M; Crawley, Joseph; Sasane, Rahul; Joshua-Gotlib, Sandra; Brixner, Diana I

    2005-04-01

    The objective of this study was to examine the relationship of work loss associated with gastro- the relationship of work loss associated with gastro- the relationship of work loss associated with gastro-esophageal reflux disease (GERD) and peptic ulcer disease (GERD) and peptic ulcer disease (PUD) in a large population of employed individuals in the United States (US) and quantify the individuals in the United States (US) and quantify the economic impact of these diseases to the employer. A proprietary database that contained work place absence, disability and workers' compensation data in addition to prescription drug and medical claims was used to answer the objectives. Employees with a medical claim with an ICD-9 code for GERD or PUD were identified from 1 January 1997 to 31 December 2000. A cohort of controls was identified for the same time period using the method of frequency matching on age, gender, industry type, occupational status, and employment status. Work absence rates and health care costs were compared between the groups after adjusting for demo graphic, and employment differences using analysis of covariance models. There were significantly lower (p rate of adjusted all-cause absenteeism and sickness-related absenteeism were observed between the disease groups versus the controls. In particular, controls had an average of 1.2 to 1.6 days and 0.4 to 0.6 lower all-cause and sickness-related absenteeism compared to the disease groups. The incremental economic impact projected to a hypothetical employed population was estimated to be $3441 for GERD, $1374 for PUD, and $4803 for GERD + PUD per employee per year compared to employees without these diseases. Direct medical cost and work absence in employees with GERD, PUD and GERD + PUD represent a significant burden to employees and employers.

  15. Biofuel Database

    Science.gov (United States)

    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.

  16. Community Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This excel spreadsheet is the result of merging at the port level of several of the in-house fisheries databases in combination with other demographic databases such...

  17. Database Administrator

    Science.gov (United States)

    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…

  18. Overlap of proteomics biomarkers between women with pre-eclampsia and PCOS: a systematic review and biomarker database integration.

    Science.gov (United States)

    Khan, Gulafshana Hafeez; Galazis, Nicolas; Docheva, Nikolina; Layfield, Robert; Atiomo, William

    2015-01-01

    Do any proteomic biomarkers previously identified for pre-eclampsia (PE) overlap with those identified in women with polycystic ovary syndrome (PCOS). Five previously identified proteomic biomarkers were found to be common in women with PE and PCOS when compared with controls. Various studies have indicated an association between PCOS and PE; however, the pathophysiological mechanisms supporting this association are not known. A systematic review and update of our PCOS proteomic biomarker database was performed, along with a parallel review of PE biomarkers. The study included papers from 1980 to December 2013. In all the studies analysed, there were a total of 1423 patients and controls. The number of proteomic biomarkers that were catalogued for PE was 192. Five proteomic biomarkers were shown to be differentially expressed in women with PE and PCOS when compared with controls: transferrin, fibrinogen α, β and γ chain variants, kininogen-1, annexin 2 and peroxiredoxin 2. In PE, the biomarkers were identified in serum, plasma and placenta and in PCOS, the biomarkers were identified in serum, follicular fluid, and ovarian and omental biopsies. The techniques employed to detect proteomics have limited ability in identifying proteins that are of low abundance, some of which may have a diagnostic potential. The sample sizes and number of biomarkers identified from these studies do not exclude the risk of false positives, a limitation of all biomarker studies. The biomarkers common to PE and PCOS were identified from proteomic analyses of different tissues. This data amalgamation of the proteomic studies in PE and in PCOS, for the first time, discovered a panel of five biomarkers for PE which are common to women with PCOS, including transferrin, fibrinogen α, β and γ chain variants, kininogen-1, annexin 2 and peroxiredoxin 2. If validated, these biomarkers could provide a useful framework for the knowledge infrastructure in this area. To accomplish this goal, a

  19. Exploration of a Vision for Actor Database Systems

    DEFF Research Database (Denmark)

    Shah, Vivek

    of these services. Existing popular approaches to building these services either use an in-memory database system or an actor runtime. We observe that these approaches have complementary strengths and weaknesses. In this dissertation, we propose the integration of actor programming models in database systems....... In doing so, we lay down a vision for a new class of systems called actor database systems. To explore this vision, this dissertation crystallizes the notion of an actor database system by defining its feature set in light of current application and hardware trends. In order to explore the viability...... of the outlined vision, a new programming model named Reactors has been designed to enrich classic relational database programming models with logical actor programming constructs. To support the reactor programming model, a high-performance in-memory multi-core OLTP database system named REACTDB has been built...

  20. Elastic-Plastic J-Integral Solutions or Surface Cracks in Tension Using an Interpolation Methodology. Appendix C -- Finite Element Models Solution Database File, Appendix D -- Benchmark Finite Element Models Solution Database File

    Science.gov (United States)

    Allen, Phillip A.; Wells, Douglas N.

    2013-01-01

    No closed form solutions exist for the elastic-plastic J-integral for surface cracks due to the nonlinear, three-dimensional nature of the problem. Traditionally, each surface crack must be analyzed with a unique and time-consuming nonlinear finite element analysis. To overcome this shortcoming, the authors have developed and analyzed an array of 600 3D nonlinear finite element models for surface cracks in flat plates under tension loading. The solution space covers a wide range of crack shapes and depths (shape: 0.2 less than or equal to a/c less than or equal to 1, depth: 0.2 less than or equal to a/B less than or equal to 0.8) and material flow properties (elastic modulus-to-yield ratio: 100 less than or equal to E/ys less than or equal to 1,000, and hardening: 3 less than or equal to n less than or equal to 20). The authors have developed a methodology for interpolating between the goemetric and material property variables that allows the user to reliably evaluate the full elastic-plastic J-integral and force versus crack mouth opening displacement solution; thus, a solution can be obtained very rapidly by users without elastic-plastic fracture mechanics modeling experience. Complete solutions for the 600 models and 25 additional benchmark models are provided in tabular format.

  1. The Integrated Status and Effectiveness Monitoring Program : Expansion of Existing Smolt Trapping Program and Steelhead Spawner Surveys : March 1st, 2008 - February 28th, 2009.

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Todd; Tonseth, Michael

    2009-01-01

    The Integrated Status and Effectiveness Monitoring Program (ISEMP - BPA project No.2003-0017) has been created as a cost effective means of developing protocols and new technologies, novel indicators, sample designs, analytical, data management and communication tools and skills, and restoration experiments that support the development of a region-wide Research, Monitoring and Evaluation (RME) program to assess the status of anadromous salmonid populations, their tributary habitat and restoration and management actions. The most straightforward approach to developing a regional-scale monitoring and evaluation program would be to increase standardization among status and trend monitoring programs. However, the diversity of species and their habitat, as well as the overwhelming uncertainty surrounding indicators, metrics, and data interpretation methods, requires the testing of multiple approaches. Thus, the approach ISEMP has adopted is to develop a broad template that may differ in the details among subbasins, but one that will ultimately lead to the formation of a unified RME process for the management of anadromous salmonid populations and habitat across the Columbia River Basin. ISEMP has been initiated in three pilot subbasins, the Wenatchee/Entiat, John Day, and Salmon. To balance replicating experimental approaches with the goal of developing monitoring and evaluation tools that apply as broadly as possible across the Pacific Northwest, these subbasins were chosen as representative of a wide range of potential challenges and conditions, e.g., differing fish species composition and life histories, ecoregions, institutional settings, and existing data. ISEMP has constructed a framework that builds on current status and trend monitoring infrastructures in these pilot subbasins, but challenges current programs by testing alternative monitoring approaches. In addition, the ISEMP is: (1) Collecting information over a hierarchy of spatial scales, allowing for a

  2. In-situ databases and comparison of ESA Ocean Colour Climate Change Initiative (OC-CCI) products with precursor data, towards an integrated approach for ocean colour validation and climate studies

    Science.gov (United States)

    Brotas, Vanda; Valente, André; Couto, André B.; Grant, Mike; Chuprin, Andrei; Jackson, Thomas; Groom, Steve; Sathyendranath, Shubha

    2014-05-01

    Ocean colour (OC) is an Oceanic Essential Climate Variable, which is used by climate modellers and researchers. The European Space Agency (ESA) Climate Change Initiative project, is the ESA response for the need of climate-quality satellite data, with the goal of providing stable, long-term, satellite-based ECV data products. The ESA Ocean Colour CCI focuses on the production of Ocean Colour ECV uses remote sensing reflectances to derive inherent optical properties and chlorophyll a concentration from ESA's MERIS (2002-2012) and NASA's SeaWiFS (1997 - 2010) and MODIS (2002-2012) sensor archives. This work presents an integrated approach by setting up a global database of in situ measurements and by inter-comparing OC-CCI products with pre-cursor datasets. The availability of in situ databases is fundamental for the validation of satellite derived ocean colour products. A global distribution in situ database was assembled, from several pre-existing datasets, with data spanning between 1997 and 2012. It includes in-situ measurements of remote sensing reflectances, concentration of chlorophyll-a, inherent optical properties and diffuse attenuation coefficient. The database is composed from observations of the following datasets: NOMAD, SeaBASS, MERMAID, AERONET-OC, BOUSSOLE and HOTS. The result was a merged dataset tuned for the validation of satellite-derived ocean colour products. This was an attempt to gather, homogenize and merge, a large high-quality bio-optical marine in situ data, as using all datasets in a single validation exercise increases the number of matchups and enhances the representativeness of different marine regimes. An inter-comparison analysis between OC-CCI chlorophyll-a product and satellite pre-cursor datasets was done with single missions and merged single mission products. Single mission datasets considered were SeaWiFS, MODIS-Aqua and MERIS; merged mission datasets were obtained from the GlobColour (GC) as well as the Making Earth Science

  3. Directory of IAEA databases

    International Nuclear Information System (INIS)

    1992-12-01

    This second edition of the Directory of IAEA Databases has been prepared within the Division of Scientific and Technical Information (NESI). Its main objective is to describe the computerized information sources available to staff members. This directory contains all databases produced at the IAEA, including databases stored on the mainframe, LAN's and PC's. All IAEA Division Directors have been requested to register the existence of their databases with NESI. For the second edition database owners were requested to review the existing entries for their databases and answer four additional questions. The four additional questions concerned the type of database (e.g. Bibliographic, Text, Statistical etc.), the category of database (e.g. Administrative, Nuclear Data etc.), the available documentation and the type of media used for distribution. In the individual entries on the following pages the answers to the first two questions (type and category) is always listed, but the answers to the second two questions (documentation and media) is only listed when information has been made available

  4. Unheimlichkeit: Alienated and Integrated Identities and Criminal Existence(s

    Directory of Open Access Journals (Sweden)

    Anthony Amatrudo

    2015-09-01

    Full Text Available This essay argues that we should reinterpret Merton’s retreatist category by using Heidegger’s notion of unheimlichkeit (uncanniness which relates to the claim that our consciousness and sense-making are grounded in our own openness to finitude. It will also make use of Heidegger’s concept of Dasein which relates to the uncovering of a primal nature of Being (Sein. When we do this we note how the existential potential of this category are at once released from the bonds of an overly objectivised Sociology and open to the possibility of a richer understanding of action and motivation within this class of persons. It argues that we should make Durkheim compatible with Marx. This is if one allows that the empirical basis for Durkheim’s ‘social condition’ is as set out by Marx. Durkheim was preoccupied by the micro-level of analysis and Marx with wider economic conditions of the nineteenth century. Merton was tied up with detailing the America of his day and with individualized goal-setting and means-ends rationality. By employing the concept of unheimlichkeit in relation to Merton’s work we open up a new form of explanation able to understand the psychic and existential striving for meaning, that Heidegger terms Dasein. Este ensayo defiende que debemos reinterpretar la categoría retraída de Merton utilizando la noción de unheimlichkeit (extrañeza de Heidegger, que se refiere a la exigencia de que nuestra consciencia y toma de decisiones se basan en nuestra aceptación de la finitud. También emplea el concepto de Heidegger del Dasein que se refiere al descubrimiento de una naturaleza primigenia del ser (Sein. Al hacer esto se observa cómo el potencial existencial de esta categoría se libera de las ataduras de una sociología excesivamente objetivizada, y se abre a la posibilidad de un entendimiento más rico de la acción y motivación entre este tipo de personas. Se defiende que deberíamos hacer que Durkheim sea compatible con Marx. Esto ocurriría si se permitiera que la base empírica de la “condición social” de Durkheim fuera como presentada por Marx. Durkheim estaba preocupado por un análisis micro-nivel y Marx con las condiciones económicas, más amplias, del siglo XIX. Merton estaba comprometido con describir la América de su época, y con establecer metas individualizadas, y racionalidad de medios y fines. Al emplear el concepto de unheimlichkeit en relación con el trabajo de Merton, se abre una nueva forma de explicación capaz de comprender el esfuerzo de comprensión psíquico y existencial que Heidegger denomina Dasein. DOWNLOAD THIS PAPER FROM SSRN: http://ssrn.com/abstract=2624580

  5. Clinical databases in physical therapy.

    NARCIS (Netherlands)

    Swinkels, I.C.S.; Ende, C.H.M. van den; Bakker, D. de; Wees, Ph.J van der; Hart, D.L.; Deutscher, D.; Bosch, W.J.H. van den; Dekker, J.

    2007-01-01

    Clinical databases in physical therapy provide increasing opportunities for research into physical therapy theory and practice. At present, information on the characteristics of existing databases is lacking. The purpose of this study was to identify clinical databases in which physical therapists

  6. ORACLE DATABASE SECURITY

    OpenAIRE

    Cristina-Maria Titrade

    2011-01-01

    This paper presents some security issues, namely security database system level, data level security, user-level security, user management, resource management and password management. Security is a constant concern in the design and database development. Usually, there are no concerns about the existence of security, but rather how large it should be. A typically DBMS has several levels of security, in addition to those offered by the operating system or network. Typically, a DBMS has user a...

  7. Mycobacteriophage genome database.

    Science.gov (United States)

    Joseph, Jerrine; Rajendran, Vasanthi; Hassan, Sameer; Kumar, Vanaja

    2011-01-01

    Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification in a rational way. The other objective is to browse the existing and new genomes and describe their functional annotation. The database is available for free at http://mpgdb.ibioinformatics.org/mpgdb.php.

  8. Database Security: A Historical Perspective

    OpenAIRE

    Lesov, Paul

    2010-01-01

    The importance of security in database research has greatly increased over the years as most of critical functionality of the business and military enterprises became digitized. Database is an integral part of any information system and they often hold sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing data or degrading availability of the database. Over the last 30 ye...

  9. Challenges in horizontal integration of eye care services into the pre-existing rural primary care structure: an operations research perspective from Nigeria

    OpenAIRE

    Chinyere Nkemdilim Ezisi; Boniface Ikenna Eze; Obiekwe Okoye; Chimdi Memnofu Chuka-Okosa; Jude Obinna Shiweobi

    2017-01-01

    Background . The provision of population-wide, accessible, affordable, acceptable and evenly distributed qualitative eye care services remains a recurrent challenge to eye care organizations worldwide. Objectives . To report the challenges encountered in setting up eye care service in a pre-existing primary health care facility in rural Nigeria and also audit the common causes of eye disorders in rural setting southeast of Nigeria. Material and methods . The study was an operations ...

  10. LandIT Database

    DEFF Research Database (Denmark)

    Iftikhar, Nadeem; Pedersen, Torben Bach

    2010-01-01

    and reporting purposes. This paper presents the LandIT database; which is result of the LandIT project, which refers to an industrial collaboration project that developed technologies for communication and data integration between farming devices and systems. The LandIT database in principal is based...... on the ISOBUS standard; however the standard is extended with additional requirements, such as gradual data aggregation and flexible exchange of farming data. This paper describes the conceptual and logical schemas of the proposed database based on a real-life farming case study....

  11. JICST Factual Database(2)

    Science.gov (United States)

    Araki, Keisuke

    The computer programme, which builds atom-bond connection tables from nomenclatures, is developed. Chemical substances with their nomenclature and varieties of trivial names or experimental code numbers are inputted. The chemical structures of the database are stereospecifically stored and are able to be searched and displayed according to stereochemistry. Source data are from laws and regulations of Japan, RTECS of US and so on. The database plays a central role within the integrated fact database service of JICST and makes interrelational retrieval possible.

  12. Federal databases

    International Nuclear Information System (INIS)

    Welch, M.J.; Welles, B.W.

    1988-01-01

    Accident statistics on all modes of transportation are available as risk assessment analytical tools through several federal agencies. This paper reports on the examination of the accident databases by personal contact with the federal staff responsible for administration of the database programs. This activity, sponsored by the Department of Energy through Sandia National Laboratories, is an overview of the national accident data on highway, rail, air, and marine shipping. For each mode, the definition or reporting requirements of an accident are determined and the method of entering the accident data into the database is established. Availability of the database to others, ease of access, costs, and who to contact were prime questions to each of the database program managers. Additionally, how the agency uses the accident data was of major interest

  13. Scale out databases for CERN use cases

    International Nuclear Information System (INIS)

    Baranowski, Zbigniew; Grzybek, Maciej; Canali, Luca; Garcia, Daniel Lanza; Surdy, Kacper

    2015-01-01

    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. (paper)

  14. XML: James Webb Space Telescope Database Issues, Lessons, and Status

    Science.gov (United States)

    Detter, Ryan; Mooney, Michael; Fatig, Curtis

    2003-01-01

    This paper will present the current concept using extensible Markup Language (XML) as the underlying structure for the James Webb Space Telescope (JWST) database. The purpose of using XML is to provide a JWST database, independent of any portion of the ground system, yet still compatible with the various systems using a variety of different structures. The testing of the JWST Flight Software (FSW) started in 2002, yet the launch is scheduled for 2011 with a planned 5-year mission and a 5-year follow on option. The initial database and ground system elements, including the commands, telemetry, and ground system tools will be used for 19 years, plus post mission activities. During the Integration and Test (I&T) phases of the JWST development, 24 distinct laboratories, each geographically dispersed, will have local database tools with an XML database. Each of these laboratories database tools will be used for the exporting and importing of data both locally and to a central database system, inputting data to the database certification process, and providing various reports. A centralized certified database repository will be maintained by the Space Telescope Science Institute (STScI), in Baltimore, Maryland, USA. One of the challenges for the database is to be flexible enough to allow for the upgrade, addition or changing of individual items without effecting the entire ground system. Also, using XML should allow for the altering of the import and export formats needed by the various elements, tracking the verification/validation of each database item, allow many organizations to provide database inputs, and the merging of the many existing database processes into one central database structure throughout the JWST program. Many National Aeronautics and Space Administration (NASA) projects have attempted to take advantage of open source and commercial technology. Often this causes a greater reliance on the use of Commercial-Off-The-Shelf (COTS), which is often limiting

  15. The human keratinocyte two-dimensional protein database (update 1994): towards an integrated approach to the study of cell proliferation, differentiation and skin diseases

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Olsen, E

    1994-01-01

    The master two-dimensional (2-D) gel database of human keratinocytes currently lists 3087 cellular proteins (2168 isoelectric focusing, IEF; and 919 none-quilibrium pH gradient electrophoresis, NEPHGE), many of which correspond to posttranslational modifications, 890 polypeptides have been...... in the database. We also report a database of proteins recovered from the medium of noncultured, unfractionated keratinocytes. This database lists 398 polypeptides (309 IEF; 89 NEPHGE) of which 76 have been identified. The aim of the comprehensive databases is to gather, through a systematic study...

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

    International Nuclear Information System (INIS)

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

    2013-01-01

    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. -- Highlights: • A new, interactive version of the HITRAN database is presented. • The data is stored in a structured fashion in a relational database. • The new HITRANonline interface offers increased functionality and easier error correction

  17. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  18. The on scene command and control system (OSC2) : an integrated incident command system (ICS) forms-database management system and oil spill trajectory and fates model

    International Nuclear Information System (INIS)

    Anderson, E.; Galagan, C.; Howlett, E.

    1998-01-01

    The On Scene Command and Control (OSC 2 ) system is an oil spill modeling tool which was developed to combine Incident Command System (ICS) forms, an underlying database, an integrated geographical information system (GIS) and an oil spill trajectory and fate model. The first use of the prototype OSC 2 system was at a PREP drill conducted at the U.S. Coast Guard Marine Safety Office, San Diego, in April 1998. The goal of the drill was to simulate a real-time response over a 36-hour period using the Unified Command System. The simulated spill was the result of a collision between two vessels inside San Diego Bay that caused the release of 2,000 barrels of fuel oil. The hardware component of the system which was tested included three notebook computers, two laser printers, and a poster printer. The field test was a success but it was not a rigorous test of the system's capabilities. The map display was useful in quickly setting up the ICS divisions and groups and in deploying resources. 6 refs., 1 tab., 5 figs

  19. Integration of the Ovation Based Distributed Turbine Control System into the Existing Process Information System and Full Scope Simulator at NPP Krsko

    International Nuclear Information System (INIS)

    Cicvaric, D.

    2010-01-01

    Programmable Digital Electro Hydraulic System (PDEH) is Turbine Control System (TCS), built on Emerson OVATION Distributed Control System (DCS) platform and installed by the Westinghouse Electric Company at the Krsko Nuclear Power Plant as the replacement for the DEH Mod II turbine control system. Core of the PDEH system consist of three pairs of redundant controllers (ETS, OA/OPC and ATC/MSR) configured for the Turbine Generator (TG) set protection, control and monitoring functions. Existing serial data link between replaced DEH Mod II and Process Information System (PIS) was removed and replaced with redundant bi-directional Ethernet TCP/IP data link via two Data Link servers in client-server architecture configuration. All hardwired signals and some of the important calculated signals are being transferred from PDEH to PIS. Main purpose of PIS data link is trending utilization at the existing PIS workstations with pre-configured trend groups and centralized data archiving. Most of the PDEH display screens (mimics) were also replicated on the PIS platform, so that TG set monitoring and operation overview can be performed over the PIS network as well as over the Process Computer Network (PCN) with PMSNT-view utility. The simulator is implemented using a stimulated Windows based Ovation platform and a SGI IRIX based Plant Model Computer (PMC) using the L-3 MAPPS simulation software platform. Two PDEH stimulated systems are installed at the Krsko Full Scope Simulator (KFSS), one for foreground and another for background simulation. Stimulated PDEH hardware is essentially identical to that installed in the plant with the exception of hardware redundancy, isolation features and interface with physical plant I/O. The Ovation control logic sheets are executed with virtual controllers hosted on a simulator specific Virtual Controller Host (VCH) Workstation. The data interface between the simulator Ovation system and the PMC is accomplished through the Ethernet

  20. Cadastral Database Positional Accuracy Improvement

    Science.gov (United States)

    Hashim, N. M.; Omar, A. H.; Ramli, S. N. M.; Omar, K. M.; Din, N.

    2017-10-01

    Positional Accuracy Improvement (PAI) is the refining process of the geometry feature in a geospatial dataset to improve its actual position. This actual position relates to the absolute position in specific coordinate system and the relation to the neighborhood features. With the growth of spatial based technology especially Geographical Information System (GIS) and Global Navigation Satellite System (GNSS), the PAI campaign is inevitable especially to the legacy cadastral database. Integration of legacy dataset and higher accuracy dataset like GNSS observation is a potential solution for improving the legacy dataset. However, by merely integrating both datasets will lead to a distortion of the relative geometry. The improved dataset should be further treated to minimize inherent errors and fitting to the new accurate dataset. The main focus of this study is to describe a method of angular based Least Square Adjustment (LSA) for PAI process of legacy dataset. The existing high accuracy dataset known as National Digital Cadastral Database (NDCDB) is then used as bench mark to validate the results. It was found that the propose technique is highly possible for positional accuracy improvement of legacy spatial datasets.

  1. Refactoring databases evolutionary database design

    CERN Document Server

    Ambler, Scott W

    2006-01-01

    Refactoring has proven its value in a wide range of development projects–helping software professionals improve system designs, maintainability, extensibility, and performance. Now, for the first time, leading agile methodologist Scott Ambler and renowned consultant Pramodkumar Sadalage introduce powerful refactoring techniques specifically designed for database systems. Ambler and Sadalage demonstrate how small changes to table structures, data, stored procedures, and triggers can significantly enhance virtually any database design–without changing semantics. You’ll learn how to evolve database schemas in step with source code–and become far more effective in projects relying on iterative, agile methodologies. This comprehensive guide and reference helps you overcome the practical obstacles to refactoring real-world databases by covering every fundamental concept underlying database refactoring. Using start-to-finish examples, the authors walk you through refactoring simple standalone databas...

  2. Experience using a distributed object oriented database for a DAQ system

    International Nuclear Information System (INIS)

    Bee, C.P.; Eshghi, S.; Jones, R.

    1996-01-01

    To configure the RD13 data acquisition system, we need many parameters which describe the various hardware and software components. Such information has been defined using an entity-relation model and stored in a commercial memory-resident database. during the last year, Itasca, an object oriented database management system (OODB), was chosen as a replacement database system. We have ported the existing databases (hs and sw configurations, run parameters etc.) to Itasca and integrated it with the run control system. We believe that it is possible to use an OODB in real-time environments such as DAQ systems. In this paper, we present our experience and impression: why we wanted to change from an entity-relational approach, some useful features of Itasca, the issues we meet during this project including integration of the database into an existing distributed environment and factors which influence performance. (author)

  3. RDD Databases

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database was established to oversee documents issued in support of fishery research activities including experimental fishing permits (EFP), letters of...

  4. Snowstorm Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Snowstorm Database is a collection of over 500 snowstorms dating back to 1900 and updated operationally. Only storms having large areas of heavy snowfall (10-20...

  5. Dealer Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dealer reporting databases contain the primary data reported by federally permitted seafood dealers in the northeast. Electronic reporting was implemented May 1,...

  6. National database

    DEFF Research Database (Denmark)

    Kristensen, Helen Grundtvig; Stjernø, Henrik

    1995-01-01

    Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen.......Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen....

  7. Integrating a Typhoon Event Database with an Optimal Flood Operation Model on the Real-Time Flood Control of the Tseng-Wen Reservoir

    Science.gov (United States)

    Chen, Y. W.; Chang, L. C.

    2012-04-01

    Typhoons which normally bring a great amount of precipitation are the primary natural hazard in Taiwan during flooding season. Because the plentiful rainfall quantities brought by typhoons are normally stored for the usage of the next draught period, the determination of release strategies for flood operation of reservoirs which is required to simultaneously consider not only the impact of reservoir safety and the flooding damage in plain area but also for the water resource stored in the reservoir after typhoon becomes important. This study proposes a two-steps study process. First, this study develop an optimal flood operation model (OFOM) for the planning of flood control and also applies the OFOM on Tseng-wun reservoir and the downstream plain related to the reservoir. Second, integrating a typhoon event database with the OFOM mentioned above makes the proposed planning model have ability to deal with a real-time flood control problem and names as real-time flood operation model (RTFOM). Three conditions are considered in the proposed models, OFOM and RTFOM, include the safety of the reservoir itself, the reservoir storage after typhoons and the impact of flooding in the plain area. Besides, the flood operation guideline announced by government is also considered in the proposed models. The these conditions and the guideline can be formed as an optimization problem which is solved by the genetic algorithm (GA) in this study. Furthermore, a distributed runoff model, kinematic-wave geomorphic instantaneous unit hydrograph (KW-GIUH), and a river flow simulation model, HEC-RAS, are used to simulate the river water level of Tseng-wun basin in the plain area and the simulated level is shown as an index of the impact of flooding. Because the simulated levels are required to re-calculate iteratively in the optimization model, applying a recursive artificial neural network (recursive ANN) instead of the HEC-RAS model can significantly reduce the computational burden of

  8. INIST: databases reorientation

    International Nuclear Information System (INIS)

    Bidet, J.C.

    1995-01-01

    INIST is a CNRS (Centre National de la Recherche Scientifique) laboratory devoted to the treatment of scientific and technical informations and to the management of these informations compiled in a database. Reorientation of the database content has been proposed in 1994 to increase the transfer of research towards enterprises and services, to develop more automatized accesses to the informations, and to create a quality assurance plan. The catalog of publications comprises 5800 periodical titles (1300 for fundamental research and 4500 for applied research). A science and technology multi-thematic database will be created in 1995 for the retrieval of applied and technical informations. ''Grey literature'' (reports, thesis, proceedings..) and human and social sciences data will be added to the base by the use of informations selected in the existing GRISELI and Francis databases. Strong modifications are also planned in the thematic cover of Earth sciences and will considerably reduce the geological information content. (J.S.). 1 tab

  9. Cultural consonance, constructions of science and co-existence: a review of the integration of traditional, complementary and alternative medicine in low- and middle-income countries

    Science.gov (United States)

    Lakshmi, Josyula K; Nambiar, Devaki; Narayan, Venkatesh; Sathyanarayana, Tamysetty N; Porter, John; Sheikh, Kabir

    2015-01-01

    This review examined the determinants, patterns and imports of official recognition, and incorporation of different traditional, complementary and alternative systems of medicine (TCAM) in the public health establishment of low- and middle-income countries, with a particular focus on India. Public health systems in most countries have tended to establish health facilities centred on allopathy, and then to recognize or derecognize different TCAM based on evidence or judgement, to arrive at health-care configurations that include several systems of medicine with disparate levels of authority, jurisdiction and government support. The rationale for the inclusion of TCAM providers in the public health workforce ranges from the need for personnel to address the disease burden borne by the public health system, to the desirability of providing patients with a choice of therapeutic modalities, and the nurturing of local culture. Integration, mostly described as a juxtaposition of different systems of medical practice, is often implemented as a system of establishing personnel with certification in different medical systems, in predominantly allopathic health-care facilities, to practise allopathic medicine. A hierarchy of systems of medicine, often unacknowledged, is exercised in most societies, with allopathy at the top, certain TCAM systems next and local healing traditions last. The tools employed by TCAM practitioners in diagnosis, research, pharmacy, marketing and education and training, which are seen to increasingly emulate those of allopathy, are sometimes inappropriate for use in therapeutic systems with widely divergent epistemologies, which call for distinct research paradigms. The coexistence of numerous systems of medicine, while offering the population greater choice, and presumably enhancing geographical access to health care as well, is often fraught with tensions related to the coexistence of philosophically disparate, even opposed, disciplines, with

  10. Challenges in horizontal integration of eye care services into the pre-existing rural primary care structure: an operations research perspective from Nigeria

    Directory of Open Access Journals (Sweden)

    Chinyere Nkemdilim Ezisi

    2017-12-01

    Full Text Available Background . The provision of population-wide, accessible, affordable, acceptable and evenly distributed qualitative eye care services remains a recurrent challenge to eye care organizations worldwide. Objectives . To report the challenges encountered in setting up eye care service in a pre-existing primary health care facility in rural Nigeria and also audit the common causes of eye disorders in rural setting southeast of Nigeria. Material and methods . The study was an operations research study conducted at Akpuoga-Nike between February and April 2011. Demographic and ophthalmic clinical data were collected. Health system-, community- and patient-determined challenges were catalogued and analyzed using Epi Info Statistical software for Windows, version 6. Univariate analysis was performed for data distribution testing. Analytical statistics were performed, with p < 0.05 considered statistically significant. Results . A total of 481 (males, 144 (29.9%; females, 377(70.1% patients aged 42.3 ± 20.2 SD years (range 4–80 years were seen. The leading eye disorders were refractive error – 28.9%, and cataract – 16.4%. The operations challenges encountered included difficulties with community sensitization/advocacies, inadequate infrastructure and mobile equipment, as well as lack of eye care manpower, consumables and funding deficits. Conclusions . Health system-related issues were the main challenges encountered. Recruitment of an adequate number of rural eye care workforce, provision of needed material resources, adequate funding and engendering community participation in rural eye care delivery through grass roots advocacy and health service public education would overcome the challenges.

  11. Enhancing continental-scale understanding of agriculture: Integrating the National Ecological Observatory Network (NEON) with existing research networks to address global change.

    Science.gov (United States)

    Kelly, G.

    2015-12-01

    Over the past decade, there has been a resurgence of interest in the sustainability of the world's food system and its contributions to feeding the world's population as well as to ensuring environmental sustainability of the planet. The elements of this grand challenge are by now well known. Analysis of agricultural sustainability is made more challenging by the fact that the local responses to these global drivers of change are extremely variable in space and time due to the biophysical and geopolitical heterogeneity across the United States, and the world. Utilizing research networks allows the scientific community to leverage existing knowledge, models and data to develop a framework for understanding the interplay between global change drivers, regional, and continental sustainability of US agriculture. For example, well-established instrumented and calibrated research networks will allow for the examination of the potential tradeoffs between: 1) crop production, 2) land use and carbon emissions and sequestration, 3) groundwater depletion, and 4) nitrogen dynamics. NEON represents a major investment in scientific infrastructure in support of ecological research at a continental scale and is intended to address multiple ecological grand challenges. NEON will collect data from automated sensors and sample organisms and ecological variables in 20 eco-climatic domains. We will provide examples of how NEON's full potential can be realized when these data are combined with long term experimental results and other sensor networks [e.g., Ameriflux, Fluxnet, the Long-term Ecological Research Program (LTER), the Long-term Agroecosystem Research Network (LTAR)], Critical Zone Observatory (CZO).

  12. ZAGRADA - A New Radiocarbon Database

    International Nuclear Information System (INIS)

    Portner, A.; Obelic, B.; Krajcar Bornic, I.

    2008-01-01

    In the Radiocarbon and Tritium Laboratory at the Rudjer Boskovic Institute three different techniques for 14C dating have been used: Gas Proportional Counting (GPC), Liquid Scintillation Counting (LSC) and preparation of milligram-sized samples for AMS dating (Accelerator Mass Spectrometry). The use of several measurement techniques has initiated a need for development of a new relational database ZAGRADA (Zagreb Radiocarbon Database) since the existing software package CARBO could not satisfy the requirements for parallel processing/using of several techniques. Using the SQL procedures, and constraints defined by primary and foreign keys, ZAGRADA enforces high data integrity and provides better performances in data filtering and sorting. Additionally, the new database for 14C samples is a multi-user oriented application that can be accessed from remote computers in the work group providing thus better efficiency of laboratory activities. In order to facilitate data handling and processing in ZAGRADA, the graphical user interface is designed to be user-friendly and to perform various actions on data like input, corrections, searching, sorting and output to printer. All invalid actions performed in user interface are registered with short textual description of an error occurred and appearing on screen in message boxes. Unauthorized access is also prevented by login control and each application window has implemented support to track last changes made by the user. The implementation of a new database for 14C samples has significant contribution to scientific research performed in the Radiocarbon and Tritium Laboratory and will provide better and easier communication with customers.(author)

  13. Integrated Tsunami Database: simulation and identification of seismic tsunami sources, 3D visualization and post-disaster assessment on the shore

    Science.gov (United States)

    Krivorot'ko, Olga; Kabanikhin, Sergey; Marinin, Igor; Karas, Adel; Khidasheli, David

    2013-04-01

    One of the most important problems of tsunami investigation is the problem of seismic tsunami source reconstruction. Non-profit organization WAPMERR (http://wapmerr.org) has provided a historical database of alleged tsunami sources around the world that obtained with the help of information about seaquakes. WAPMERR also has a database of observations of the tsunami waves in coastal areas. The main idea of presentation consists of determining of the tsunami source parameters using seismic data and observations of the tsunami waves on the shore, and the expansion and refinement of the database of presupposed tsunami sources for operative and accurate prediction of hazards and assessment of risks and consequences. Also we present 3D visualization of real-time tsunami wave propagation and loss assessment, characterizing the nature of the building stock in cities at risk, and monitoring by satellite images using modern GIS technology ITRIS (Integrated Tsunami Research and Information System) developed by WAPMERR and Informap Ltd. The special scientific plug-in components are embedded in a specially developed GIS-type graphic shell for easy data retrieval, visualization and processing. The most suitable physical models related to simulation of tsunamis are based on shallow water equations. We consider the initial-boundary value problem in Ω := {(x,y) ?R2 : x ?(0,Lx ), y ?(0,Ly ), Lx,Ly > 0} for the well-known linear shallow water equations in the Cartesian coordinate system in terms of the liquid flow components in dimensional form Here ?(x,y,t) defines the free water surface vertical displacement, i.e. amplitude of a tsunami wave, q(x,y) is the initial amplitude of a tsunami wave. The lateral boundary is assumed to be a non-reflecting boundary of the domain, that is, it allows the free passage of the propagating waves. Assume that the free surface oscillation data at points (xm, ym) are given as a measured output data from tsunami records: fm(t) := ? (xm, ym,t), (xm

  14. A study of existing experimental data and validation process for evaluated high energy nuclear data. Report of task force on integral test for JENDL High Energy File in Japanese Nuclear Data Committee

    International Nuclear Information System (INIS)

    Oyama, Yukio; Baba, Mamoru; Watanabe, Yukinobu

    1998-11-01

    JENDL High Energy File (JENDL-HE) is being produced by Japanese Nuclear Data Committee (JNDC) to provide common fundamental nuclear data in the intermediate energy region for many applications concerning a basic research, an accelerator-driven nuclear waste transmutation, a fusion material study, and medical applications like the radiation therapy. The first version of JENDL-HE, which contains the evaluated nuclear data up to 50 MeV, is planned to release in 1998. However, a method of integral test with which we can validate the high-energy nuclear data file has not been established. The validation of evaluated nuclear data through the integral tests is necessary to promote utilization of JENDL-HE. JNDC set up a task force in 1997 to discuss the problems concerning the integral tests of JENDL-HE. The task force members have surveyed and studied the current status of the problems for a year to obtain a guideline for development of the high-energy nuclear database. This report summarizes the results of the survey and study done by the task force for JNDC. (author)

  15. Integrated Synthesis of the Permian Basin: Data and Models for Recovering Existing and Undiscovered Oil Resources from the Largest Oil-Bearing Basin in the U.S.

    Energy Technology Data Exchange (ETDEWEB)

    John Jackson; Katherine Jackson

    2008-09-30

    Large volumes of oil and gas remain in the mature basins of North America. This is nowhere more true than in the Permian Basin of Texas and New Mexico. A critical barrier to recovery of this vast remaining resource, however, is information. Access to accurate geological data and analyses of the controls of hydrocarbon distribution is the key to the knowledge base as well as the incentives needed by oil and gas companies. The goals of this project were to collect, analyze, synthesize, and deliver to industry and the public fundamental information and data on the geology of oil and gas systems in the Permian Basin. This was accomplished in two ways. First we gathered all available data, organized it, and placed it on the web for ready access. Data include core analysis data, lists of pertinent published reports, lists of available cores, type logs, and selected PowerPoint presentations. We also created interpretive data such as type logs, geological cross sections, and geological maps and placed them in a geospatially-registered framework in ARC/GIS. Second, we created new written syntheses of selected reservoir plays in the Permian basin. Although only 8 plays were targeted for detailed analysis in the project proposal to DOE, 14 were completed. These include Ellenburger, Simpson, Montoya, Fusselman, Wristen, Thirtyone, Mississippian, Morrow, Atoka, Strawn, Canyon/Cisco, Wolfcamp, Artesia Group, and Delaware Mountain Group. These fully illustrated reports include critical summaries of published literature integrated with new unpublished research conducted during the project. As such these reports provide the most up-to-date analysis of the geological controls on reservoir development available. All reports are available for download on the project website and are also included in this final report. As stated in our proposal, technology transfer is perhaps the most important component of the project. In addition to providing direct access to data and reports through

  16. Grid integration of electric-powered vehicles in existing and future energy supply structures. Advances in systems analyses 1. Final report; Netzintegration von Fahrzeugen mit elektrifizierten Antriebssystemen in bestehende und zukuenftige Energieversorgungsstrukturen. Advances in System Analyses 1. Endbericht

    Energy Technology Data Exchange (ETDEWEB)

    Linssen, Jochen; Bickert, Stefan; Hennings, Wilfried [Forschungszentrum Juelich GmbH (Germany). Inst. fuer Energie- und Klimaforschung, Systemforschung und Technologische Entwicklung (IEK-STE); and others

    2012-07-01

    The research project examines whether a fleet of vehicles with electric propulsion system (xEV) can be integrated into existing and future energy supply systems for effective integration of fluctuating power production as well as for energy storage. A multi-sectoral, system-wide scenario analysis is performed to evaluate the grid integration of electric vehicles. The effect of an xEV fleet and the impacts of various battery charging scenarios, including the option of feeding power back into the grid, are addressed by detailed technical and economic models and summarized by an energy system model. The suitability of different powertrain concepts is analysed, giving consideration to their individual applications by users. Based on the results of a German nationwide survey of mobility patterns and analyses of 47 test subjects, individual driving profiles for private cars are drawn up and stored in a database. They are used as input for the vehicle energy model. This model calculates the energy requirements of different xEV concepts and facilitates optimized powertrain design and battery sizing for the respective applications. The results show that if the batteries are charged overnight it is possible to cover a major fraction of daily driving distances by electric power. Additional charging during the day does not significantly improve this fraction. The auxiliaries have a greater influence on the vehicle's energy demand than individual driving patterns. Battery lifetime is extended by recharging the battery as required and preferably as late as possible before the next trip. In most cases, using the batteries for grid services reduces battery lifetime and leads to higher specific costs. Models of the transmission grid and typical distribution grids are developed. It is shown that charging one million xEV in 2020 and six million in 2030 (as envisaged by the German Federal Government) is technically feasible without major structural modifications of the transmission

  17. Grid integration of electric-powered vehicles in existing and future energy supply structures. Advances in systems analyses 1. Final report; Netzintegration von Fahrzeugen mit elektrifizierten Antriebssystemen in bestehende und zukuenftige Energieversorgungsstrukturen. Advances in System Analyses 1. Endbericht

    Energy Technology Data Exchange (ETDEWEB)

    Linssen, Jochen; Bickert, Stefan; Hennings, Wilfried [Forschungszentrum Juelich GmbH (Germany). Inst. fuer Energie- und Klimaforschung, Systemforschung und Technologische Entwicklung (IEK-STE)] [and others

    2012-07-01

    The research project examines whether a fleet of vehicles with electric propulsion system (xEV) can be integrated into existing and future energy supply systems for effective integration of fluctuating power production as well as for energy storage. A multi-sectoral, system-wide scenario analysis is performed to evaluate the grid integration of electric vehicles. The effect of an xEV fleet and the impacts of various battery charging scenarios, including the option of feeding power back into the grid, are addressed by detailed technical and economic models and summarized by an energy system model. The suitability of different powertrain concepts is analysed, giving consideration to their individual applications by users. Based on the results of a German nationwide survey of mobility patterns and analyses of 47 test subjects, individual driving profiles for private cars are drawn up and stored in a database. They are used as input for the vehicle energy model. This model calculates the energy requirements of different xEV concepts and facilitates optimized powertrain design and battery sizing for the respective applications. The results show that if the batteries are charged overnight it is possible to cover a major fraction of daily driving distances by electric power. Additional charging during the day does not significantly improve this fraction. The auxiliaries have a greater influence on the vehicle's energy demand than individual driving patterns. Battery lifetime is extended by recharging the battery as required and preferably as late as possible before the next trip. In most cases, using the batteries for grid services reduces battery lifetime and leads to higher specific costs. Models of the transmission grid and typical distribution grids are developed. It is shown that charging one million xEV in 2020 and six million in 2030 (as envisaged by the German Federal Government) is technically feasible without major structural modifications of the

  18. Scale out databases for CERN use cases

    CERN Document Server

    Baranowski, Zbigniew; Canali, Luca; Garcia, Daniel Lanza; Surdy, Kacper

    2015-01-01

    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 dat...

  19. Texas flexible pavements overlays : review and analysis of existing databases.

    Science.gov (United States)

    2011-12-01

    Proper calibration of pavement design and rehabilitation performance models to : conditions in Texas is essential for cost-effective flexible pavement design. The degree of : excellence with which TxDOTs pavement design models is calibrated will d...

  20. A Generative Approach for Building Database Federations

    Directory of Open Access Journals (Sweden)

    Uwe Hohenstein

    1999-11-01

    Full Text Available A comprehensive, specification-based approach for building database federations is introduced that supports an integrated ODMG2.0 conforming access to heterogeneous data sources seamlessly done in C++. The approach is centered around several generators. A first set of generators produce ODMG adapters for local sources in order to homogenize them. Each adapter represents an ODMG view and supports the ODMG manipulation and querying. The adapters can be plugged into a federation framework. Another generator produces an homogeneous and uniform view by putting an ODMG conforming federation layer on top of the adapters. Input to these generators are schema specifications. Schemata are defined in corresponding specification languages. There are languages to homogenize relational and object-oriented databases, as well as ordinary file systems. Any specification defines an ODMG schema and relates it to an existing data source. An integration language is then used to integrate the schemata and to build system-spanning federated views thereupon. The generative nature provides flexibility with respect to schema modification of component databases. Any time a schema changes, only the specification has to be adopted; new adapters are generated automatically

  1. The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci

    Directory of Open Access Journals (Sweden)

    Xavier Suresh R

    2006-06-01

    Full Text Available Abstract Background Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these data available in a genomic context to researchers via a user friendly query interface. Description The QTL (Quantitative Trait Locus data and related information for bovine QTL are gathered from published work and from existing databases. An integrated database schema was designed and the database (MySQL populated with the gathered data. The bovine QTL Viewer was developed for the integration of QTL data available for cattle. The tool consists of an integrated database of bovine QTL and the QTL viewer to display QTL and their chromosomal position. Conclusion We present a web accessible, integrated database of bovine (dairy and beef cattle QTL for use by animal geneticists. The viewer and database are of general applicability to any livestock species for which there are public QTL data. The viewer can be accessed at http://bovineqtl.tamu.edu.

  2. Constructing a Geology Ontology Using a Relational Database

    Science.gov (United States)

    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. InterAction Database (IADB)

    Science.gov (United States)

    The InterAction Database includes demographic and prescription information for more than 500,000 patients in the northern and middle Netherlands and has been integrated with other systems to enhance data collection and analysis.

  4. EXIST Perspective for SFXTs

    Science.gov (United States)

    Ubertini, Pietro; Sidoli, L.; Sguera, V.; Bazzano, A.

    2009-12-01

    Supergiant Fast X-ray Transients (SFXTs) are one of the most interesting (and unexpected) results of the INTEGRAL mission. They are a new class of HMXBs displaying short hard X-ray outbursts (duration less tha a day) characterized by fast flares (few hours timescale) and large dinamic range (10E3-10E4). The physical mechanism driving their peculiar behaviour is still unclear and highly debated: some models involve the structure of the supergiant companion donor wind (likely clumpy, in a spherical or non spherical geometry) and the orbital properties (wide separation with eccentric or circular orbit), while others involve the properties of the neutron star compact object and invoke very low magnetic field values (B 1E14 G, magnetars). The picture is still highly unclear from the observational point of view as well: no cyclotron lines have been detected in the spectra, thus the strength of the neutron star magnetic field is unknown. Orbital periods have been measured in only 4 systems, spanning from 3.3 days to 165 days. Even the duty cycle seems to be quite different from source to source. The Energetic X-ray Imaging Survey Telescope (EXIST), with its hard X-ray all-sky survey and large improved limiting sensitivity, will allow us to get a clearer picture of SFXTs. A complete census of their number is essential to enlarge the sample. A long term and continuous as possible X-ray monitoring is crucial to -(1) obtain the duty cycle, -(2 )investigate their unknown orbital properties (separation, orbital period, eccentricity),- (3) to completely cover the whole outburst activity, (4)-to search for cyclotron lines in the high energy spectra. EXIST observations will provide crucial informations to test the different models and shed light on the peculiar behaviour of SFXTs.

  5. Integration

    DEFF Research Database (Denmark)

    Emerek, Ruth

    2004-01-01

    Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration......Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration...

  6. The human interactome knowledge base (hint-kb): An integrative human protein interaction database enriched with predicted protein–protein interaction scores using a novel hybrid technique

    KAUST Repository

    Theofilatos, Konstantinos A.; Dimitrakopoulos, Christos M.; Likothanassis, Spiridon D.; Kleftogiannis, Dimitrios A.; Moschopoulos, Charalampos N.; Alexakos, Christos; Papadimitriou, Stergios; Mavroudi, Seferina P.

    2013-01-01

    Proteins are the functional components of many cellular processes and the identification of their physical protein–protein interactions (PPIs) is an area of mature academic research. Various databases have been developed containing information about

  7. A Novel Approach: Chemical Relational Databases, and the ...

    Science.gov (United States)

    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

  8. Database Vs Data Warehouse

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Data warehouse technology includes a set of concepts and methods that offer the users useful information for decision making. The necessity to build a data warehouse arises from the necessity to improve the quality of information in the organization. The date proceeding from different sources, having a variety of forms - both structured and unstructured, are filtered according to business rules and are integrated in a single large data collection. Using informatics solutions, managers have understood that data stored in operational systems - including databases, are an informational gold mine that must be exploited. Data warehouses have been developed to answer the increasing demands for complex analysis, which could not be properly achieved with operational databases. The present paper emphasizes some of the criteria that information application developers can use in order to choose between a database solution or a data warehouse one.

  9. RODOS database adapter

    International Nuclear Information System (INIS)

    Xie Gang

    1995-11-01

    Integrated data management is an essential aspect of many automatical information systems such as RODOS, a real-time on-line decision support system for nuclear emergency management. In particular, the application software must provide access management to different commercial database systems. This report presents the tools necessary for adapting embedded SQL-applications to both HP-ALLBASE/SQL and CA-Ingres/SQL databases. The design of the database adapter and the concept of RODOS embedded SQL syntax are discussed by considering some of the most important features of SQL-functions and the identification of significant differences between SQL-implementations. Finally fully part of the software developed and the administrator's and installation guides are described. (orig.) [de

  10. Database Application Schema Forensics

    Directory of Open Access Journals (Sweden)

    Hector Quintus Beyers

    2014-12-01

    Full Text Available The application schema layer of a Database Management System (DBMS can be modified to deliver results that may warrant a forensic investigation. Table structures can be corrupted by changing the metadata of a database or operators of the database can be altered to deliver incorrect results when used in queries. This paper will discuss categories of possibilities that exist to alter the application schema with some practical examples. Two forensic environments are introduced where a forensic investigation can take place in. Arguments are provided why these environments are important. Methods are presented how these environments can be achieved for the application schema layer of a DBMS. A process is proposed on how forensic evidence should be extracted from the application schema layer of a DBMS. The application schema forensic evidence identification process can be applied to a wide range of forensic settings.

  11. Tibetan Magmatism Database

    Science.gov (United States)

    Chapman, James B.; Kapp, Paul

    2017-11-01

    A database containing previously published geochronologic, geochemical, and isotopic data on Mesozoic to Quaternary igneous rocks in the Himalayan-Tibetan orogenic system are presented. The database is intended to serve as a repository for new and existing igneous rock data and is publicly accessible through a web-based platform that includes an interactive map and data table interface with search, filtering, and download options. To illustrate the utility of the database, the age, location, and ɛHft composition of magmatism from the central Gangdese batholith in the southern Lhasa terrane are compared. The data identify three high-flux events, which peak at 93, 50, and 15 Ma. They are characterized by inboard arc migration and a temporal and spatial shift to more evolved isotopic compositions.

  12. [Integrity].

    Science.gov (United States)

    Gómez Rodríguez, Rafael Ángel

    2014-01-01

    To say that someone possesses integrity is to claim that that person is almost predictable about responses to specific situations, that he or she can prudentially judge and to act correctly. There is a closed interrelationship between integrity and autonomy, and the autonomy rests on the deeper moral claim of all humans to integrity of the person. Integrity has two senses of significance for medical ethic: one sense refers to the integrity of the person in the bodily, psychosocial and intellectual elements; and in the second sense, the integrity is the virtue. Another facet of integrity of the person is la integrity of values we cherish and espouse. The physician must be a person of integrity if the integrity of the patient is to be safeguarded. The autonomy has reduced the violations in the past, but the character and virtues of the physician are the ultimate safeguard of autonomy of patient. A field very important in medicine is the scientific research. It is the character of the investigator that determines the moral quality of research. The problem arises when legitimate self-interests are replaced by selfish, particularly when human subjects are involved. The final safeguard of moral quality of research is the character and conscience of the investigator. Teaching must be relevant in the scientific field, but the most effective way to teach virtue ethics is through the example of the a respected scientist.

  13. Network-based Database Course

    DEFF Research Database (Denmark)

    Nielsen, J.N.; Knudsen, Morten; Nielsen, Jens Frederik Dalsgaard

    A course in database design and implementation has been de- signed, utilizing existing network facilities. The course is an elementary course for students of computer engineering. Its purpose is to give the students a theoretical database knowledge as well as practical experience with design...... and implementation. A tutorial relational database and the students self-designed databases are implemented on the UNIX system of Aalborg University, thus giving the teacher the possibility of live demonstrations in the lecture room, and the students the possibility of interactive learning in their working rooms...

  14. Active in-database processing to support ambient assisted living systems.

    Science.gov (United States)

    de Morais, Wagner O; Lundström, Jens; Wickström, Nicholas

    2014-08-12

    As an alternative to the existing software architectures that underpin the development of smart homes and ambient assisted living (AAL) systems, this work presents a database-centric architecture that takes advantage of active databases and in-database processing. Current platforms supporting AAL systems use database management systems (DBMSs) exclusively for data storage. Active databases employ database triggers to detect and react to events taking place inside or outside of the database. DBMSs can be extended with stored procedures and functions that enable in-database processing. This means that the data processing is integrated and performed within the DBMS. The feasibility and flexibility of the proposed approach were demonstrated with the implementation of three distinct AAL services. The active database was used to detect bed-exits and to discover common room transitions and deviations during the night. In-database machine learning methods were used to model early night behaviors. Consequently, active in-database processing avoids transferring sensitive data outside the database, and this improves performance, security and privacy. Furthermore, centralizing the computation into the DBMS facilitates code reuse, adaptation and maintenance. These are important system properties that take into account the evolving heterogeneity of users, their needs and the devices that are characteristic of smart homes and AAL systems. Therefore, DBMSs can provide capabilities to address requirements for scalability, security, privacy, dependability and personalization in applications of smart environments in healthcare.

  15. Active In-Database Processing to Support Ambient Assisted Living Systems

    Directory of Open Access Journals (Sweden)

    Wagner O. de Morais

    2014-08-01

    Full Text Available As an alternative to the existing software architectures that underpin the development of smart homes and ambient assisted living (AAL systems, this work presents a database-centric architecture that takes advantage of active databases and in-database processing. Current platforms supporting AAL systems use database management systems (DBMSs exclusively for data storage. Active databases employ database triggers to detect and react to events taking place inside or outside of the database. DBMSs can be extended with stored procedures and functions that enable in-database processing. This means that the data processing is integrated and performed within the DBMS. The feasibility and flexibility of the proposed approach were demonstrated with the implementation of three distinct AAL services. The active database was used to detect bed-exits and to discover common room transitions and deviations during the night. In-database machine learning methods were used to model early night behaviors. Consequently, active in-database processing avoids transferring sensitive data outside the database, and this improves performance, security and privacy. Furthermore, centralizing the computation into the DBMS facilitates code reuse, adaptation and maintenance. These are important system properties that take into account the evolving heterogeneity of users, their needs and the devices that are characteristic of smart homes and AAL systems. Therefore, DBMSs can provide capabilities to address requirements for scalability, security, privacy, dependability and personalization in applications of smart environments in healthcare.

  16. The CUTLASS database facilities

    International Nuclear Information System (INIS)

    Jervis, P.; Rutter, P.

    1988-09-01

    The enhancement of the CUTLASS database management system to provide improved facilities for data handling is seen as a prerequisite to its effective use for future power station data processing and control applications. This particularly applies to the larger projects such as AGR data processing system refurbishments, and the data processing systems required for the new Coal Fired Reference Design stations. In anticipation of the need for improved data handling facilities in CUTLASS, the CEGB established a User Sub-Group in the early 1980's to define the database facilities required by users. Following the endorsement of the resulting specification and a detailed design study, the database facilities have been implemented as an integral part of the CUTLASS system. This paper provides an introduction to the range of CUTLASS Database facilities, and emphasises the role of Database as the central facility around which future Kit 1 and (particularly) Kit 6 CUTLASS based data processing and control systems will be designed and implemented. (author)

  17. ADANS database specification

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-01-16

    The purpose of the Air Mobility Command (AMC) Deployment Analysis System (ADANS) Database Specification (DS) is to describe the database organization and storage allocation and to provide the detailed data model of the physical design and information necessary for the construction of the parts of the database (e.g., tables, indexes, rules, defaults). The DS includes entity relationship diagrams, table and field definitions, reports on other database objects, and a description of the ADANS data dictionary. ADANS is the automated system used by Headquarters AMC and the Tanker Airlift Control Center (TACC) for airlift planning and scheduling of peacetime and contingency operations as well as for deliberate planning. ADANS also supports planning and scheduling of Air Refueling Events by the TACC and the unit-level tanker schedulers. ADANS receives input in the form of movement requirements and air refueling requests. It provides a suite of tools for planners to manipulate these requirements/requests against mobility assets and to develop, analyze, and distribute schedules. Analysis tools are provided for assessing the products of the scheduling subsystems, and editing capabilities support the refinement of schedules. A reporting capability provides formatted screen, print, and/or file outputs of various standard reports. An interface subsystem handles message traffic to and from external systems. The database is an integral part of the functionality summarized above.

  18. DisFace: A Database of Human Facial Disorders

    Directory of Open Access Journals (Sweden)

    Paramjit Kaur

    2017-10-01

    Full Text Available Face is an integral part of human body by which an individual communicates in the society. Its importance can be highlighted by the fact that a person deprived of face cannot sustain in the living world. In the past few decades, human face has gained attention of several researchers, whether it is related to facial anthropometry, facial disorder, face transplantation or face reconstruction. Several researches have also shown the correlation between neuropsychiatry disorders and human face and also that how face recognition abilities are correlated with these disorders. Currently, several databases exist which contain the facial images of several individuals captured from different sources. The advantage of these databases is that the images in these databases can be used for testing and training purpose. However, in current date no such database exists which would provide not only facial images of individuals; but also the literature concerning the human face, list of several genes controlling human face, list of facial disorders and various tools which work on facial images. Thus, the current research aims at developing a database of human facial disorders using bioinformatics approach. The database will contain information about facial diseases, medications, symptoms, findings, etc. The information will be extracted from several other databases like OMIM, PubChem, Radiopedia, Medline Plus, FDA, etc. and links to them will also be provided. Initially, the diseases specific for human face have been obtained from already created published corpora of literature using text mining approach. Becas tool was used to obtain the specific task.  A dataset will be created and stored in the form of database. It will be a database containing cross-referenced index of human facial diseases, medications, symptoms, signs, etc. Thus, a database on human face with complete existing information about human facial disorders will be developed. The novelty of the

  19. Building spatio-temporal database model based on ontological approach using relational database environment

    International Nuclear Information System (INIS)

    Mahmood, N.; Burney, S.M.A.

    2017-01-01

    Everything in this world is encapsulated by space and time fence. Our daily life activities are utterly linked and related with other objects in vicinity. Therefore, a strong relationship exist with our current location, time (including past, present and future) and event through with we are moving as an object also affect our activities in life. Ontology development and its integration with database are vital for the true understanding of the complex systems involving both spatial and temporal dimensions. In this paper we propose a conceptual framework for building spatio-temporal database model based on ontological approach. We have used relational data model for modelling spatio-temporal data content and present our methodology with spatio-temporal ontological accepts and its transformation into spatio-temporal database model. We illustrate the implementation of our conceptual model through a case study related to cultivated land parcel used for agriculture to exhibit the spatio-temporal behaviour of agricultural land and related entities. Moreover, it provides a generic approach for designing spatiotemporal databases based on ontology. The proposed model is capable to understand the ontological and somehow epistemological commitments and to build spatio-temporal ontology and transform it into a spatio-temporal data model. Finally, we highlight the existing and future research challenges. (author)

  20. GigaDB: announcing the GigaScience database

    Directory of Open Access Journals (Sweden)

    Sneddon Tam P

    2012-07-01

    Full Text Available Abstract With the launch of GigaScience journal, here we provide insight into the accompanying database GigaDB, which allows the integration of manuscript publication with supporting data and tools. Reinforcing and upholding GigaScience’s goals to promote open-data and reproducibility of research, GigaDB also aims to provide a home, when a suitable public repository does not exist, for the supporting data or tools featured in the journal and beyond.

  1. Efficient Incremental Garbage Collection for Workstation/Server Database Systems

    OpenAIRE

    Amsaleg , Laurent; Gruber , Olivier; Franklin , Michael

    1994-01-01

    Projet RODIN; We describe an efficient server-based algorithm for garbage collecting object-oriented databases in a workstation/server environment. The algorithm is incremental and runs concurrently with client transactions, however, it does not hold any locks on data and does not require callbacks to clients. It is fault tolerant, but performs very little logging. The algorithm has been designed to be integrated into existing OODB systems, and therefore it works with standard implementation ...

  2. Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals

    Science.gov (United States)

    Rothwell, Joseph A.; Urpi-Sarda, Mireia; Boto-Ordoñez, Maria; Knox, Craig; Llorach, Rafael; Eisner, Roman; Cruz, Joseph; Neveu, Vanessa; Wishart, David; Manach, Claudine; Andres-Lacueva, Cristina; Scalbert, Augustin

    2012-01-01

    Phenol-Explorer, launched in 2009, is the only comprehensive web-based database on the content in foods of polyphenols, a major class of food bioactives that receive considerable attention due to their role in the prevention of diseases. Polyphenols are rarely absorbed and excreted in their ingested forms, but extensively metabolized in the body, and until now, no database has allowed the recall of identities and concentrations of polyphenol metabolites in biofluids after the consumption of polyphenol-rich sources. Knowledge of these metabolites is essential in the planning of experiments whose aim is to elucidate the effects of polyphenols on health. Release 2.0 is the first major update of the database, allowing the rapid retrieval of data on the biotransformations and pharmacokinetics of dietary polyphenols. Data on 375 polyphenol metabolites identified in urine and plasma were collected from 236 peer-reviewed publications on polyphenol metabolism in humans and experimental animals and added to the database by means of an extended relational design. Pharmacokinetic parameters have been collected and can be retrieved in both tabular and graphical form. The web interface has been enhanced and now allows the filtering of information according to various criteria. Phenol-Explorer 2.0, which will be periodically updated, should prove to be an even more useful and capable resource for polyphenol scientists because bioactivities and health effects of polyphenols are dependent on the nature and concentrations of metabolites reaching the target tissues. The Phenol-Explorer database is publicly available and can be found online at http://www.phenol-explorer.eu. Database URL: http://www.phenol-explorer.eu PMID:22879444

  3. Molecule database framework: a framework for creating database applications with chemical structure search capability.

    Science.gov (United States)

    Kiener, Joos

    2013-12-11

    Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework

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

    Science.gov (United States)

    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.

  5. Requirements for existing buildings

    DEFF Research Database (Denmark)

    Thomsen, Kirsten Engelund; Wittchen, Kim Bjarne

    This report collects energy performance requirements for existing buildings in European member states by June 2012.......This report collects energy performance requirements for existing buildings in European member states by June 2012....

  6. Greening Existing Tribal Buildings

    Science.gov (United States)

    Guidance about improving sustainability in existing tribal casinos and manufactured homes. Many steps can be taken to make existing buildings greener and healthier. They may also reduce utility and medical costs.

  7. Column-oriented database management systems

    OpenAIRE

    Možina, David

    2013-01-01

    In the following thesis I will present column-oriented database. Among other things, I will answer on a question why there is a need for a column-oriented database. In recent years there have been a lot of attention regarding a column-oriented database, even if the existence of a columnar database management systems dates back in the early seventies of the last century. I will compare both systems for a database management – a colum-oriented database system and a row-oriented database system ...

  8. kpath: integration of metabolic pathway linked data.

    Science.gov (United States)

    Navas-Delgado, Ismael; García-Godoy, María Jesús; López-Camacho, Esteban; Rybinski, Maciej; Reyes-Palomares, Armando; Medina, Miguel Ángel; Aldana-Montes, José F

    2015-01-01

    In the last few years, the Life Sciences domain has experienced a rapid growth in the amount of available biological databases. The heterogeneity of these databases makes data integration a challenging issue. Some integration challenges are locating resources, relationships, data formats, synonyms or ambiguity. The Linked Data approach partially solves the heterogeneity problems by introducing a uniform data representation model. Linked Data refers to a set of best practices for publishing and connecting structured data on the Web. This article introduces kpath, a database that integrates information related to metabolic pathways. kpath also provides a navigational interface that enables not only the browsing, but also the deep use of the integrated data to build metabolic networks based on existing disperse knowledge. This user interface has been used to showcase relationships that can be inferred from the information available in several public databases. © The Author(s) 2015. Published by Oxford University Press.

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

    Science.gov (United States)

    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…

  10. The Danish Testicular Cancer database.

    Science.gov (United States)

    Daugaard, Gedske; Kier, Maria Gry Gundgaard; Bandak, Mikkel; Mortensen, Mette Saksø; Larsson, Heidi; Søgaard, Mette; Toft, Birgitte Groenkaer; Engvad, Birte; Agerbæk, Mads; Holm, Niels Vilstrup; Lauritsen, Jakob

    2016-01-01

    The nationwide Danish Testicular Cancer database consists of a retrospective research database (DaTeCa database) and a prospective clinical database (Danish Multidisciplinary Cancer Group [DMCG] DaTeCa database). The aim is to improve the quality of care for patients with testicular cancer (TC) in Denmark, that is, by identifying risk factors for relapse, toxicity related to treatment, and focusing on late effects. All Danish male patients with a histologically verified germ cell cancer diagnosis in the Danish Pathology Registry are included in the DaTeCa databases. Data collection has been performed from 1984 to 2007 and from 2013 onward, respectively. The retrospective DaTeCa database contains detailed information with more than 300 variables related to histology, stage, treatment, relapses, pathology, tumor markers, kidney function, lung function, etc. A questionnaire related to late effects has been conducted, which includes questions regarding social relationships, life situation, general health status, family background, diseases, symptoms, use of medication, marital status, psychosocial issues, fertility, and sexuality. TC survivors alive on October 2014 were invited to fill in this questionnaire including 160 validated questions. Collection of questionnaires is still ongoing. A biobank including blood/sputum samples for future genetic analyses has been established. Both samples related to DaTeCa and DMCG DaTeCa database are included. The prospective DMCG DaTeCa database includes variables regarding histology, stage, prognostic group, and treatment. The DMCG DaTeCa database has existed since 2013 and is a young clinical database. It is necessary to extend the data collection in the prospective database in order to answer quality-related questions. Data from the retrospective database will be added to the prospective data. This will result in a large and very comprehensive database for future studies on TC patients.

  11. Database Description - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us tRNAD...B-CE Database Description General information of database Database name tRNADB-CE Alter...CC BY-SA Detail Background and funding Name: MEXT Integrated Database Project Reference(s) Article title: tRNAD... 2009 Jan;37(Database issue):D163-8. External Links: Article title: tRNADB-CE 2011: tRNA gene database curat...n Download License Update History of This Database Site Policy | Contact Us Database Description - tRNADB-CE | LSDB Archive ...

  12. Professional iPhone and iPad Database Application Programming

    CERN Document Server

    Alessi, Patrick

    2010-01-01

    A much-needed resource on database development and enterprise integration for the iPhone. An enormous demand exists for getting iPhone applications into the enterprise and this book guides you through all the necessary steps for integrating an iPhone app within an existing enterprise. Experienced iPhone developers will learn how to take advantage of the built-in capabilities of the iPhone to confidently implement a data-driven application for the iPhone.: Shows you how to integrate iPhone applications into enterprise class systems; Introduces development of data-driven applications on the iPho

  13. Integrated remote sensing and visualization (IRSV) system for transportation infrastructure operations and management, phase one, volume 2 : knowledge modeling and database development.

    Science.gov (United States)

    2009-12-01

    The Integrated Remote Sensing and Visualization System (IRSV) is being designed to accommodate the needs of todays Bridge Engineers at the : state and local level from several aspects that were documented in Volume One, Summary Report. The followi...

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

    Science.gov (United States)

    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...

  15. A performance study on the synchronisation of heterogeneous Grid databases using CONStanza

    CERN Document Server

    Pucciani, G; Domenici, Andrea; Stockinger, Heinz

    2010-01-01

    In Grid environments, several heterogeneous database management systems are used in various administrative domains. However, data exchange and synchronisation need to be available across different sites and different database systems. In this article we present our data consistency service CONStanza and give details on how we achieve relaxed update synchronisation between different database implementations. The integration in existing Grid environments is one of the major goals of the system. Performance tests have been executed following a factorial approach. Detailed experimental results and a statistical analysis are presented to evaluate the system components and drive future developments. (C) 2010 Elsevier B.V. All rights reserved.

  16. DistiLD Database

    DEFF Research Database (Denmark)

    Palleja, Albert; Horn, Heiko; Eliasson, Sabrina

    2012-01-01

    Genome-wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) associated with the risk of hundreds of diseases. However, there is currently no database that enables non-specialists to answer the following simple questions: which SNPs associated...... with diseases are in linkage disequilibrium (LD) with a gene of interest? Which chromosomal regions have been associated with a given disease, and which are the potentially causal genes in each region? To answer these questions, we use data from the HapMap Project to partition each chromosome into so-called LD...... blocks, so that SNPs in LD with each other are preferentially in the same block, whereas SNPs not in LD are in different blocks. By projecting SNPs and genes onto LD blocks, the DistiLD database aims to increase usage of existing GWAS results by making it easy to query and visualize disease...

  17. Customer database for Watrec Oy

    OpenAIRE

    Melnichikhina, Ekaterina

    2016-01-01

    This thesis is a development project for Watrec Oy. Watrec Oy is a Finnish company specializes in “waste-to-energy” issues. Customer Relation Management (CRM) strategies are now being applied within the company. The customer database is the first and trial step towards CRM strategy in Watrec Oy. The reasons for database project lie in lacking of clear customers’ data. The main objectives are: - To integrate the customers’ and project data; - To improve the level of sales and mar...

  18. Physical database design using Oracle

    CERN Document Server

    Burleson, Donald K

    2004-01-01

    INTRODUCTION TO ORACLE PHYSICAL DESIGNPrefaceRelational Databases and Physical DesignSystems Analysis and Physical Database DesignIntroduction to Logical Database DesignEntity/Relation ModelingBridging between Logical and Physical ModelsPhysical Design Requirements Validation PHYSICAL ENTITY DESIGN FOR ORACLEData Relationships and Physical DesignMassive De-Normalization: STAR Schema DesignDesigning Class HierarchiesMaterialized Views and De-NormalizationReferential IntegrityConclusionORACLE HARDWARE DESIGNPlanning the Server EnvironmentDesigning the Network Infrastructure for OracleOracle Netw

  19. Improving the thermal integrity of new single-family detached residential buildings: Documentation for a regional database of capital costs and space conditioning load savings

    International Nuclear Information System (INIS)

    Koomey, J.G.; McMahon, J.E.; Wodley, C.

    1991-07-01

    This report summarizes the costs and space-conditioning load savings from improving new single-family building shells. It relies on survey data from the National Association of Home-builders (NAHB) to assess current insulation practices for these new buildings, and NAHB cost data (aggregated to the Federal region level) to estimate the costs of improving new single-family buildings beyond current practice. Space-conditioning load savings are estimated using a database of loads for prototype buildings developed at Lawrence Berkeley Laboratory, adjusted to reflect population-weighted average weather in each of the ten federal regions and for the nation as a whole

  20. Nuclear plant operations, maintenance, and configuration management using three-dimensional computer graphics and databases

    International Nuclear Information System (INIS)

    Tutos, N.C.; Reinschmidt, K.F.

    1987-01-01

    Stone and Webster Engineering Corporation has developed the Plant Digital Model concept as a new approach to Configuration Mnagement of nuclear power plants. The Plant Digital Model development is a step-by-step process, based on existing manual procedures and computer applications, and is fully controllable by the plant managers and engineers. The Plant Digital Model is based on IBM computer graphics and relational database management systems, and therefore can be easily integrated with existing plant databases and corporate management-information systems

  1. A computational platform to maintain and migrate manual functional annotations for BioCyc databases.

    Science.gov (United States)

    Walsh, Jesse R; Sen, Taner Z; Dickerson, Julie A

    2014-10-12

    BioCyc databases are an important resource for information on biological pathways and genomic data. Such databases represent the accumulation of biological data, some of which has been manually curated from literature. An essential feature of these databases is the continuing data integration as new knowledge is discovered. As functional annotations are improved, scalable methods are needed for curators to manage annotations without detailed knowledge of the specific design of the BioCyc database. We have developed CycTools, a software tool which allows curators to maintain functional annotations in a model organism database. This tool builds on existing software to improve and simplify annotation data imports of user provided data into BioCyc databases. Additionally, CycTools automatically resolves synonyms and alternate identifiers contained within the database into the appropriate internal identifiers. Automating steps in the manual data entry process can improve curation efforts for major biological databases. The functionality of CycTools is demonstrated by transferring GO term annotations from MaizeCyc to matching proteins in CornCyc, both maize metabolic pathway databases available at MaizeGDB, and by creating strain specific databases for metabolic engineering.

  2. Psychology's struggle for existence: Second edition, 1913.

    Science.gov (United States)

    Wundt, Wilhelm; Lamiell, James T

    2013-08-01

    Presents an English translation of Wilhelm Wundt's Psychology's struggle for existence: Second edition, 1913, by James T. Lamiell in August, 2012. In his essay, Wundt advised against the impending divorce of psychology from philosophy. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

  3. The Danish Testicular Cancer database

    Directory of Open Access Journals (Sweden)

    Daugaard G

    2016-10-01

    . Collection of questionnaires is still ongoing. A biobank including blood/sputum samples for future genetic analyses has been established. Both samples related to DaTeCa and DMCG DaTeCa database are included. The prospective DMCG DaTeCa database includes variables regarding histology, stage, prognostic group, and treatment. Conclusion: The DMCG DaTeCa database has existed since 2013 and is a young clinical database. It is necessary to extend the data collection in the prospective database in order to answer quality-related questions. Data from the retrospective database will be added to the prospective data. This will result in a large and very comprehensive database for future studies on TC patients. Keywords: testis cancer, clinical indicators, database research, DaTeCa, DMCG DaTeCa database, hypogonadism

  4. Network and Database Security: Regulatory Compliance, Network, and Database Security - A Unified Process and Goal

    Directory of Open Access Journals (Sweden)

    Errol A. Blake

    2007-12-01

    Full Text Available Database security has evolved; data security professionals have developed numerous techniques and approaches to assure data confidentiality, integrity, and availability. This paper will show that the Traditional Database Security, which has focused primarily on creating user accounts and managing user privileges to database objects are not enough to protect data confidentiality, integrity, and availability. This paper is a compilation of different journals, articles and classroom discussions will focus on unifying the process of securing data or information whether it is in use, in storage or being transmitted. Promoting a change in Database Curriculum Development trends may also play a role in helping secure databases. This paper will take the approach that if one make a conscientious effort to unifying the Database Security process, which includes Database Management System (DBMS selection process, following regulatory compliances, analyzing and learning from the mistakes of others, Implementing Networking Security Technologies, and Securing the Database, may prevent database breach.

  5. NNDC database migration project

    Energy Technology Data Exchange (ETDEWEB)

    Burrows, Thomas W; Dunford, Charles L [U.S. Department of Energy, Brookhaven Science Associates (United States)

    2004-03-01

    NNDC Database Migration was necessary to replace obsolete hardware and software, to be compatible with the industry standard in relational databases (mature software, large base of supporting software for administration and dissemination and replication and synchronization tools) and to improve the user access in terms of interface and speed. The Relational Database Management System (RDBMS) consists of a Sybase Adaptive Server Enterprise (ASE), which is relatively easy to move between different RDB systems (e.g., MySQL, MS SQL-Server, or MS Access), the Structured Query Language (SQL) and administrative tools written in Java. Linux or UNIX platforms can be used. The existing ENSDF datasets are often VERY large and will need to be reworked and both the CRP (adopted) and CRP (Budapest) datasets give elemental cross sections (not relative I{gamma}) in the RI field (so it is not immediately obvious which of the old values has been changed). But primary and secondary intensities are now available on the same scale. The intensity normalization has been done for us. We will gain access to a large volume of data from Budapest and some of those gamma-ray intensity and energy data will be superior to what we already have.

  6. Database development and management

    CERN Document Server

    Chao, Lee

    2006-01-01

    Introduction to Database Systems Functions of a DatabaseDatabase Management SystemDatabase ComponentsDatabase Development ProcessConceptual Design and Data Modeling Introduction to Database Design Process Understanding Business ProcessEntity-Relationship Data Model Representing Business Process with Entity-RelationshipModelTable Structure and NormalizationIntroduction to TablesTable NormalizationTransforming Data Models to Relational Databases .DBMS Selection Transforming Data Models to Relational DatabasesEnforcing ConstraintsCreating Database for Business ProcessPhysical Design and Database

  7. 'Integration'

    DEFF Research Database (Denmark)

    Olwig, Karen Fog

    2011-01-01

    , while the countries have adopted disparate policies and ideologies, differences in the actual treatment and attitudes towards immigrants and refugees in everyday life are less clear, due to parallel integration programmes based on strong similarities in the welfare systems and in cultural notions...... of equality in the three societies. Finally, it shows that family relations play a central role in immigrants’ and refugees’ establishment of a new life in the receiving societies, even though the welfare society takes on many of the social and economic functions of the family....

  8. KALIMER design database development and operation manual

    International Nuclear Information System (INIS)

    Jeong, Kwan Seong; Hahn, Do Hee; Lee, Yong Bum; Chang, Won Pyo

    2000-12-01

    KALIMER Design Database is developed to utilize the integration management for Liquid Metal Reactor Design Technology Development using Web Applications. KALIMER Design database consists of Results Database, Inter-Office Communication (IOC), 3D CAD database, Team Cooperation System, and Reserved Documents. Results Database is a research results database for mid-term and long-term nuclear R and D. IOC is a linkage control system inter sub project to share and integrate the research results for KALIMER. 3D CAD Database is a schematic design overview for KALIMER. Team Cooperation System is to inform team member of research cooperation and meetings. Finally, KALIMER Reserved Documents is developed to manage collected data and several documents since project accomplishment

  9. KALIMER design database development and operation manual

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Kwan Seong; Hahn, Do Hee; Lee, Yong Bum; Chang, Won Pyo

    2000-12-01

    KALIMER Design Database is developed to utilize the integration management for Liquid Metal Reactor Design Technology Development using Web Applications. KALIMER Design database consists of Results Database, Inter-Office Communication (IOC), 3D CAD database, Team Cooperation System, and Reserved Documents. Results Database is a research results database for mid-term and long-term nuclear R and D. IOC is a linkage control system inter sub project to share and integrate the research results for KALIMER. 3D CAD Database is a schematic design overview for KALIMER. Team Cooperation System is to inform team member of research cooperation and meetings. Finally, KALIMER Reserved Documents is developed to manage collected data and several documents since project accomplishment.

  10. Applying AN Object-Oriented Database Model to a Scientific Database Problem: Managing Experimental Data at Cebaf.

    Science.gov (United States)

    Ehlmann, Bryon K.

    Current scientific experiments are often characterized by massive amounts of very complex data and the need for complex data analysis software. Object-oriented database (OODB) systems have the potential of improving the description of the structure and semantics of this data and of integrating the analysis software with the data. This dissertation results from research to enhance OODB functionality and methodology to support scientific databases (SDBs) and, more specifically, to support a nuclear physics experiments database for the Continuous Electron Beam Accelerator Facility (CEBAF). This research to date has identified a number of problems related to the practical application of OODB technology to the conceptual design of the CEBAF experiments database and other SDBs: the lack of a generally accepted OODB design methodology, the lack of a standard OODB model, the lack of a clear conceptual level in existing OODB models, and the limited support in existing OODB systems for many common object relationships inherent in SDBs. To address these problems, the dissertation describes an Object-Relationship Diagram (ORD) and an Object-oriented Database Definition Language (ODDL) that provide tools that allow SDB design and development to proceed systematically and independently of existing OODB systems. These tools define multi-level, conceptual data models for SDB design, which incorporate a simple notation for describing common types of relationships that occur in SDBs. ODDL allows these relationships and other desirable SDB capabilities to be supported by an extended OODB system. A conceptual model of the CEBAF experiments database is presented in terms of ORDs and the ODDL to demonstrate their functionality and use and provide a foundation for future development of experimental nuclear physics software using an OODB approach.

  11. DBGC: A Database of Human Gastric Cancer

    Science.gov (United States)

    Wang, Chao; Zhang, Jun; Cai, Mingdeng; Zhu, Zhenggang; Gu, Wenjie; Yu, Yingyan; Zhang, Xiaoyan

    2015-01-01

    The Database of Human Gastric Cancer (DBGC) is a comprehensive database that integrates various human gastric cancer-related data resources. Human gastric cancer-related transcriptomics projects, proteomics projects, mutations, biomarkers and drug-sensitive genes from different sources were collected and unified in this database. Moreover, epidemiological statistics of gastric cancer patients in China and clinicopathological information annotated with gastric cancer cases were also integrated into the DBGC. We believe that this database will greatly facilitate research regarding human gastric cancer in many fields. DBGC is freely available at http://bminfor.tongji.edu.cn/dbgc/index.do PMID:26566288

  12. A coordination language for databases

    DEFF Research Database (Denmark)

    Li, Ximeng; Wu, Xi; Lluch Lafuente, Alberto

    2017-01-01

    We present a coordination language for the modeling of distributed database applications. The language, baptized Klaim-DB, borrows the concepts of localities and nets of the coordination language Klaim but re-incarnates the tuple spaces of Klaim as databases. It provides high-level abstractions...... and primitives for the access and manipulation of structured data, with integrity and atomicity considerations. We present the formal semantics of Klaim-DB and develop a type system that avoids potential runtime errors such as certain evaluation errors and mismatches of data format in tables, which are monitored...... in the semantics. The use of the language is illustrated in a scenario where the sales from different branches of a chain of department stores are aggregated from their local databases. Raising the abstraction level and encapsulating integrity checks in the language primitives have benefited the modeling task...

  13. Design and implementation of typical target image database system

    International Nuclear Information System (INIS)

    Qin Kai; Zhao Yingjun

    2010-01-01

    It is necessary to provide essential background data and thematic data timely in image processing and application. In fact, application is an integrating and analyzing procedure with different kinds of data. In this paper, the authors describe an image database system which classifies, stores, manages and analyzes database of different types, such as image database, vector database, spatial database, spatial target characteristics database, its design and structure. (authors)

  14. Danish Colorectal Cancer Group Database

    DEFF Research Database (Denmark)

    Ingeholm, Peter; Gögenur, Ismail; Iversen, Lene H

    2016-01-01

    AIM OF DATABASE: The aim of the database, which has existed for registration of all patients with colorectal cancer in Denmark since 2001, is to improve the prognosis for this patient group. STUDY POPULATION: All Danish patients with newly diagnosed colorectal cancer who are either diagnosed......, and other pathological risk factors. DESCRIPTIVE DATA: The database has had >95% completeness in including patients with colorectal adenocarcinoma with >54,000 patients registered so far with approximately one-third rectal cancers and two-third colon cancers and an overrepresentation of men among rectal...... diagnosis, surgical interventions, and short-term outcomes. The database does not have high-resolution oncological data and does not register recurrences after primary surgery. The Danish Colorectal Cancer Group provides high-quality data and has been documenting an increase in short- and long...

  15. Why preeclampsia still exists?

    Science.gov (United States)

    Chelbi, Sonia T; Veitia, Reiner A; Vaiman, Daniel

    2013-08-01

    Preeclampsia (PE) is a deadly gestational disease affecting up to 10% of women and specific of the human species. Preeclampsia is clearly multifactorial, but the existence of a genetic basis for this disease is now clearly established by the existence of familial cases, epidemiological studies and known predisposing gene polymorphisms. PE is very common despite the fact that Darwinian pressure should have rapidly eliminated or strongly minimized the frequency of predisposing alleles. Consecutive pregnancies with the same partner decrease the risk and severity of PE. Here, we show that, due to this peculiar feature, preeclampsia predisposing-alleles can be differentially maintained according to the familial structure. Thus, we suggest that an optimal frequency of PE-predisposing alleles in human populations can be achieved as a result of a trade-off between benefits of exogamy, importance for maintaining genetic diversity and increase of the fitness owing to a stable paternal investment. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Database Systems - Present and Future

    Directory of Open Access Journals (Sweden)

    2009-01-01

    Full Text Available The database systems have nowadays an increasingly important role in the knowledge-based society, in which computers have penetrated all fields of activity and the Internet tends to develop worldwide. In the current informatics context, the development of the applications with databases is the work of the specialists. Using databases, reach a database from various applications, and also some of related concepts, have become accessible to all categories of IT users. This paper aims to summarize the curricular area regarding the fundamental database systems issues, which are necessary in order to train specialists in economic informatics higher education. The database systems integrate and interfere with several informatics technologies and therefore are more difficult to understand and use. Thus, students should know already a set of minimum, mandatory concepts and their practical implementation: computer systems, programming techniques, programming languages, data structures. The article also presents the actual trends in the evolution of the database systems, in the context of economic informatics.

  17. Existence of Projective Planes

    OpenAIRE

    Perrott, Xander

    2016-01-01

    This report gives an overview of the history of finite projective planes and their properties before going on to outline the proof that no projective plane of order 10 exists. The report also investigates the search carried out by MacWilliams, Sloane and Thompson in 1970 [12] and confirms their result by providing independent verification that there is no vector of weight 15 in the code generated by the projective plane of order 10.

  18. Does bioethics exist?

    Science.gov (United States)

    Turner, L

    2009-12-01

    Bioethicists disagree over methods, theories, decision-making guides, case analyses and public policies. Thirty years ago, the thinking of many scholars coalesced around a principlist approach to bioethics. That mid-level mode of moral reasoning is now one of many approaches to moral deliberation. Significant variation in contemporary approaches to the study of ethical issues related to medicine, biotechnology and health care raises the question of whether bioethics exists as widely shared method, theory, normative framework or mode of moral reasoning.

  19. Mathematics for Databases

    NARCIS (Netherlands)

    ir. Sander van Laar

    2007-01-01

    A formal description of a database consists of the description of the relations (tables) of the database together with the constraints that must hold on the database. Furthermore the contents of a database can be retrieved using queries. These constraints and queries for databases can very well be

  20. Databases and their application

    NARCIS (Netherlands)

    Grimm, E.C.; Bradshaw, R.H.W; Brewer, S.; Flantua, S.; Giesecke, T.; Lézine, A.M.; Takahara, H.; Williams, J.W.,Jr; Elias, S.A.; Mock, C.J.

    2013-01-01

    During the past 20 years, several pollen database cooperatives have been established. These databases are now constituent databases of the Neotoma Paleoecology Database, a public domain, multiproxy, relational database designed for Quaternary-Pliocene fossil data and modern surface samples. The

  1. DOT Online Database

    Science.gov (United States)

    Page Home Table of Contents Contents Search Database Search Login Login Databases Advisory Circulars accessed by clicking below: Full-Text WebSearch Databases Database Records Date Advisory Circulars 2092 5 data collection and distribution policies. Document Database Website provided by MicroSearch

  2. SmallSat Database

    Science.gov (United States)

    Petropulos, Dolores; Bittner, David; Murawski, Robert; Golden, Bert

    2015-01-01

    The SmallSat has an unrealized potential in both the private industry and in the federal government. Currently over 70 companies, 50 universities and 17 governmental agencies are involved in SmallSat research and development. In 1994, the U.S. Army Missile and Defense mapped the moon using smallSat imagery. Since then Smart Phones have introduced this imagery to the people of the world as diverse industries watched this trend. The deployment cost of smallSats is also greatly reduced compared to traditional satellites due to the fact that multiple units can be deployed in a single mission. Imaging payloads have become more sophisticated, smaller and lighter. In addition, the growth of small technology obtained from private industries has led to the more widespread use of smallSats. This includes greater revisit rates in imagery, significantly lower costs, the ability to update technology more frequently and the ability to decrease vulnerability of enemy attacks. The popularity of smallSats show a changing mentality in this fast paced world of tomorrow. What impact has this created on the NASA communication networks now and in future years? In this project, we are developing the SmallSat Relational Database which can support a simulation of smallSats within the NASA SCaN Compatability Environment for Networks and Integrated Communications (SCENIC) Modeling and Simulation Lab. The NASA Space Communications and Networks (SCaN) Program can use this modeling to project required network support needs in the next 10 to 15 years. The SmallSat Rational Database could model smallSats just as the other SCaN databases model the more traditional larger satellites, with a few exceptions. One being that the smallSat Database is designed to be built-to-order. The SmallSat database holds various hardware configurations that can be used to model a smallSat. It will require significant effort to develop as the research material can only be populated by hand to obtain the unique data

  3. Self-Esteem Challenges of Nursing Students: An Integrative Review

    OpenAIRE

    KEOGH, BRIAN

    2016-01-01

    Introduction: Self-esteem among nursing students is important in providing high-quality serviceto clients, yet each study in this field has described only a portion of existing relevant knowledge.Integrative review studies are the best practice for identification of existing nursing knowledge.The purpose of this study was to determine self-esteem challenges among nursing students. Methods: An integrative review was conducted in this study. The databases ProQuest, Medlineon PubMed, Science Dir...

  4. Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE), Version 5.0: Models and Results Database (MAR-D) reference manual. Volume 8

    International Nuclear Information System (INIS)

    Russell, K.D.; Skinner, N.L.

    1994-07-01

    The Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) refers to a set of several microcomputer programs that were developed to create and analyze probabilistic risk assessments (PRAs), primarily for nuclear power plants. The primary function of MAR-D is to create a data repository for completed PRAs and Individual Plant Examinations (IPEs) by providing input, conversion, and output capabilities for data used by IRRAS, SARA, SETS, and FRANTIC software. As probabilistic risk assessments and individual plant examinations are submitted to the NRC for review, MAR-D can be used to convert the models and results from the study for use with IRRAS and SARA. Then, these data can be easily accessed by future studies and will be in a form that will enhance the analysis process. This reference manual provides an overview of the functions available within MAR-D and step-by-step operating instructions

  5. Database on aircraft accidents

    International Nuclear Information System (INIS)

    Nishio, Masahide; Koriyama, Tamio

    2013-11-01

    The Reactor Safety Subcommittee in the Nuclear Safety and Preservation Committee published 'The criteria on assessment of probability of aircraft crash into light water reactor facilities' as the standard method for evaluating probability of aircraft crash into nuclear reactor facilities in July 2002. In response to this issue, Japan Nuclear Energy Safety Organization has been collecting open information on aircraft accidents of commercial airplanes, self-defense force (SDF) airplanes and US force airplanes every year since 2003, sorting out them and developing the database of aircraft accidents for the latest 20 years to evaluate probability of aircraft crash into nuclear reactor facilities. In this report the database was revised by adding aircraft accidents in 2011 to the existing database and deleting aircraft accidents in 1991 from it, resulting in development of the revised 2012 database for the latest 20 years from 1992 to 2011. Furthermore, the flight information on commercial aircrafts was also collected to develop the flight database for the latest 20 years from 1992 to 2011 to evaluate probability of aircraft crash into reactor facilities. The method for developing the database of aircraft accidents to evaluate probability of aircraft crash into reactor facilities is based on the report 'The criteria on assessment of probability of aircraft crash into light water reactor facilities' described above. The 2012 revised database for the latest 20 years from 1992 to 2011 shows the followings. The trend of the 2012 database changes little as compared to the last year's report. (1) The data of commercial aircraft accidents is based on 'Aircraft accident investigation reports of Japan transport safety board' of Ministry of Land, Infrastructure, Transport and Tourism. The number of commercial aircraft accidents is 4 for large fixed-wing aircraft, 58 for small fixed-wing aircraft, 5 for large bladed aircraft and 99 for small bladed aircraft. The relevant accidents

  6. Database on aircraft accidents

    International Nuclear Information System (INIS)

    Nishio, Masahide; Koriyama, Tamio

    2012-09-01

    The Reactor Safety Subcommittee in the Nuclear Safety and Preservation Committee published the report 'The criteria on assessment of probability of aircraft crash into light water reactor facilities' as the standard method for evaluating probability of aircraft crash into nuclear reactor facilities in July 2002. In response to the report, Japan Nuclear Energy Safety Organization has been collecting open information on aircraft accidents of commercial airplanes, self-defense force (SDF) airplanes and US force airplanes every year since 2003, sorting out them and developing the database of aircraft accidents for latest 20 years to evaluate probability of aircraft crash into nuclear reactor facilities. This year, the database was revised by adding aircraft accidents in 2010 to the existing database and deleting aircraft accidents in 1991 from it, resulting in development of the revised 2011 database for latest 20 years from 1991 to 2010. Furthermore, the flight information on commercial aircrafts was also collected to develop the flight database for latest 20 years from 1991 to 2010 to evaluate probability of aircraft crash into reactor facilities. The method for developing the database of aircraft accidents to evaluate probability of aircraft crash into reactor facilities is based on the report 'The criteria on assessment of probability of aircraft crash into light water reactor facilities' described above. The 2011 revised database for latest 20 years from 1991 to 2010 shows the followings. The trend of the 2011 database changes little as compared to the last year's one. (1) The data of commercial aircraft accidents is based on 'Aircraft accident investigation reports of Japan transport safety board' of Ministry of Land, Infrastructure, Transport and Tourism. 4 large fixed-wing aircraft accidents, 58 small fixed-wing aircraft accidents, 5 large bladed aircraft accidents and 114 small bladed aircraft accidents occurred. The relevant accidents for evaluating

  7. Network and Database Security: Regulatory Compliance, Network, and Database Security - A Unified Process and Goal

    OpenAIRE

    Errol A. Blake

    2007-01-01

    Database security has evolved; data security professionals have developed numerous techniques and approaches to assure data confidentiality, integrity, and availability. This paper will show that the Traditional Database Security, which has focused primarily on creating user accounts and managing user privileges to database objects are not enough to protect data confidentiality, integrity, and availability. This paper is a compilation of different journals, articles and classroom discussions ...

  8. Energy Consumption Database

    Science.gov (United States)

    Consumption Database The California Energy Commission has created this on-line database for informal reporting ) classifications. The database also provides easy downloading of energy consumption data into Microsoft Excel (XLSX

  9. A Survey of Privacy on Data Integration

    OpenAIRE

    Do Son, Thanh

    2015-01-01

    This survey is an integrated view of other surveys on privacy preserving for data integration. First, we review the database context and challenges and research questions. Second, we formulate the privacy problems for schema matching and data matching. Next, we introduce the elements of privacy models. Then, we summarize the existing privacy techniques and the analysis (proofs) of privacy guarantees. Finally, we describe the privacy frameworks and their applications.

  10. Draft secure medical database standard.

    Science.gov (United States)

    Pangalos, George

    2002-01-01

    Medical database security is a particularly important issue for all Healthcare establishments. Medical information systems are intended to support a wide range of pertinent health issues today, for example: assure the quality of care, support effective management of the health services institutions, monitor and contain the cost of care, implement technology into care without violating social values, ensure the equity and availability of care, preserve humanity despite the proliferation of technology etc.. In this context, medical database security aims primarily to support: high availability, accuracy and consistency of the stored data, the medical professional secrecy and confidentiality, and the protection of the privacy of the patient. These properties, though of technical nature, basically require that the system is actually helpful for medical care and not harmful to patients. These later properties require in turn not only that fundamental ethical principles are not violated by employing database systems, but instead, are effectively enforced by technical means. This document reviews the existing and emerging work on the security of medical database systems. It presents in detail the related problems and requirements related to medical database security. It addresses the problems of medical database security policies, secure design methodologies and implementation techniques. It also describes the current legal framework and regulatory requirements for medical database security. The issue of medical database security guidelines is also examined in detailed. The current national and international efforts in the area are studied. It also gives an overview of the research work in the area. The document also presents in detail the most complete to our knowledge set of security guidelines for the development and operation of medical database systems.

  11. An object-oriented framework for managing cooperating legacy databases

    NARCIS (Netherlands)

    Balsters, H; de Brock, EO

    2003-01-01

    We describe a general semantic framework for precise specification of so-called database federations. A database federation provides for tight coupling of a collection of heterogeneous legacy databases into a global integrated system. Our approach to database federation is based on the UML/OCL data

  12. An inductive database system based on virtual mining views

    NARCIS (Netherlands)

    Blockeel, H.; Calders, T.G.K.; Fromont, É.; Goethals, B.; Prado, A.; Robardet, C.

    2012-01-01

    Inductive databases integrate database querying with database mining. In this article, we present an inductive database system that does not rely on a new data mining query language, but on plain SQL. We propose an intuitive and elegant framework based on virtual mining views, which are relational

  13. Object-oriented modeling and design of database federations

    NARCIS (Netherlands)

    Balsters, H.

    2003-01-01

    We describe a logical architecture and a general semantic framework for precise specification of so-called database federations. A database federation provides for tight coupling of a collection of heterogeneous component databases into a global integrated system. Our approach to database federation

  14. Collecting Taxes Database

    Data.gov (United States)

    US Agency for International Development — The Collecting Taxes Database contains performance and structural indicators about national tax systems. The database contains quantitative revenue performance...

  15. USAID Anticorruption Projects Database

    Data.gov (United States)

    US Agency for International Development — The Anticorruption Projects Database (Database) includes information about USAID projects with anticorruption interventions implemented worldwide between 2007 and...

  16. NoSQL databases

    OpenAIRE

    Mrozek, Jakub

    2012-01-01

    This thesis deals with database systems referred to as NoSQL databases. In the second chapter, I explain basic terms and the theory of database systems. A short explanation is dedicated to database systems based on the relational data model and the SQL standardized query language. Chapter Three explains the concept and history of the NoSQL databases, and also presents database models, major features and the use of NoSQL databases in comparison with traditional database systems. In the fourth ...

  17. BIOSPIDA: A Relational Database Translator for NCBI.

    Science.gov (United States)

    Hagen, Matthew S; Lee, Eva K

    2010-11-13

    As the volume and availability of biological databases continue widespread growth, it has become increasingly difficult for research scientists to identify all relevant information for biological entities of interest. Details of nucleotide sequences, gene expression, molecular interactions, and three-dimensional structures are maintained across many different databases. To retrieve all necessary information requires an integrated system that can query multiple databases with minimized overhead. This paper introduces a universal parser and relational schema translator that can be utilized for all NCBI databases in Abstract Syntax Notation (ASN.1). The data models for OMIM, Entrez-Gene, Pubmed, MMDB and GenBank have been successfully converted into relational databases and all are easily linkable helping to answer complex biological questions. These tools facilitate research scientists to locally integrate databases from NCBI without significant workload or development time.

  18. Recovery actions in PRA [probabilistic risk assessment] for the Risk Methods Integration and Evaluation Program (RMIEP): Volume 1, Development of the data-based method

    International Nuclear Information System (INIS)

    Weston, L.M.; Whitehead, D.W.; Graves, N.L.

    1987-06-01

    In a probabilistic risk assessment (PRA) for a nuclear power plant, the analyst identifies a set of potential core damage events consisting of equipment failures and human errors and their estimated probabilities of occurrence. If operator recovery from an event within some specified time is considered, then the probability of this recovery can be included in the PRA. This report provides PRA analysts with an improved methodology for including recovery actions in a PRA. A recovery action can be divided into two distinct phases: a Diagnosis Phase (realizing that there is a problem with a critical parameter and deciding upon the correct course of action) and an Action Phase (physically accomplishing the required action). In this methodology, simulator data are used to estimate recovery probabilities for the diagnosis phase. Different time-reliability curves showing the probability of failure of diagnosis as a function of time from the compelling cue for the event are presented. These curves are based on simulator exercises, and the actions are grouped based upon their operational similarities. This is an improvement over existing diagnosis models that rely greatly upon subjective judgment to obtain such estimates. The action phase is modeled using estimates from available sources. The methodology also includes a recommendation on where and when to apply the recovery action in the PRA process

  19. O Ponto G Existe?

    Directory of Open Access Journals (Sweden)

    Carlos Alexandre Molina Noccioli

    2016-07-01

    Full Text Available Este trabalho busca analisar o tratamento linguístico-discursivo das informações acerca de um tópicotemático tradicionalmente visto como tabu, relacionado a questões sexuais, na notícia O ponto G existe?, publicada em 2008, na revista brasileira Superinteressante, destacando-se como o conhecimento em questão é representado socialmente ao se considerar a linha editorial da revista. A notícia caracteriza-se como um campo fértil para a análise das estratégias divulgativas, já que atrai, inclusive pelas escolhas temáticas, a curiosidade dos leitores. Imbuído de um tema excêntrico, o texto consegue angariar um público jovem interessado em discussões polêmicas relacionadas ao seu universo.

  20. Legume and Lotus japonicus Databases

    DEFF Research Database (Denmark)

    Hirakawa, Hideki; Mun, Terry; Sato, Shusei

    2014-01-01

    Since the genome sequence of Lotus japonicus, a model plant of family Fabaceae, was determined in 2008 (Sato et al. 2008), the genomes of other members of the Fabaceae family, soybean (Glycine max) (Schmutz et al. 2010) and Medicago truncatula (Young et al. 2011), have been sequenced. In this sec....... In this section, we introduce representative, publicly accessible online resources related to plant materials, integrated databases containing legume genome information, and databases for genome sequence and derived marker information of legume species including L. japonicus...

  1. The UCSC Genome Browser Database: 2008 update

    DEFF Research Database (Denmark)

    Karolchik, D; Kuhn, R M; Baertsch, R

    2007-01-01

    The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrat...

  2. Mining Views : database views for data mining

    NARCIS (Netherlands)

    Blockeel, H.; Calders, T.; Fromont, É.; Goethals, B.; Prado, A.

    2008-01-01

    We present a system towards the integration of data mining into relational databases. To this end, a relational database model is proposed, based on the so called virtual mining views. We show that several types of patterns and models over the data, such as itemsets, association rules and decision

  3. Mining Views : database views for data mining

    NARCIS (Netherlands)

    Blockeel, H.; Calders, T.; Fromont, É.; Goethals, B.; Prado, A.; Nijssen, S.; De Raedt, L.

    2007-01-01

    We propose a relational database model towards the integration of data mining into relational database systems, based on the so called virtual mining views. We show that several types of patterns and models over the data, such as itemsets, association rules, decision trees and clusterings, can be

  4. Bibliography - Existing Guidance for External Hazard Modelling

    International Nuclear Information System (INIS)

    Decker, Kurt

    2015-01-01

    The bibliography of deliverable D21.1 includes existing international and national guidance documents and standards on external hazard assessment together with a selection of recent scientific papers, which are regarded to provide useful information on the state of the art of external event modelling. The literature database is subdivided into International Standards, National Standards, and Science Papers. The deliverable is treated as a 'living document' which is regularly updated as necessary during the lifetime of ASAMPSA-E. The current content of the database is about 140 papers. Most of the articles are available as full-text versions in PDF format. The deliverable is available as an EndNote X4 database and as text files. The database includes the following information: Reference, Key words, Abstract (if available), PDF file of the original paper (if available), Notes (comments by the ASAMPSA-E consortium if available) The database is stored at the ASAMPSA-E FTP server hosted by IRSN. PDF files of original papers are accessible through the EndNote software

  5. Databases for INDUS-1 and INDUS-2

    International Nuclear Information System (INIS)

    Merh, Bhavna N.; Fatnani, Pravin

    2003-01-01

    The databases for Indus are relational databases designed to store various categories of data related to the accelerator. The data archiving and retrieving system in Indus is based on a client/sever model. A general purpose commercial database is used to store parameters and equipment data for the whole machine. The database manages configuration, on-line and historical databases. On line and off line applications distributed in several systems can store and retrieve the data from the database over the network. This paper describes the structure of databases for Indus-1 and Indus-2 and their integration within the software architecture. The data analysis, design, resulting data-schema and implementation issues are discussed. (author)

  6. PrimateLit Database

    Science.gov (United States)

    Primate Info Net Related Databases NCRR PrimateLit: A bibliographic database for primatology Top of any problems with this service. We welcome your feedback. The PrimateLit database is no longer being Resources, National Institutes of Health. The database is a collaborative project of the Wisconsin Primate

  7. Development of a geotechnical information database.

    Science.gov (United States)

    2009-06-01

    The purpose of this project was to create a database for existing, current, and future geotechnical records and data. : The project originated from the Geotechnical Design Section at the Louisiana Department of Transportation and : Development (LADOT...

  8. Issues in Big-Data Database Systems

    Science.gov (United States)

    2014-06-01

    that big data will not be manageable using conventional relational database technology, and it is true that alternative paradigms, such as NoSQL systems...conventional relational database technology, and it is true that alternative paradigms, such as NoSQL systems and search engines, have much to offer...scale well, and because integration with external data sources is so difficult. NoSQL systems are more open to this integration, and provide excellent

  9. An effective suggestion method for keyword search of databases

    KAUST Repository

    Huang, Hai; Chen, Zonghai; Liu, Chengfei; Huang, He; Zhang, Xiangliang

    2016-01-01

    This paper solves the problem of providing high-quality suggestions for user keyword queries over databases. With the assumption that the returned suggestions are independent, existing query suggestion methods over databases score candidate

  10. Logical database design principles

    CERN Document Server

    Garmany, John; Clark, Terry

    2005-01-01

    INTRODUCTION TO LOGICAL DATABASE DESIGNUnderstanding a Database Database Architectures Relational Databases Creating the Database System Development Life Cycle (SDLC)Systems Planning: Assessment and Feasibility System Analysis: RequirementsSystem Analysis: Requirements Checklist Models Tracking and Schedules Design Modeling Functional Decomposition DiagramData Flow Diagrams Data Dictionary Logical Structures and Decision Trees System Design: LogicalSYSTEM DESIGN AND IMPLEMENTATION The ER ApproachEntities and Entity Types Attribute Domains AttributesSet-Valued AttributesWeak Entities Constraint

  11. Software listing: CHEMTOX database

    International Nuclear Information System (INIS)

    Moskowitz, P.D.

    1993-01-01

    Initially launched in 1983, the CHEMTOX Database was among the first microcomputer databases containing hazardous chemical information. The database is used in many industries and government agencies in more than 17 countries. Updated quarterly, the CHEMTOX Database provides detailed environmental and safety information on 7500-plus hazardous substances covered by dozens of regulatory and advisory sources. This brief listing describes the method of accessing data and provides ordering information for those wishing to obtain the CHEMTOX Database

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

    Science.gov (United States)

    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.

  13. Assessing land use/cover changes: a nationwide multidate spatial database for Mexico

    Science.gov (United States)

    Mas, Jean-François; Velázquez, Alejandro; Díaz-Gallegos, José Reyes; Mayorga-Saucedo, Rafael; Alcántara, Camilo; Bocco, Gerardo; Castro, Rutilio; Fernández, Tania; Pérez-Vega, Azucena

    2004-10-01

    A nationwide multidate GIS database was generated in order to carry out the quantification and spatial characterization of land use/cover changes (LUCC) in Mexico. Existing cartography on land use/cover at a 1:250,000 scale was revised to select compatible inputs regarding the scale, the classification scheme and the mapping method. Digital maps from three different dates (the late 1970s, 1993 and 2000) were revised, evaluated, corrected and integrated into a GIS database. In order to improve the reliability of the database, an attempt was made to assess the accuracy of the digitalisation procedure and to detect and correct unlikely changes due to thematic errors in the maps. Digital maps were overlaid in order to generate LUCC maps, transition matrices and to calculate rates of conversion. Based upon this database, rates of deforestation between 1976 and 2000 were evaluated as 0.25 and 0.76% per year for temperate and tropical forests, respectively.

  14. Secure Distributed Databases Using Cryptography

    Directory of Open Access Journals (Sweden)

    Ion IVAN

    2006-01-01

    Full Text Available The computational encryption is used intensively by different databases management systems for ensuring privacy and integrity of information that are physically stored in files. Also, the information is sent over network and is replicated on different distributed systems. It is proved that a satisfying level of security is achieved if the rows and columns of tables are encrypted independently of table or computer that sustains the data. Also, it is very important that the SQL - Structured Query Language query requests and responses to be encrypted over the network connection between the client and databases server. All this techniques and methods must be implemented by the databases administrators, designer and developers in a consistent security policy.

  15. RA radiological characterization database application

    International Nuclear Information System (INIS)

    Steljic, M.M; Ljubenov, V.Lj. . E-mail address of corresponding author: milijanas@vin.bg.ac.yu; Steljic, M.M.)

    2005-01-01

    Radiological characterization of the RA research reactor is one of the main activities in the first two years of the reactor decommissioning project. The raw characterization data from direct measurements or laboratory analyses (defined within the existing sampling and measurement programme) have to be interpreted, organized and summarized in order to prepare the final characterization survey report. This report should be made so that the radiological condition of the entire site is completely and accurately shown with the radiological condition of the components clearly depicted. This paper presents an electronic database application, designed as a serviceable and efficient tool for characterization data storage, review and analysis, as well as for the reports generation. Relational database model was designed and the application is made by using Microsoft Access 2002 (SP1), a 32-bit RDBMS for the desktop and client/server database applications that run under Windows XP. (author)

  16. Electronic database of arterial aneurysms

    Directory of Open Access Journals (Sweden)

    Fabiano Luiz Erzinger

    2014-12-01

    Full Text Available Background:The creation of an electronic database facilitates the storage of information, as well as streamlines the exchange of data, making easier the exchange of knowledge for future research.Objective:To construct an electronic database containing comprehensive and up-to-date clinical and surgical data on the most common arterial aneurysms, to help advance scientific research.Methods:The most important specialist textbooks and articles found in journals and on internet databases were reviewed in order to define the basic structure of the protocol. Data were computerized using the SINPE© system for integrated electronic protocols and tested in a pilot study.Results:The data entered onto the system was first used to create a Master protocol, organized into a structure of top-level directories covering a large proportion of the content on vascular diseases as follows: patient history; physical examination; supplementary tests and examinations; diagnosis; treatment; and clinical course. By selecting items from the Master protocol, Specific protocols were then created for the 22 arterial sites most often involved by aneurysms. The program provides a method for collection of data on patients including clinical characteristics (patient history and physical examination, supplementary tests and examinations, treatments received and follow-up care after treatment. Any information of interest on these patients that is contained in the protocol can then be used to query the database and select data for studies.Conclusions:It proved possible to construct a database of clinical and surgical data on the arterial aneurysms of greatest interest and, by adapting the data to specific software, the database was integrated into the SINPE© system, thereby providing a standardized method for collection of data on these patients and tools for retrieving this information in an organized manner for use in scientific studies.

  17. The CATDAT damaging earthquakes database

    Directory of Open Access Journals (Sweden)

    J. E. Daniell

    2011-08-01

    Full Text Available The global CATDAT damaging earthquakes and secondary effects (tsunami, fire, landslides, liquefaction and fault rupture database was developed to validate, remove discrepancies, and expand greatly upon existing global databases; and to better understand the trends in vulnerability, exposure, and possible future impacts of such historic earthquakes.

    Lack of consistency and errors in other earthquake loss databases frequently cited and used in analyses was a major shortcoming in the view of the authors which needed to be improved upon.

    Over 17 000 sources of information have been utilised, primarily in the last few years, to present data from over 12 200 damaging earthquakes historically, with over 7000 earthquakes since 1900 examined and validated before insertion into the database. Each validated earthquake includes seismological information, building damage, ranges of social losses to account for varying sources (deaths, injuries, homeless, and affected, and economic losses (direct, indirect, aid, and insured.

    Globally, a slightly increasing trend in economic damage due to earthquakes is not consistent with the greatly increasing exposure. The 1923 Great Kanto ($214 billion USD damage; 2011 HNDECI-adjusted dollars compared to the 2011 Tohoku (>$300 billion USD at time of writing, 2008 Sichuan and 1995 Kobe earthquakes show the increasing concern for economic loss in urban areas as the trend should be expected to increase. Many economic and social loss values not reported in existing databases have been collected. Historical GDP (Gross Domestic Product, exchange rate, wage information, population, HDI (Human Development Index, and insurance information have been collected globally to form comparisons.

    This catalogue is the largest known cross-checked global historic damaging earthquake database and should have far-reaching consequences for earthquake loss estimation, socio-economic analysis, and the global

  18. The CATDAT damaging earthquakes database

    Science.gov (United States)

    Daniell, J. E.; Khazai, B.; Wenzel, F.; Vervaeck, A.

    2011-08-01

    The global CATDAT damaging earthquakes and secondary effects (tsunami, fire, landslides, liquefaction and fault rupture) database was developed to validate, remove discrepancies, and expand greatly upon existing global databases; and to better understand the trends in vulnerability, exposure, and possible future impacts of such historic earthquakes. Lack of consistency and errors in other earthquake loss databases frequently cited and used in analyses was a major shortcoming in the view of the authors which needed to be improved upon. Over 17 000 sources of information have been utilised, primarily in the last few years, to present data from over 12 200 damaging earthquakes historically, with over 7000 earthquakes since 1900 examined and validated before insertion into the database. Each validated earthquake includes seismological information, building damage, ranges of social losses to account for varying sources (deaths, injuries, homeless, and affected), and economic losses (direct, indirect, aid, and insured). Globally, a slightly increasing trend in economic damage due to earthquakes is not consistent with the greatly increasing exposure. The 1923 Great Kanto (214 billion USD damage; 2011 HNDECI-adjusted dollars) compared to the 2011 Tohoku (>300 billion USD at time of writing), 2008 Sichuan and 1995 Kobe earthquakes show the increasing concern for economic loss in urban areas as the trend should be expected to increase. Many economic and social loss values not reported in existing databases have been collected. Historical GDP (Gross Domestic Product), exchange rate, wage information, population, HDI (Human Development Index), and insurance information have been collected globally to form comparisons. This catalogue is the largest known cross-checked global historic damaging earthquake database and should have far-reaching consequences for earthquake loss estimation, socio-economic analysis, and the global reinsurance field.

  19. The STRING database in 2011

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Franceschini, Andrea; Kuhn, Michael

    2011-01-01

    present an update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING); it provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information. Interactions in STRING are provided with a confidence score...... models, extensive data updates and strongly improved connectivity and integration with third-party resources. Version 9.0 of STRING covers more than 1100 completely sequenced organisms; the resource can be reached at http://string-db.org....

  20. Secure Distributed Databases Using Cryptography

    OpenAIRE

    Ion IVAN; Cristian TOMA

    2006-01-01

    The computational encryption is used intensively by different databases management systems for ensuring privacy and integrity of information that are physically stored in files. Also, the information is sent over network and is replicated on different distributed systems. It is proved that a satisfying level of security is achieved if the rows and columns of tables are encrypted independently of table or computer that sustains the data. Also, it is very important that the SQL - Structured Que...

  1. An integrable, web-based solution for easy assessment of video-recorded performances

    DEFF Research Database (Denmark)

    Subhi, Yousif; Todsen, Tobias; Konge, Lars

    2014-01-01

    , and access to this information should be restricted to select personnel. A local software solution may also ease the need for customization to local needs and integration into existing user databases or project management software. We developed an integrable web-based solution for easy assessment of video...

  2. Functional Decomposition of Modeling and Simulation Terrain Database Generation Process

    National Research Council Canada - National Science Library

    Yakich, Valerie R; Lashlee, J. D

    2008-01-01

    .... This report documents the conceptual procedure as implemented by Lockheed Martin Simulation, Training, and Support and decomposes terrain database construction using the Integration Definition for Function Modeling (IDEF...

  3. Database Description - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name PSCDB Alternative n...rial Science and Technology (AIST) Takayuki Amemiya E-mail: Database classification Structure Databases - Protein structure Database...554-D558. External Links: Original website information Database maintenance site Graduate School of Informat...available URL of Web services - Need for user registration Not available About This Database Database Descri...ption Download License Update History of This Database Site Policy | Contact Us Database Description - PSCDB | LSDB Archive ...

  4. Directory of IAEA databases

    International Nuclear Information System (INIS)

    1991-11-01

    The first edition of the Directory of IAEA Databases is intended to describe the computerized information sources available to IAEA staff members. It contains a listing of all databases produced at the IAEA, together with information on their availability

  5. Native Health Research Database

    Science.gov (United States)

    ... Indian Health Board) Welcome to the Native Health Database. Please enter your search terms. Basic Search Advanced ... To learn more about searching the Native Health Database, click here. Tutorial Video The NHD has made ...

  6. Cell Centred Database (CCDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging.

  7. E3 Staff Database

    Data.gov (United States)

    US Agency for International Development — E3 Staff database is maintained by E3 PDMS (Professional Development & Management Services) office. The database is Mysql. It is manually updated by E3 staff as...

  8. HOLLYWOOD: a comparative relational database of alternative splicing.

    Science.gov (United States)

    Holste, Dirk; Huo, George; Tung, Vivian; Burge, Christopher B

    2006-01-01

    RNA splicing is an essential step in gene expression, and is often variable, giving rise to multiple alternatively spliced mRNA and protein isoforms from a single gene locus. The design of effective databases to support experimental and computational investigations of alternative splicing (AS) is a significant challenge. In an effort to integrate accurate exon and splice site annotation with current knowledge about splicing regulatory elements and predicted AS events, and to link information about the splicing of orthologous genes in different species, we have developed the Hollywood system. This database was built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags, and links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. Hollywood was implemented as a relational database and currently contains comprehensive information for human and mouse. It is accompanied by a web query tool that allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene. A streamlined graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser. The database is accessible at http://hollywood.mit.edu.

  9. Integrating Relational Databases and Constraint Languages

    DEFF Research Database (Denmark)

    Hansen, Michael Reichhardt; Hansen, Bo S.; Lucas, Peter

    1989-01-01

    A new structure of application programs is suggested, which separates the algorithmic parts from factual information (data and rules). The latter is to be stored in a repository that can be shared among multiple applications. It is argued that rules stating pure relations are better suited...... for sharing among different applications than procedural or functional rules because these latter rules always determine inputs and outputs.To support such a repository, an extended relational algebra is explored. This algebra serves as the semantic model for a proposed rules language and is the basis...

  10. Development of a PSA information database system

    International Nuclear Information System (INIS)

    Kim, Seung Hwan

    2005-01-01

    The need to develop the PSA information database for performing a PSA has been growing rapidly. For example, performing a PSA requires a lot of data to analyze, to evaluate the risk, to trace the process of results and to verify the results. PSA information database is a system that stores all PSA related information into the database and file system with cross links to jump to the physical documents whenever they are needed. Korea Atomic Energy Research Institute is developing a PSA information database system, AIMS (Advanced Information Management System for PSA). The objective is to integrate and computerize all the distributed information of a PSA into a system and to enhance the accessibility to PSA information for all PSA related activities. This paper describes how we implemented such a database centered application in the view of two areas, database design and data (document) service

  11. Environmental comparison of intensive and integrated agriculture-aquaculture systems for striped catfish production in the Mekong Delta, Vietnam, based on two existing case studies using life cycle assessment

    NARCIS (Netherlands)

    Kluts, I.N.; Potting, J.M.B.; Bosma, R.H.; Phong, L.T.; Udo, H.M.J.

    2012-01-01

    Vietnam is the largest producer for the export of striped catfish. Traditionally striped catfish production in the Mekong Delta took place in integrated agriculture–aquaculture systems, but has shifted recently to intensive systems to meet increasing export demands. A recent study quantified the

  12. NIRS database of the original research database

    International Nuclear Information System (INIS)

    Morita, Kyoko

    1991-01-01

    Recently, library staffs arranged and compiled the original research papers that have been written by researchers for 33 years since National Institute of Radiological Sciences (NIRS) established. This papers describes how the internal database of original research papers has been created. This is a small sample of hand-made database. This has been cumulating by staffs who have any knowledge about computer machine or computer programming. (author)

  13. Scopus database: a review.

    Science.gov (United States)

    Burnham, Judy F

    2006-03-08

    The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs.

  14. Aviation Safety Issues Database

    Science.gov (United States)

    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.

  15. Relational Databases and Biomedical Big Data.

    Science.gov (United States)

    de Silva, N H Nisansa D

    2017-01-01

    In various biomedical applications that collect, handle, and manipulate data, the amounts of data tend to build up and venture into the range identified as bigdata. In such occurrences, a design decision has to be taken as to what type of database would be used to handle this data. More often than not, the default and classical solution to this in the biomedical domain according to past research is relational databases. While this used to be the norm for a long while, it is evident that there is a trend to move away from relational databases in favor of other types and paradigms of databases. However, it still has paramount importance to understand the interrelation that exists between biomedical big data and relational databases. This chapter will review the pros and cons of using relational databases to store biomedical big data that previous researches have discussed and used.

  16. Current trends and new challenges of databases and web applications for systems driven biological research

    Directory of Open Access Journals (Sweden)

    Pradeep Kumar eSreenivasaiah

    2010-12-01

    Full Text Available Dynamic and rapidly evolving nature of systems driven research imposes special requirements on the technology, approach, design and architecture of computational infrastructure including database and web application. Several solutions have been proposed to meet the expectations and novel methods have been developed to address the persisting problems of data integration. It is important for researchers to understand different technologies and approaches. Having familiarized with the pros and cons of the existing technologies, researchers can exploit its capabilities to the maximum potential for integrating data. In this review we discuss the architecture, design and key technologies underlying some of the prominent databases (DBs and web applications. We will mention their roles in integration of biological data and investigate some of the emerging design concepts and computational technologies that are likely to have a key role in the future of systems driven biomedical research.

  17. The eNanoMapper database for nanomaterial safety information

    Directory of Open Access Journals (Sweden)

    Nina Jeliazkova

    2015-07-01

    Full Text Available Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs. Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs.Results: The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API, and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms.Conclusion: We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the “representational state

  18. The eNanoMapper database for nanomaterial safety information.

    Science.gov (United States)

    Jeliazkova, Nina; Chomenidis, Charalampos; Doganis, Philip; Fadeel, Bengt; Grafström, Roland; Hardy, Barry; Hastings, Janna; Hegi, Markus; Jeliazkov, Vedrin; Kochev, Nikolay; Kohonen, Pekka; Munteanu, Cristian R; Sarimveis, Haralambos; Smeets, Bart; Sopasakis, Pantelis; Tsiliki, Georgia; Vorgrimmler, David; Willighagen, Egon

    2015-01-01

    The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the "representational state transfer" (REST) API enables building user friendly

  19. Adding Semantic Support to Existing UDDI Infrastructure

    National Research Council Canada - National Science Library

    Luo, Jim; Montrose, Bruce; Kang, Myong

    2005-01-01

    .... The advantage is that it is completely backward compatible. The add-on modules only need to be installed on the clients of users who wish to take advantage of semantic markups. They can be integrated seamlessly into existing systems and operations without any modification of the infrastructure.

  20. Automated Oracle database testing

    CERN Multimedia

    CERN. Geneva

    2014-01-01

    Ensuring database stability and steady performance in the modern world of agile computing is a major challenge. Various changes happening at any level of the computing infrastructure: OS parameters & packages, kernel versions, database parameters & patches, or even schema changes, all can potentially harm production services. This presentation shows how an automatic and regular testing of Oracle databases can be achieved in such agile environment.