Mediator infrastructure for information integration and semantic data integration environment for biomedical research.

PubMed

Grethe, Jeffrey S; Ross, Edward; Little, David; Sanders, Brian; Gupta, Amarnath; Astakhov, Vadim

2009-01-01

This paper presents current progress in the development of semantic data integration environment which is a part of the Biomedical Informatics Research Network (BIRN; http://www.nbirn.net) project. BIRN is sponsored by the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). A goal is the development of a cyberinfrastructure for biomedical research that supports advance data acquisition, data storage, data management, data integration, data mining, data visualization, and other computing and information processing services over the Internet. Each participating institution maintains storage of their experimental or computationally derived data. Mediator-based data integration system performs semantic integration over the databases to enable researchers to perform analyses based on larger and broader datasets than would be available from any single institution's data. This paper describes recent revision of the system architecture, implementation, and capabilities of the semantically based data integration environment for BIRN.

An integrated approach to reservoir modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Donaldson, K.

1993-08-01

The purpose of this research is to evaluate the usefulness of the following procedural and analytical methods in investigating the heterogeneity of the oil reserve for the Mississipian Big Injun Sandstone of the Granny Creek field, Clay and Roane counties, West Virginia: (1) relational database, (2) two-dimensional cross sections, (3) true three-dimensional modeling, (4) geohistory analysis, (5) a rule-based expert system, and (6) geographical information systems. The large data set could not be effectively integrated and interpreted without this approach. A relational database was designed to fully integrate three- and four-dimensional data. The database provides an effective means for maintainingmore » and manipulating the data. A two-dimensional cross section program was designed to correlate stratigraphy, depositional environments, porosity, permeability, and petrographic data. This flexible design allows for additional four-dimensional data. Dynamic Graphics[sup [trademark

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

PubMed

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.

DSSTOX: NEW ON-LINE RESOURCE FOR PUBLISHING AND INTEGRATING STANDARDIZED STRUCTURE-INCLUSIVE TOXICITY DATABASES

EPA Science Inventory

DSSTox: New On-line Resource for Publishing Structure-Standardized Toxicity Databases

Ann M Richard1, Jamie Burch2, ClarLynda Williams3
1Nat. Health and Environ. Effects Res. Lb, US EP& Ret Triangle Park, NC 27711; 2EPA-NC
Central Univ Student COOP, US EPA, lies. Tri...

Individuals and Environments: Linking Ability and Skill Ratings with Interests

ERIC Educational Resources Information Center

Anthoney, Sarah Fetter; Armstrong, Patrick Ian

2010-01-01

Holland's (1997) theory of corresponding person and work environment structures was evaluated by comparing the integration of individual and occupational ratings of interests, abilities, and skills. Occupational ratings were obtained from the U.S. Department of Labor's O*NET database (U.S. Department of Labor, 2007). College students (494 women,…

Heterogeneity in Health Care Computing Environments

PubMed Central

Sengupta, Soumitra

1989-01-01

This paper discusses issues of heterogeneity in computer systems, networks, databases, and presentation techniques, and the problems it creates in developing integrated medical information systems. The need for institutional, comprehensive goals are emphasized. Using the Columbia-Presbyterian Medical Center's computing environment as the case study, various steps to solve the heterogeneity problem are presented.

Integrating forensic information in a crime intelligence database.

PubMed

Rossy, Quentin; Ioset, Sylvain; Dessimoz, Damien; Ribaux, Olivier

2013-07-10

Since 2008, intelligence units of six states of the western part of Switzerland have been sharing a common database for the analysis of high volume crimes. On a daily basis, events reported to the police are analysed, filtered and classified to detect crime repetitions and interpret the crime environment. Several forensic outcomes are integrated in the system such as matches of traces with persons, and links between scenes detected by the comparison of forensic case data. Systematic procedures have been settled to integrate links assumed mainly through DNA profiles, shoemarks patterns and images. A statistical outlook on a retrospective dataset of series from 2009 to 2011 of the database informs for instance on the number of repetition detected or confirmed and increased by forensic case data. Time needed to obtain forensic intelligence in regard with the type of marks treated, is seen as a critical issue. Furthermore, the underlying integration process of forensic intelligence into the crime intelligence database raised several difficulties in regards of the acquisition of data and the models used in the forensic databases. Solutions found and adopted operational procedures are described and discussed. This process form the basis to many other researches aimed at developing forensic intelligence models. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

An integrated knowledge system for wind tunnel testing - Project Engineers' Intelligent Assistant

NASA Technical Reports Server (NTRS)

Lo, Ching F.; Shi, George Z.; Hoyt, W. A.; Steinle, Frank W., Jr.

1993-01-01

The Project Engineers' Intelligent Assistant (PEIA) is an integrated knowledge system developed using artificial intelligence technology, including hypertext, expert systems, and dynamic user interfaces. This system integrates documents, engineering codes, databases, and knowledge from domain experts into an enriched hypermedia environment and was designed to assist project engineers in planning and conducting wind tunnel tests. PEIA is a modular system which consists of an intelligent user-interface, seven modules and an integrated tool facility. Hypermedia technology is discussed and the seven PEIA modules are described. System maintenance and updating is very easy due to the modular structure and the integrated tool facility provides user access to commercial software shells for documentation, reporting, or database updating. PEIA is expected to provide project engineers with technical information, increase efficiency and productivity, and provide a realistic tool for personnel training.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bower, J.C.; Burford, M.J.; Downing, T.R.

The Integrated Baseline System (IBS) is an emergency management planning and analysis tool that is being developed under the direction of the US Army Nuclear and Chemical Agency (USANCA). The IBS Data Management Guide provides the background, as well as the operations and procedures needed to generate and maintain a site-specific map database. Data and system managers use this guide to manage the data files and database that support the administrative, user-environment, database management, and operational capabilities of the IBS. This document provides a description of the data files and structures necessary for running the IBS software and using themore » site map database.« less

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

PubMed

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. This database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

A few scenarios still do not fit all

NASA Astrophysics Data System (ADS)

Schweizer, Vanessa

2018-05-01

For integrated climate change research, the Scenario Matrix Architecture provides a tractable menu of possible emissions trajectories, socio-economic futures and policy environments. However, the future of decision support may lie in searchable databases.

Software Configuration Management Across Project Boundaries and In Distributed Development Environments.

DTIC Science & Technology

1984-01-01

between projects and between host development systems, and between projects, using an integrated Programming Support Environment. The discussion assumes...the availability of some of the facilities that were proposed for inclusion in the UK CHAPSE (CHILL Ada Programming Support Environment). C’ Accession...life cycle of a product. In a programming support envirorment (PSE) with an underlying database, the software can be stored in the databave and

An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences.

PubMed

De Oliveira, T; Miller, R; Tarin, M; Cassol, S

2003-01-01

Sequence databases encode a wealth of information needed to develop improved vaccination and treatment strategies for the control of HIV and other important pathogens. To facilitate effective utilization of these datasets, we developed a user-friendly GDE-based LINUX interface that reduces input/output file formatting. GDE was adapted to the Linux operating system, bioinformatics tools were integrated with microbe-specific databases, and up-to-date GDE menus were developed for several clinically important viral, bacterial and parasitic genomes. Each microbial interface was designed for local access and contains Genbank, BLAST-formatted and phylogenetic databases. GDE-Linux is available for research purposes by direct application to the corresponding author. Application-specific menus and support files can be downloaded from (http://www.bioafrica.net).

Building an Integrated Environment for Multimedia

NASA Technical Reports Server (NTRS)

1997-01-01

Multimedia courseware on the solar system and earth science suitable for use in elementary, middle, and high schools was developed under this grant. The courseware runs on Silicon Graphics, Incorporated (SGI) workstations and personal computers (PCs). There is also a version of the courseware accessible via the World Wide Web. Accompanying multimedia database systems were also developed to enhance the multimedia courseware. The database systems accompanying the PC software are based on the relational model, while the database systems accompanying the SGI software are based on the object-oriented model.

ELISA-BASE: An Integrated Bioinformatics Tool for Analyzing and Tracking ELISA Microarray Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Amanda M.; Collett, James L.; Seurynck-Servoss, Shannon L.

ELISA-BASE is an open-source database for capturing, organizing and analyzing protein enzyme-linked immunosorbent assay (ELISA) microarray data. ELISA-BASE is an extension of the BioArray Soft-ware Environment (BASE) database system, which was developed for DNA microarrays. In order to make BASE suitable for protein microarray experiments, we developed several plugins for importing and analyzing quantitative ELISA microarray data. Most notably, our Protein Microarray Analysis Tool (ProMAT) for processing quantita-tive ELISA data is now available as a plugin to the database.

Development of the Lymphoma Enterprise Architecture Database: A caBIG(tm) Silver level compliant System

PubMed Central

Huang, Taoying; Shenoy, Pareen J.; Sinha, Rajni; Graiser, Michael; Bumpers, Kevin W.; Flowers, Christopher R.

2009-01-01

Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid™ (caBIG™) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system™ (LEAD™), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute’s Center for Bioinformatics to establish the LEAD™ platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD™ could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG™ can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG™ to the management of clinical and biological data. PMID:19492074

Development of the Lymphoma Enterprise Architecture Database: a caBIG Silver level compliant system.

PubMed

Huang, Taoying; Shenoy, Pareen J; Sinha, Rajni; Graiser, Michael; Bumpers, Kevin W; Flowers, Christopher R

2009-04-03

Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid (caBIG) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system (LEAD), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute's Center for Bioinformatics to establish the LEAD platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG to the management of clinical and biological data.

Analysis of methods. [information systems evolution environment

NASA Technical Reports Server (NTRS)

Mayer, Richard J. (Editor); Ackley, Keith A.; Wells, M. Sue; Mayer, Paula S. D.; Blinn, Thomas M.; Decker, Louis P.; Toland, Joel A.; Crump, J. Wesley; Menzel, Christopher P.; Bodenmiller, Charles A.

1991-01-01

Information is one of an organization's most important assets. For this reason the development and maintenance of an integrated information system environment is one of the most important functions within a large organization. The Integrated Information Systems Evolution Environment (IISEE) project has as one of its primary goals a computerized solution to the difficulties involved in the development of integrated information systems. To develop such an environment a thorough understanding of the enterprise's information needs and requirements is of paramount importance. This document is the current release of the research performed by the Integrated Development Support Environment (IDSE) Research Team in support of the IISEE project. Research indicates that an integral part of any information system environment would be multiple modeling methods to support the management of the organization's information. Automated tool support for these methods is necessary to facilitate their use in an integrated environment. An integrated environment makes it necessary to maintain an integrated database which contains the different kinds of models developed under the various methodologies. In addition, to speed the process of development of models, a procedure or technique is needed to allow automatic translation from one methodology's representation to another while maintaining the integrity of both. The purpose for the analysis of the modeling methods included in this document is to examine these methods with the goal being to include them in an integrated development support environment. To accomplish this and to develop a method for allowing intra-methodology and inter-methodology model element reuse, a thorough understanding of multiple modeling methodologies is necessary. Currently the IDSE Research Team is investigating the family of Integrated Computer Aided Manufacturing (ICAM) DEFinition (IDEF) languages IDEF(0), IDEF(1), and IDEF(1x), as well as ENALIM, Entity Relationship, Data Flow Diagrams, and Structure Charts, for inclusion in an integrated development support environment.

Casimage project: a digital teaching files authoring environment.

PubMed

Rosset, Antoine; Muller, Henning; Martins, Martina; Dfouni, Natalia; Vallée, Jean-Paul; Ratib, Osman

2004-04-01

The goal of the Casimage project is to offer an authoring and editing environment integrated with the Picture Archiving and Communication Systems (PACS) for creating image-based electronic teaching files. This software is based on a client/server architecture allowing remote access of users to a central database. This authoring environment allows radiologists to create reference databases and collection of digital images for teaching and research directly from clinical cases being reviewed on PACS diagnostic workstations. The environment includes all tools to create teaching files, including textual description, annotations, and image manipulation. The software also allows users to generate stand-alone CD-ROMs and web-based teaching files to easily share their collections. The system includes a web server compatible with the Medical Imaging Resource Center standard (MIRC, http://mirc.rsna.org) to easily integrate collections in the RSNA web network dedicated to teaching files. This software could be installed on any PACS workstation to allow users to add new cases at any time and anywhere during clinical operations. Several images collections were created with this tool, including thoracic imaging that was subsequently made available on a CD-Rom and on our web site and through the MIRC network for public access.

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

PubMed

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://hive.biochemistry.gwu.edu/tools/biomuta/index.php; CSR: http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr; HIVE: http://hive.biochemistry.gwu.edu.

LONI visualization environment.

PubMed

Dinov, Ivo D; Valentino, Daniel; Shin, Bae Cheol; Konstantinidis, Fotios; Hu, Guogang; MacKenzie-Graham, Allan; Lee, Erh-Fang; Shattuck, David; Ma, Jeff; Schwartz, Craig; Toga, Arthur W

2006-06-01

Over the past decade, the use of informatics to solve complex neuroscientific problems has increased dramatically. Many of these research endeavors involve examining large amounts of imaging, behavioral, genetic, neurobiological, and neuropsychiatric data. Superimposing, processing, visualizing, or interpreting such a complex cohort of datasets frequently becomes a challenge. We developed a new software environment that allows investigators to integrate multimodal imaging data, hierarchical brain ontology systems, on-line genetic and phylogenic databases, and 3D virtual data reconstruction models. The Laboratory of Neuro Imaging visualization environment (LONI Viz) consists of the following components: a sectional viewer for imaging data, an interactive 3D display for surface and volume rendering of imaging data, a brain ontology viewer, and an external database query system. The synchronization of all components according to stereotaxic coordinates, region name, hierarchical ontology, and genetic labels is achieved via a comprehensive BrainMapper functionality, which directly maps between position, structure name, database, and functional connectivity information. This environment is freely available, portable, and extensible, and may prove very useful for neurobiologists, neurogenetisists, brain mappers, and for other clinical, pedagogical, and research endeavors.

Digital Earth system based river basin data integration

NASA Astrophysics Data System (ADS)

Zhang, Xin; Li, Wanqing; Lin, Chao

2014-12-01

Digital Earth is an integrated approach to build scientific infrastructure. The Digital Earth systems provide a three-dimensional visualization and integration platform for river basin data which include the management data, in situ observation data, remote sensing observation data and model output data. This paper studies the Digital Earth system based river basin data integration technology. Firstly, the construction of the Digital Earth based three-dimensional river basin data integration environment is discussed. Then the river basin management data integration technology is presented which is realized by general database access interface, web service and ActiveX control. Thirdly, the in situ data stored in database tables as records integration is realized with three-dimensional model of the corresponding observation apparatus display in the Digital Earth system by a same ID code. In the next two parts, the remote sensing data and the model output data integration technologies are discussed in detail. The application in the Digital Zhang River basin System of China shows that the method can effectively improve the using efficiency and visualization effect of the data.

Development of water environment information management and water pollution accident response system

NASA Astrophysics Data System (ADS)

Zhang, J.; Ruan, H.

2009-12-01

In recent years, many water pollution accidents occurred with the rapid economical development. In this study, water environment information management and water pollution accident response system are developed based on geographic information system (GIS) techniques. The system integrated spatial database, attribute database, hydraulic model, and water quality model under a user-friendly interface in a GIS environment. System ran in both Client/Server (C/S) and Browser/Server (B/S) platform which focused on model and inquiry respectively. System provided spatial and attribute data inquiry, water quality evaluation, statics, water pollution accident response case management (opening reservoir etc) and 2D and 3D visualization function, and gave assistant information to make decision on water pollution accident response. Polluted plume in Huaihe River were selected to simulate the transport of pollutes.

Design of a Multi Dimensional Database for the Archimed DataWarehouse.

PubMed

Bréant, Claudine; Thurler, Gérald; Borst, François; Geissbuhler, Antoine

2005-01-01

The Archimed data warehouse project started in 1993 at the Geneva University Hospital. It has progressively integrated seven data marts (or domains of activity) archiving medical data such as Admission/Discharge/Transfer (ADT) data, laboratory results, radiology exams, diagnoses, and procedure codes. The objective of the Archimed data warehouse is to facilitate the access to an integrated and coherent view of patient medical in order to support analytical activities such as medical statistics, clinical studies, retrieval of similar cases and data mining processes. This paper discusses three principal design aspects relative to the conception of the database of the data warehouse: 1) the granularity of the database, which refers to the level of detail or summarization of data, 2) the database model and architecture, describing how data will be presented to end users and how new data is integrated, 3) the life cycle of the database, in order to ensure long term scalability of the environment. Both, the organization of patient medical data using a standardized elementary fact representation and the use of the multi dimensional model have proved to be powerful design tools to integrate data coming from the multiple heterogeneous database systems part of the transactional Hospital Information System (HIS). Concurrently, the building of the data warehouse in an incremental way has helped to control the evolution of the data content. These three design aspects bring clarity and performance regarding data access. They also provide long term scalability to the system and resilience to further changes that may occur in source systems feeding the data warehouse.

High-Performance Secure Database Access Technologies for HEP Grids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matthew Vranicar; John Weicher

2006-04-17

The Large Hadron Collider (LHC) at the CERN Laboratory will become the largest scientific instrument in the world when it starts operations in 2007. Large Scale Analysis Computer Systems (computational grids) are required to extract rare signals of new physics from petabytes of LHC detector data. In addition to file-based event data, LHC data processing applications require access to large amounts of data in relational databases: detector conditions, calibrations, etc. U.S. high energy physicists demand efficient performance of grid computing applications in LHC physics research where world-wide remote participation is vital to their success. To empower physicists with data-intensive analysismore » capabilities a whole hyperinfrastructure of distributed databases cross-cuts a multi-tier hierarchy of computational grids. The crosscutting allows separation of concerns across both the global environment of a federation of computational grids and the local environment of a physicist’s computer used for analysis. Very few efforts are on-going in the area of database and grid integration research. Most of these are outside of the U.S. and rely on traditional approaches to secure database access via an extraneous security layer separate from the database system core, preventing efficient data transfers. Our findings are shared by the Database Access and Integration Services Working Group of the Global Grid Forum, who states that "Research and development activities relating to the Grid have generally focused on applications where data is stored in files. However, in many scientific and commercial domains, database management systems have a central role in data storage, access, organization, authorization, etc, for numerous applications.” There is a clear opportunity for a technological breakthrough, requiring innovative steps to provide high-performance secure database access technologies for grid computing. We believe that an innovative database architecture where the secure authorization is pushed into the database engine will eliminate inefficient data transfer bottlenecks. Furthermore, traditionally separated database and security layers provide an extra vulnerability, leaving a weak clear-text password authorization as the only protection on the database core systems. Due to the legacy limitations of the systems’ security models, the allowed passwords often can not even comply with the DOE password guideline requirements. We see an opportunity for the tight integration of the secure authorization layer with the database server engine resulting in both improved performance and improved security. Phase I has focused on the development of a proof-of-concept prototype using Argonne National Laboratory’s (ANL) Argonne Tandem-Linac Accelerator System (ATLAS) project as a test scenario. By developing a grid-security enabled version of the ATLAS project’s current relation database solution, MySQL, PIOCON Technologies aims to offer a more efficient solution to secure database access.« less

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

PubMed Central

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

2015-01-01

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

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE Office of Scientific and Technical Information (OSTI.GOV)

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE PAGES

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

NLCD - MODIS albedo data

EPA Pesticide Factsheets

The NLCD-MODIS land cover-albedo database integrates high-quality MODIS albedo observations with areas of homogeneous land cover from NLCD. The spatial resolution (pixel size) of the database is 480m-x-480m aligned to the standardized UGSG Albers Equal-Area projection. The spatial extent of the database is the continental United States. This dataset is associated with the following publication:Wickham , J., C.A. Barnes, and T. Wade. Combining NLCD and MODIS to Create a Land Cover-Albedo Dataset for the Continental United States. REMOTE SENSING OF ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 170(0): 143-153, (2015).

Health Assessment Document for Chromium (Final Report, 1983)

EPA Science Inventory

This final report summarizes a comprehensive database that considers all sources of chromium in the environment, the likelihood for its exposure to humans, and the possible consequences to man and lower organisms from its absorption. This information is integrated into a format t...

NCBI2RDF: enabling full RDF-based access to NCBI databases.

PubMed

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

2013-01-01

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

Developing a Cyberinfrastructure for integrated assessments of environmental contaminants.

PubMed

Kaur, Taranjit; Singh, Jatinder; Goodale, Wing M; Kramar, David; Nelson, Peter

2005-03-01

The objective of this study was to design and implement prototype software for capturing field data and automating the process for reporting and analyzing the distribution of mercury. The four phase process used to design, develop, deploy and evaluate the prototype software is described. Two different development strategies were used: (1) design of a mobile data collection application intended to capture field data in a meaningful format and automate transfer into user databases, followed by (2) a re-engineering of the original software to develop an integrated database environment with improved methods for aggregating and sharing data. Results demonstrated that innovative use of commercially available hardware and software components can lead to the development of an end-to-end digital cyberinfrastructure that captures, records, stores, transmits, compiles and integrates multi-source data as it relates to mercury.

A semantic problem solving environment for integrative parasite research: identification of intervention targets for Trypanosoma cruzi.

PubMed

Parikh, Priti P; Minning, Todd A; Nguyen, Vinh; Lalithsena, Sarasi; Asiaee, Amir H; Sahoo, Satya S; Doshi, Prashant; Tarleton, Rick; Sheth, Amit P

2012-01-01

Research on the biology of parasites requires a sophisticated and integrated computational platform to query and analyze large volumes of data, representing both unpublished (internal) and public (external) data sources. Effective analysis of an integrated data resource using knowledge discovery tools would significantly aid biologists in conducting their research, for example, through identifying various intervention targets in parasites and in deciding the future direction of ongoing as well as planned projects. A key challenge in achieving this objective is the heterogeneity between the internal lab data, usually stored as flat files, Excel spreadsheets or custom-built databases, and the external databases. Reconciling the different forms of heterogeneity and effectively integrating data from disparate sources is a nontrivial task for biologists and requires a dedicated informatics infrastructure. Thus, we developed an integrated environment using Semantic Web technologies that may provide biologists the tools for managing and analyzing their data, without the need for acquiring in-depth computer science knowledge. We developed a semantic problem-solving environment (SPSE) that uses ontologies to integrate internal lab data with external resources in a Parasite Knowledge Base (PKB), which has the ability to query across these resources in a unified manner. The SPSE includes Web Ontology Language (OWL)-based ontologies, experimental data with its provenance information represented using the Resource Description Format (RDF), and a visual querying tool, Cuebee, that features integrated use of Web services. We demonstrate the use and benefit of SPSE using example queries for identifying gene knockout targets of Trypanosoma cruzi for vaccine development. Answers to these queries involve looking up multiple sources of data, linking them together and presenting the results. The SPSE facilitates parasitologists in leveraging the growing, but disparate, parasite data resources by offering an integrative platform that utilizes Semantic Web techniques, while keeping their workload increase minimal.

Data Architecture in an Open Systems Environment.

ERIC Educational Resources Information Center

Bernbom, Gerald; Cromwell, Dennis

1993-01-01

The conceptual basis for structured data architecture, and its integration with open systems technology at Indiana University, are described. Key strategic goals guiding these efforts are discussed: commitment to improved data access; migration to relational database technology, and deployment of a high-speed, multiprotocol network; and…

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean.

PubMed

Pagliosa, Paulo R; Doria, João G; Misturini, Dairana; Otegui, Mariana B P; Oortman, Mariana S; Weis, Wilson A; Faroni-Perez, Larisse; Alves, Alexandre P; Camargo, Maurício G; Amaral, A Cecília Z; Marques, Antonio C; Lana, Paulo C

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/.

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean

PubMed Central

Pagliosa, Paulo R.; Doria, João G.; Misturini, Dairana; Otegui, Mariana B. P.; Oortman, Mariana S.; Weis, Wilson A.; Faroni-Perez, Larisse; Alves, Alexandre P.; Camargo, Maurício G.; Amaral, A. Cecília Z.; Marques, Antonio C.; Lana, Paulo C.

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/ PMID:24573879

Open source integrated modeling environment Delta Shell

NASA Astrophysics Data System (ADS)

Donchyts, G.; Baart, F.; Jagers, B.; van Putten, H.

2012-04-01

In the last decade, integrated modelling has become a very popular topic in environmental modelling since it helps solving problems, which is difficult to model using a single model. However, managing complexity of integrated models and minimizing time required for their setup remains a challenging task. The integrated modelling environment Delta Shell simplifies this task. The software components of Delta Shell are easy to reuse separately from each other as well as a part of integrated environment that can run in a command-line or a graphical user interface mode. The most components of the Delta Shell are developed using C# programming language and include libraries used to define, save and visualize various scientific data structures as well as coupled model configurations. Here we present two examples showing how Delta Shell simplifies process of setting up integrated models from the end user and developer perspectives. The first example shows coupling of a rainfall-runoff, a river flow and a run-time control models. The second example shows how coastal morphological database integrates with the coastal morphological model (XBeach) and a custom nourishment designer. Delta Shell is also available as open-source software released under LGPL license and accessible via http://oss.deltares.nl.

Clinical results of HIS, RIS, PACS integration using data integration CASE tools

NASA Astrophysics Data System (ADS)

Taira, Ricky K.; Chan, Hing-Ming; Breant, Claudine M.; Huang, Lu J.; Valentino, Daniel J.

1995-05-01

Current infrastructure research in PACS is dominated by the development of communication networks (local area networks, teleradiology, ATM networks, etc.), multimedia display workstations, and hierarchical image storage architectures. However, limited work has been performed on developing flexible, expansible, and intelligent information processing architectures for the vast decentralized image and text data repositories prevalent in healthcare environments. Patient information is often distributed among multiple data management systems. Current large-scale efforts to integrate medical information and knowledge sources have been costly with limited retrieval functionality. Software integration strategies to unify distributed data and knowledge sources is still lacking commercially. Systems heterogeneity (i.e., differences in hardware platforms, communication protocols, database management software, nomenclature, etc.) is at the heart of the problem and is unlikely to be standardized in the near future. In this paper, we demonstrate the use of newly available CASE (computer- aided software engineering) tools to rapidly integrate HIS, RIS, and PACS information systems. The advantages of these tools include fast development time (low-level code is generated from graphical specifications), and easy system maintenance (excellent documentation, easy to perform changes, and centralized code repository in an object-oriented database). The CASE tools are used to develop and manage the `middle-ware' in our client- mediator-serve architecture for systems integration. Our architecture is scalable and can accommodate heterogeneous database and communication protocols.

Collaborative Resource Allocation

NASA Technical Reports Server (NTRS)

Wang, Yeou-Fang; Wax, Allan; Lam, Raymond; Baldwin, John; Borden, Chester

2007-01-01

Collaborative Resource Allocation Networking Environment (CRANE) Version 0.5 is a prototype created to prove the newest concept of using a distributed environment to schedule Deep Space Network (DSN) antenna times in a collaborative fashion. This program is for all space-flight and terrestrial science project users and DSN schedulers to perform scheduling activities and conflict resolution, both synchronously and asynchronously. Project schedulers can, for the first time, participate directly in scheduling their tracking times into the official DSN schedule, and negotiate directly with other projects in an integrated scheduling system. A master schedule covers long-range, mid-range, near-real-time, and real-time scheduling time frames all in one, rather than the current method of separate functions that are supported by different processes and tools. CRANE also provides private workspaces (both dynamic and static), data sharing, scenario management, user control, rapid messaging (based on Java Message Service), data/time synchronization, workflow management, notification (including emails), conflict checking, and a linkage to a schedule generation engine. The data structure with corresponding database design combines object trees with multiple associated mortal instances and relational database to provide unprecedented traceability and simplify the existing DSN XML schedule representation. These technologies are used to provide traceability, schedule negotiation, conflict resolution, and load forecasting from real-time operations to long-range loading analysis up to 20 years in the future. CRANE includes a database, a stored procedure layer, an agent-based middle tier, a Web service wrapper, a Windows Integrated Analysis Environment (IAE), a Java application, and a Web page interface.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zavarin, Mavrik; Wolery, T. J.; Atkins-Duffin, C.

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.

IRIS Toxicological Review of Ammonia (External Review Draft ...

EPA Pesticide Factsheets

EPA is conducting a peer review of the scientific basis supporting the human health hazard and dose-response assessment of ammonia that will appear in the Integrated Risk Information System (IRIS) database. EPA is undertaking an Integrated Risk Information System (IRIS) health assessment for ammonia. IRIS is an EPA database containing Agency scientific positions on potential adverse human health effects that may result from chronic (or lifetime) exposure to chemicals in the environment. IRIS contains chemical-specific summaries of qualitative and quantitative health information in support of two steps of the risk assessment paradigm, i.e., hazard identification and dose-response evaluation. IRIS assessments are used in combination with specific situational exposure assessment information to evaluate potential public health risk associated with environmental contaminants.

IRIS Toxicological Review of n-Butanol (External Review Draft ...

EPA Pesticide Factsheets

EPA is conducting a peer review of the scientific basis supporting the human health hazard and dose-response assessment of n-butanol that will appear in the Integrated Risk Information System (IRIS) database. EPA is undertaking an Integrated Risk Information System (IRIS) health assessment for n-butanol. IRIS is an EPA database containing Agency scientific positions on potential adverse human health effects that may result from chronic (or lifetime) exposure to chemicals in the environment. IRIS contains chemical-specific summaries of qualitative and quantitative health information in support of two steps of the risk assessment paradigm, i.e., hazard identification and dose-response evaluation. IRIS assessments are used in combination with specific situational exposure assessment information to evaluate potential public health risk associated with environmental contaminants.

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

PubMed

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

2015-03-01

Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

ENFIN--A European network for integrative systems biology.

PubMed

Kahlem, Pascal; Clegg, Andrew; Reisinger, Florian; Xenarios, Ioannis; Hermjakob, Henning; Orengo, Christine; Birney, Ewan

2009-11-01

Integration of biological data of various types and the development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing an adapted infrastructure to connect databases, and platforms to enable both the generation of new bioinformatics tools and the experimental validation of computational predictions. With the aim of bridging the gap existing between standard wet laboratories and bioinformatics, the ENFIN Network runs integrative research projects to bring the latest computational techniques to bear directly on questions dedicated to systems biology in the wet laboratory environment. The Network maintains internally close collaboration between experimental and computational research, enabling a permanent cycling of experimental validation and improvement of computational prediction methods. The computational work includes the development of a database infrastructure (EnCORE), bioinformatics analysis methods and a novel platform for protein function analysis FuncNet.

Establishment of the Northeast Coastal Watershed Geospatial Data Network (NECWGDN)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hannigan, Robyn

The goals of NECWGDN were to establish integrated geospatial databases that interfaced with existing open-source (water.html) environmental data server technologies (e.g., HydroDesktop) and included ecological and human data to enable evaluation, prediction, and adaptation in coastal environments to climate- and human-induced threats to the coastal marine resources within the Gulf of Maine. We have completed the development and testing of a "test bed" architecture that is compatible with HydroDesktop and have identified key metadata structures that will enable seamless integration and delivery of environmental, ecological, and human data as well as models to predict threats to end-users. Uniquely this databasemore » integrates point as well as model data and so offers capacities to end-users that are unique among databases. Future efforts will focus on the development of integrated environmental-human dimension models that can serve, in near real time, visualizations of threats to coastal resources and habitats.« less

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases

PubMed Central

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

2013-01-01

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

Korean Ministry of Environment's web-based visual consumer product exposure and risk assessment system (COPER).

PubMed

Lee, Hunjoo; Lee, Kiyoung; Park, Ji Young; Min, Sung-Gi

2017-05-01

With support from the Korean Ministry of the Environment (ME), our interdisciplinary research staff developed the COnsumer Product Exposure and Risk assessment system (COPER). This system includes various databases and features that enable the calculation of exposure and determination of risk caused by consumer products use. COPER is divided into three tiers: the integrated database layer (IDL), the domain specific service layer (DSSL), and the exposure and risk assessment layer (ERAL). IDL is organized by the form of the raw data (mostly non-aggregated data) and includes four sub-databases: a toxicity profile, an inventory of Korean consumer products, the weight fractions of chemical substances in the consumer products determined by chemical analysis and national representative exposure factors. DSSL provides web-based information services corresponding to each database within IDL. Finally, ERAL enables risk assessors to perform various exposure and risk assessments, including exposure scenario design via either inhalation or dermal contact by using or organizing each database in an intuitive manner. This paper outlines the overall architecture of the system and highlights some of the unique features of COPER based on visual and dynamic rendering engine for exposure assessment model on web.

Qualitative Comparison of IGRA and ESRL Radiosonde Archived Databases

NASA Technical Reports Server (NTRS)

Walker, John R.

2014-01-01

Multiple databases of atmospheric profile information are freely available to individuals and groups such as the Natural Environments group. Two of the primary database archives provided by NOAA that are most frequently used are those from the Earth Science Research Laboratory (ESRL) and the Integrated Global Radiosonde Archive (IGRA). Inquiries have been made as to why one database is used as opposed to the other, yet to the best of knowledge, no formal comparison has been performed. The goal of this study is to provide a qualitative comparison of the ESRL and IGRA radiosonde databases. For part of this analyses, 14 upper air observation sites were selected. These sites all have the common attribute of having been used or are planned for use in the development of Range Reference Atmospheres (RRAs) in support of NASA's and DOD's current and future goals.

Enabling heterogenous multi-scale database for emergency service functions through geoinformation technologies

NASA Astrophysics Data System (ADS)

Bhanumurthy, V.; Venugopala Rao, K.; Srinivasa Rao, S.; Ram Mohan Rao, K.; Chandra, P. Satya; Vidhyasagar, J.; Diwakar, P. G.; Dadhwal, V. K.

2014-11-01

Geographical Information Science (GIS) is now graduated from traditional desktop system to Internet system. Internet GIS is emerging as one of the most promising technologies for addressing Emergency Management. Web services with different privileges are playing an important role in dissemination of the emergency services to the decision makers. Spatial database is one of the most important components in the successful implementation of Emergency Management. It contains spatial data in the form of raster, vector, linked with non-spatial information. Comprehensive data is required to handle emergency situation in different phases. These database elements comprise core data, hazard specific data, corresponding attribute data, and live data coming from the remote locations. Core data sets are minimum required data including base, thematic, infrastructure layers to handle disasters. Disaster specific information is required to handle a particular disaster situation like flood, cyclone, forest fire, earth quake, land slide, drought. In addition to this Emergency Management require many types of data with spatial and temporal attributes that should be made available to the key players in the right format at right time. The vector database needs to be complemented with required resolution satellite imagery for visualisation and analysis in disaster management. Therefore, the database is interconnected and comprehensive to meet the requirement of an Emergency Management. This kind of integrated, comprehensive and structured database with appropriate information is required to obtain right information at right time for the right people. However, building spatial database for Emergency Management is a challenging task because of the key issues such as availability of data, sharing policies, compatible geospatial standards, data interoperability etc. Therefore, to facilitate using, sharing, and integrating the spatial data, there is a need to define standards to build emergency database systems. These include aspects such as i) data integration procedures namely standard coding scheme, schema, meta data format, spatial format ii) database organisation mechanism covering data management, catalogues, data models iii) database dissemination through a suitable environment, as a standard service for effective service dissemination. National Database for Emergency Management (NDEM) is such a comprehensive database for addressing disasters in India at the national level. This paper explains standards for integrating, organising the multi-scale and multi-source data with effective emergency response using customized user interfaces for NDEM. It presents standard procedure for building comprehensive emergency information systems for enabling emergency specific functions through geospatial technologies.

CONNJUR Workflow Builder: A software integration environment for spectral reconstruction

PubMed Central

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J.C.; Gryk, Michael R.

2015-01-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses. PMID:26066803

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

PubMed

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R

2015-07-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

Managing Data in a GIS Environment

NASA Technical Reports Server (NTRS)

Beltran, Maria; Yiasemis, Haris

1997-01-01

A Geographic Information System (GIS) is a computer-based system that enables capture, modeling, manipulation, retrieval, analysis and presentation of geographically referenced data. A GIS operates in a dynamic environment of spatial and temporal information. This information is held in a database like any other information system, but performance is more of an issue for a geographic database than a traditional database due to the nature of the data. What distinguishes a GIS from other information systems is the spatial and temporal dimensions of the data and the volume of data (several gigabytes). Most traditional information systems are usually based around tables and textual reports, whereas GIS requires the use of cartographic forms and other visualization techniques. Much of the data can be represented using computer graphics, but a GIS is not a graphics database. A graphical system is concerned with the manipulation and presentation of graphical objects whereas a GIS handles geographic objects that have not only spatial dimensions but non-visual, i e., attribute and components. Furthermore, the nature of the data on which a GIS operates makes the traditional relational database approach inadequate for retrieving data and answering queries that reference spatial data. The purpose of this paper is to describe the efficiency issues behind storage and retrieval of data within a GIS database. Section 2 gives a general background on GIS, and describes the issues involved in custom vs. commercial and hybrid vs. integrated geographic information systems. Section 3 describes the efficiency issues concerning the management of data within a GIS environment. The paper ends with a summary of the main concerns of this paper.

Calculation of Coupled Vibroacoustics Response Estimates from a Library of Available Uncoupled Transfer Function Sets

NASA Technical Reports Server (NTRS)

Smith, Andrew; LaVerde, Bruce; Hunt, Ron; Fulcher, Clay; Towner, Robert; McDonald, Emmett

2012-01-01

The design and theoretical basis of a new database tool that quickly generates vibroacoustic response estimates using a library of transfer functions (TFs) is discussed. During the early stages of a launch vehicle development program, these response estimates can be used to provide vibration environment specification to hardware vendors. The tool accesses TFs from a database, combines the TFs, and multiplies these by input excitations to estimate vibration responses. The database is populated with two sets of uncoupled TFs; the first set representing vibration response of a bare panel, designated as H(sup s), and the second set representing the response of the free-free component equipment by itself, designated as H(sup c). For a particular configuration undergoing analysis, the appropriate H(sup s) and H(sup c) are selected and coupled to generate an integrated TF, designated as H(sup s +c). This integrated TF is then used with the appropriate input excitations to estimate vibration responses. This simple yet powerful tool enables a user to estimate vibration responses without directly using finite element models, so long as suitable H(sup s) and H(sup c) sets are defined in the database libraries. The paper discusses the preparation of the database tool and provides the assumptions and methodologies necessary to combine H(sup s) and H(sup c) sets into an integrated H(sup s + c). An experimental validation of the approach is also presented.

Managing vulnerabilities and achieving compliance for Oracle databases in a modern ERP environment

NASA Astrophysics Data System (ADS)

Hölzner, Stefan; Kästle, Jan

In this paper we summarize good practices on how to achieve compliance for an Oracle database in combination with an ERP system. We use an integrated approach to cover both the management of vulnerabilities (preventive measures) and the use of logging and auditing features (detective controls). This concise overview focusses on the combination Oracle and SAP and it’s dependencies, but also outlines security issues that arise with other ERP systems. Using practical examples, we demonstrate common vulnerabilities and coutermeasures as well as guidelines for the use of auditing features.

An integrated toolbox for processing and analysis of remote sensing data of inland and coastal waters - atmospheric correction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haan, J.F. de; Kokke, J.M.M.; Hoogenboom, H.J.

1997-06-01

Deriving thematic maps of water quality parameters from a remote sensing image requires a number of processing steps, such as calibration, atmospheric correction, air-water interface correction, and application of water quality algorithms. A prototype version of an integrated software environment has recently been developed that enables the user to perform and control these processing steps. Major parts of this environment are: (i) access to the MODTRAN 3 radiative transfer code, (ii) a database of water quality algorithms, and (iii) a spectral library of Dutch coastal and inland waters, containing subsurface irradiance reflectance spectra and associated water quality parameters. The atmosphericmore » correction part of this environment is discussed here. It is shown that this part can be used to accurately retrieve spectral signatures of inland water for wavelengths between 450 and 750 nm, provided in situ measurements are used to determine atmospheric model parameters. Assessment of the usefulness of the completely integrated software system in an operational environment requires a revised version that is presently being developed.« less

Hospital integrated parallel cluster for fast and cost-efficient image analysis: clinical experience and research evaluation

NASA Astrophysics Data System (ADS)

Erberich, Stephan G.; Hoppe, Martin; Jansen, Christian; Schmidt, Thomas; Thron, Armin; Oberschelp, Walter

2001-08-01

In the last few years more and more University Hospitals as well as private hospitals changed to digital information systems for patient record, diagnostic files and digital images. Not only that patient management becomes easier, it is also very remarkable how clinical research can profit from Picture Archiving and Communication Systems (PACS) and diagnostic databases, especially from image databases. Since images are available on the finger tip, difficulties arise when image data needs to be processed, e.g. segmented, classified or co-registered, which usually demands a lot computational power. Today's clinical environment does support PACS very well, but real image processing is still under-developed. The purpose of this paper is to introduce a parallel cluster of standard distributed systems and its software components and how such a system can be integrated into a hospital environment. To demonstrate the cluster technique we present our clinical experience with the crucial but cost-intensive motion correction of clinical routine and research functional MRI (fMRI) data, as it is processed in our Lab on a daily basis.

Information management systems for pharmacogenomics.

PubMed

Thallinger, Gerhard G; Trajanoski, Slave; Stocker, Gernot; Trajanoski, Zlatko

2002-09-01

The value of high-throughput genomic research is dramatically enhanced by association with key patient data. These data are generally available but of disparate quality and not typically directly associated. A system that could bring these disparate data sources into a common resource connected with functional genomic data would be tremendously advantageous. However, the integration of clinical and accurate interpretation of the generated functional genomic data requires the development of information management systems capable of effectively capturing the data as well as tools to make that data accessible to the laboratory scientist or to the clinician. In this review these challenges and current information technology solutions associated with the management, storage and analysis of high-throughput data are highlighted. It is suggested that the development of a pharmacogenomic data management system which integrates public and proprietary databases, clinical datasets, and data mining tools embedded in a high-performance computing environment should include the following components: parallel processing systems, storage technologies, network technologies, databases and database management systems (DBMS), and application services.

IRIS Toxicological Review of Tetrahydrofuran (THF) (External ...

EPA Pesticide Factsheets

EPA is conducting a peer review and public comment of the scientific basis supporting the human health hazard and dose-response assessment of tetrahydrofuran (THF) that when finalized will appear on the Integrated Risk Information System (IRIS) database. EPA is undertaking an Integrated Risk Information System (IRIS) health assessment for tetrahydrofuran. IRIS is an EPA database containing Agency scientific positions on potential adverse human health effects that may result from chronic (or lifetime) exposure to chemicals in the environment. IRIS contains chemical-specific summaries of qualitative and quantitative health information in support of two steps of the risk assessment paradigm, i.e., hazard identification and dose-response evaluation. IRIS assessments are used in combination with specific situational exposure assessment information to evaluate potential public health risk associated with environmental contaminants.

QuakeSim 2.0

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay W.; Lyzenga, Gregory A.; Granat, Robert A.; Norton, Charles D.; Rundle, John B.; Pierce, Marlon E.; Fox, Geoffrey C.; McLeod, Dennis; Ludwig, Lisa Grant

2012-01-01

QuakeSim 2.0 improves understanding of earthquake processes by providing modeling tools and integrating model applications and various heterogeneous data sources within a Web services environment. QuakeSim is a multisource, synergistic, data-intensive environment for modeling the behavior of earthquake faults individually, and as part of complex interacting systems. Remotely sensed geodetic data products may be explored, compared with faults and landscape features, mined by pattern analysis applications, and integrated with models and pattern analysis applications in a rich Web-based and visualization environment. Integration of heterogeneous data products with pattern informatics tools enables efficient development of models. Federated database components and visualization tools allow rapid exploration of large datasets, while pattern informatics enables identification of subtle, but important, features in large data sets. QuakeSim is valuable for earthquake investigations and modeling in its current state, and also serves as a prototype and nucleus for broader systems under development. The framework provides access to physics-based simulation tools that model the earthquake cycle and related crustal deformation. Spaceborne GPS and Inter ferometric Synthetic Aperture (InSAR) data provide information on near-term crustal deformation, while paleoseismic geologic data provide longerterm information on earthquake fault processes. These data sources are integrated into QuakeSim's QuakeTables database system, and are accessible by users or various model applications. UAVSAR repeat pass interferometry data products are added to the QuakeTables database, and are available through a browseable map interface or Representational State Transfer (REST) interfaces. Model applications can retrieve data from Quake Tables, or from third-party GPS velocity data services; alternatively, users can manually input parameters into the models. Pattern analysis of GPS and seismicity data has proved useful for mid-term forecasting of earthquakes, and for detecting subtle changes in crustal deformation. The GPS time series analysis has also proved useful as a data-quality tool, enabling the discovery of station anomalies and data processing and distribution errors. Improved visualization tools enable more efficient data exploration and understanding. Tools provide flexibility to science users for exploring data in new ways through download links, but also facilitate standard, intuitive, and routine uses for science users and end users such as emergency responders.

Evolution of the Tropical Cyclone Integrated Data Exchange And Analysis System (TC-IDEAS)

NASA Technical Reports Server (NTRS)

Turk, J.; Chao, Y.; Haddad, Z.; Hristova-Veleva, S.; Knosp, B.; Lambrigtsen, B.; Li, P.; Licata, S.; Poulsen, W.; Su, H.;

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

PubMed

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 combining population-based cohort data with publicly available datasets not typically used for ageing and mental well-being research. Integration of various data sources and observational units into a single platform will help to explain the differences in ageing-related mental and cognitive disorders both within as well as between cities in Europe, the US, Canada, and Russia and to assess the causal pathways and interactions between the urban environment and the individual determinants of mental well-being and cognitive ageing in older adults.

EWB: The Environment WorkBench Version 4.0

NASA Technical Reports Server (NTRS)

1995-01-01

The Environment WorkBench EWB is a desktop integrated analysis tool for studying a spacecraft's interactions with its environment. Over 100 environment and analysis models are integrated into the menu-based tool. EWB, which was developed for and under the guidance of the NASA Lewis Research Center, is built atop the Module Integrator and Rule-based Intelligent Analytic Database (MIRIAD) architecture. This allows every module in EWB to communicate information to other modules in a transparent manner from the user's point of view. It removes the tedious and error-prone steps of entering data by hand from one model to another. EWB runs under UNIX operating systems (SGI and SUN workstations) and under MS Windows (3.x, 95, and NT) operating systems. MIRIAD, the unique software that makes up the core of EWB, provides the flexibility to easily modify old models and incorporate new ones as user needs change. The MIRIAD approach separates the computer assisted engineering (CAE) tool into three distinct units: 1) A modern graphical user interface to present information; 2) A data dictionary interpreter to coordinate analysis; and 3) A database for storing system designs and analysis results. The user interface is externally programmable through ASCII data files, which contain the location and type of information to be displayed on the screen. This approach provides great flexibility in tailoring the look and feel of the code to individual user needs. MIRIADbased applications, such as EWB, have utilities for viewing tabulated parametric study data, XY line plots, contour plots, and three-dimensional plots of contour data and system geometries. In addition, a Monte Carlo facility is provided to allow statistical assessments (including uncertainties) in models or data.

Experiences with DCE: the pro7 communication server based on OSF-DCE functionality.

PubMed

Schulte, M; Lordieck, W

1997-01-01

The pro7-communication server is a new approach to manage communication between different applications on different hardware platforms in a hospital environment. The most important features are the use of OSF/DCE for realising remote procedure calls between different platforms, the use of an SQL-92 compatible relational database and the design of a new software development tool (called protocol definition language compiler) for describing the interface of a new application, which is to integrate in a hospital environment.

MMpI: A WideRange of Available Compounds of Matrix Metalloproteinase Inhibitors

PubMed Central

Muvva, Charuvaka; Patra, Sanjukta; Venkatesan, Subramanian

2016-01-01

Matrix metalloproteinases (MMPs) are a family of zinc-dependent proteinases involved in the regulation of the extracellular signaling and structural matrix environment of cells and tissues. MMPs are considered as promising targets for the treatment of many diseases. Therefore, creation of database on the inhibitors of MMP would definitely accelerate the research activities in this area due to its implication in above-mentioned diseases and associated limitations in the first and second generation inhibitors. In this communication, we report the development of a new MMpI database which provides resourceful information for all researchers working in this field. It is a web-accessible, unique resource that contains detailed information on the inhibitors of MMP including small molecules, peptides and MMP Drug Leads. The database contains entries of ~3000 inhibitors including ~72 MMP Drug Leads and ~73 peptide based inhibitors. This database provides the detailed molecular and structural details which are necessary for the drug discovery and development. The MMpI database contains physical properties, 2D and 3D structures (mol2 and pdb format files) of inhibitors of MMP. Other data fields are hyperlinked to PubChem, ChEMBL, BindingDB, DrugBank, PDB, MEROPS and PubMed. The database has extensive searching facility with MMpI ID, IUPAC name, chemical structure and with the title of research article. The MMP inhibitors provided in MMpI database are optimized using Python-based Hierarchical Environment for Integrated Xtallography (Phenix) software. MMpI Database is unique and it is the only public database that contains and provides the complete information on the inhibitors of MMP. Database URL: http://clri.res.in/subramanian/databases/mmpi/index.php. PMID:27509041

PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.

PubMed

Demir, E; Babur, O; Dogrusoz, U; Gursoy, A; Nisanci, G; Cetin-Atalay, R; Ozturk, M

2002-07-01

Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named Patika (Pathway Analysis Tool for Integration and Knowledge Acquisition). Patika is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that Patika will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development. A prototype of Patika is available upon request from the authors.

SmallSat Database

NASA Technical Reports Server (NTRS)

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 required. When completed it will interface with the SCENIC environment to allow modeling of smallSats. The SmallSat Relational Database can also be integrated with the SCENIC Simulation modeling system that is currently in development. The SmallSat Relational Database simulation will be of great significance in assisting the NASA SCaN group to understand the impact the smallSats have made which have populated the lower orbit around our mother earth. What I have created and worked on this summer session 2015, is the basis for a tool that will be of value to the NASA SCaN SCENIC Simulation Environment for years to come.

EarthRef.org: Exploring aspects of a Cyber Infrastructure in Earth Science and Education

NASA Astrophysics Data System (ADS)

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

2004-12-01

EarthRef.org is the common host and (co-) developer of a range of earth science databases and IT resources providing a test bed for a Cyberinfrastructure in Earth Science and Education (CIESE). EarthRef.org data base efforts include in particular the Geochemical Earth Reference Model (GERM), the Magnetics Information Consortium (MagIC), the Educational Resources for Earth Science Education (ERESE) project, the Seamount Catalog, the Mid-Ocean Ridge Catalog, the Radio-Isotope Geochronology (RiG) initiative for CHRONOS, and the Microbial Observatory for Fe oxidizing microbes on Loihi Seamount (FeMO; the most recent development). These diverse databases are developed under a single database umbrella and webserver at the San Diego Supercomputing Center. All the data bases have similar structures, with consistent metadata concepts, a common database layout, and automated upload wizards. Shared resources include supporting databases like an address book, a reference/publication catalog, and a common digital archive making database development and maintenance cost-effective, while guaranteeing interoperability. The EarthRef.org CIESE provides a common umbrella for synthesis information as well as sample-based data, and it bridges the gap between science and science education in middle and high schools, validating the potential for a system wide data infrastructure in a CIESE. EarthRef.org experiences have shown that effective communication with the respective communities is a key part of a successful CIESE facilitating both utility and community buy-in. GERM has been particularly successful at developing a metadata scheme for geochemistry and in the development of a new electronic journal (G-cubed) that has made much progress in data publication and linkages between journals and community data bases. GERM also has worked, through editors and publishers, towards interfacing databases with the publication process, to accomplish a more scholarly and database friendly data publication environment, and to interface with the respective science communities. MagIC has held several workshops that have resulted in an integrated data archival environment using metadata that are interchangeable with the geochemical metadata. MagIC archives a wide array of paleo and rock magnetic directional, intensity and magnetic property data as well as integrating computational tools. ERESE brought together librarians, teachers, and scientists to create an educational environment that supports inquiry driven education and the use of science data. Experiences in EarthRef.org demonstrates the feasibility of an effective, community wide CIESE for data publication, archival and modeling, as well as the outreach to the educational community.

Beyond these walls: Can psychosocial clubhouses promote the social integration of adults with serious mental illness in the community?

PubMed

Gumber, Shinakee; Stein, Catherine H

2018-03-01

The study examined factors associated with community integration experiences of adults with serious mental illness who were members of psychosocial rehabilitation clubhouses in New York City. Ninety-two clubhouse members completed an online survey. The study examined relative contribution of adults' reports of individual factors (self-reported psychiatric symptoms, self-esteem), community supports (self-reported employment status and perceived family support), and the clubhouse environment (self-reported time spent in the clubhouse, clubhouse supportiveness, and practical orientation) in accounting for variation in members' reports of social integration within the clubhouse and within the larger community. Hierarchical linear regression results suggest a differential pattern of variables associated with participants' experience of social integration within the clubhouse versus outside the clubhouse with the larger non-mental-health consumers. Adults' reports of more time spent in the clubhouse and perceptions of clubhouse environment as having a more practical orientation were associated with adults' reports of greater social integration within the clubhouse. In contrast, greater self-esteem and being independently employed were associated with greater social integration outside the clubhouse. Perceived family support was associated with higher levels of social integration both within and outside the clubhouse setting. Conclusion and Implication for Practice: Greater social integration of clubhouse members both in and outside the clubhouse environment is essential in understanding community integration. Recommendations for the clubhouse model to improve community integration experiences of its members are discussed. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Development of an Integrated Hydrologic Modeling System for Rainfall-Runoff Simulation

NASA Astrophysics Data System (ADS)

Lu, B.; Piasecki, M.

2008-12-01

This paper aims to present the development of an integrated hydrological model which involves functionalities of digital watershed processing, online data retrieval, hydrologic simulation and post-event analysis. The proposed system is intended to work as a back end to the CUAHSI HIS cyberinfrastructure developments. As a first step into developing this system, a physics-based distributed hydrologic model PIHM (Penn State Integrated Hydrologic Model) is wrapped into OpenMI(Open Modeling Interface and Environment ) environment so as to seamlessly interact with OpenMI compliant meteorological models. The graphical user interface is being developed from the openGIS application called MapWindows which permits functionality expansion through the addition of plug-ins. . Modules required to set up through the GUI workboard include those for retrieving meteorological data from existing database or meteorological prediction models, obtaining geospatial data from the output of digital watershed processing, and importing initial condition and boundary condition. They are connected to the OpenMI compliant PIHM to simulate rainfall-runoff processes and includes a module for automatically displaying output after the simulation. Online databases are accessed through the WaterOneFlow web services, and the retrieved data are either stored in an observation database(OD) following the schema of Observation Data Model(ODM) in case for time series support, or a grid based storage facility which may be a format like netCDF or a grid-based-data database schema . Specific development steps include the creation of a bridge to overcome interoperability issue between PIHM and the ODM, as well as the embedding of TauDEM (Terrain Analysis Using Digital Elevation Models) into the model. This module is responsible for developing watershed and stream network using digital elevation models. Visualizing and editing geospatial data is achieved by the usage of MapWinGIS, an ActiveX control developed by MapWindow team. After applying to the practical watershed, the performance of the model can be tested by the post-event analysis module.

Integrating Technologies, Methodologies, and Databases into a Comprehensive Terminology Management Environment to Support Interoperability among Clinical Information Systems

ERIC Educational Resources Information Center

Shakib, Shaun Cameron

2013-01-01

Controlled clinical terminologies are essential to realizing the benefits of electronic health record systems. However, implementing consistent and sustainable use of terminology has proven to be both intellectually and practically challenging. First, this project derives a conceptual understanding of the scope and intricacies of the challenge by…

Facilitators and barriers to adjustment of international nurses: an integrative review.

PubMed

Kawi, J; Xu, Y

2009-06-01

There is a scarcity of research focusing on issues encountered by international nurses (INs) in their adjustment to foreign health-care environments. Increasingly, INs are relied upon to address staffing shortages in many Western countries. As such, it is vital to identify what facilitates and what the barriers are to the successful adjustment in order to assist their integration into new workplace environments. This integrative review identifies facilitators and barriers encountered by INs as they adjust to foreign health-care environments. Based on Cooper's Five Stages of Integrative Research Review, a systematic search of eight electronic databases was conducted, combined with hand and ancestral searches. Two authors independently reviewed each qualified study for relevance and significance. Subsequently, facilitators and barriers were identified and categorized into themes and subthemes. Twenty-nine studies conducted in Australia, Canada, Iceland, UK and the USA were included in this review. Findings indicated that positive work ethic, persistence, psychosocial and logistical support, learning to be assertive and continuous learning facilitated the adjustment of INs to their new workplace environments. In contrast, language and communication difficulties, differences in culture-based lifeways, lack of support, inadequate orientation, differences in nursing practice and inequality were barriers. The review findings provide the basis for the development and testing of an evidence-informed programme to facilitate the successful adjustment of INs to their new work environments.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

PubMed

Shannon, Paul; Markiel, Andrew; Ozier, Owen; Baliga, Nitin S; Wang, Jonathan T; Ramage, Daniel; Amin, Nada; Schwikowski, Benno; Ideker, Trey

2003-11-01

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

Coastal resource and sensitivity mapping of Vietnam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Odin, L.M.

1997-08-01

This paper describes a project to establish a relationship between environmental sensitivity (primarily to oil pollution) and response planning and prevention priorities for Vietnamese coastal regions. An inventory of coastal environmental sensitivity and the creation of index mapping was performed. Satellite and geographical information system data were integrated and used for database creation. The database was used to create a coastal resource map, coastal sensitivity map, and a field inventory base map. The final coastal environment sensitivity classification showed that almost 40 percent of the 7448 km of mapped shoreline has a high to medium high sensitivity to oil pollution.

The multi-modal Australian ScienceS Imaging and Visualization Environment (MASSIVE) high performance computing infrastructure: applications in neuroscience and neuroinformatics research

PubMed Central

Goscinski, Wojtek J.; McIntosh, Paul; Felzmann, Ulrich; Maksimenko, Anton; Hall, Christopher J.; Gureyev, Timur; Thompson, Darren; Janke, Andrew; Galloway, Graham; Killeen, Neil E. B.; Raniga, Parnesh; Kaluza, Owen; Ng, Amanda; Poudel, Govinda; Barnes, David G.; Nguyen, Toan; Bonnington, Paul; Egan, Gary F.

2014-01-01

The Multi-modal Australian ScienceS Imaging and Visualization Environment (MASSIVE) is a national imaging and visualization facility established by Monash University, the Australian Synchrotron, the Commonwealth Scientific Industrial Research Organization (CSIRO), and the Victorian Partnership for Advanced Computing (VPAC), with funding from the National Computational Infrastructure and the Victorian Government. The MASSIVE facility provides hardware, software, and expertise to drive research in the biomedical sciences, particularly advanced brain imaging research using synchrotron x-ray and infrared imaging, functional and structural magnetic resonance imaging (MRI), x-ray computer tomography (CT), electron microscopy and optical microscopy. The development of MASSIVE has been based on best practice in system integration methodologies, frameworks, and architectures. The facility has: (i) integrated multiple different neuroimaging analysis software components, (ii) enabled cross-platform and cross-modality integration of neuroinformatics tools, and (iii) brought together neuroimaging databases and analysis workflows. MASSIVE is now operational as a nationally distributed and integrated facility for neuroinfomatics and brain imaging research. PMID:24734019

Collaboration systems for classroom instruction

NASA Astrophysics Data System (ADS)

Chen, C. Y. Roger; Meliksetian, Dikran S.; Chang, Martin C.

1996-01-01

In this paper we discuss how classroom instruction can benefit from state-of-the-art technologies in networks, worldwide web access through Internet, multimedia, databases, and computing. Functional requirements for establishing such a high-tech classroom are identified, followed by descriptions of our current experimental implementations. The focus of the paper is on the capabilities of distributed collaboration, which supports both synchronous multimedia information sharing as well as a shared work environment for distributed teamwork and group decision making. Our ultimate goal is to achieve the concept of 'living world in a classroom' such that live and dynamic up-to-date information and material from all over the world can be integrated into classroom instruction on a real-time basis. We describe how we incorporate application developments in a geography study tool, worldwide web information retrievals, databases, and programming environments into the collaborative system.

Multifunctional millimeter-wave radar system for helicopter safety

NASA Astrophysics Data System (ADS)

Goshi, Darren S.; Case, Timothy J.; McKitterick, John B.; Bui, Long Q.

2012-06-01

A multi-featured sensor solution has been developed that enhances the operational safety and functionality of small airborne platforms, representing an invaluable stride toward enabling higher-risk, tactical missions. This paper demonstrates results from a recently developed multi-functional sensor system that integrates a high performance millimeter-wave radar front end, an evidence grid-based integration processing scheme, and the incorporation into a 3D Synthetic Vision System (SVS) display. The front end architecture consists of a w-band real-beam scanning radar that generates a high resolution real-time radar map and operates with an adaptable antenna architecture currently configured with an interferometric capability for target height estimation. The raw sensor data is further processed within an evidence grid-based integration functionality that results in high-resolution maps in the region surrounding the platform. Lastly, the accumulated radar results are displayed in a fully rendered 3D SVS environment integrated with local database information to provide the best representation of the surrounding environment. The integrated system concept will be discussed and initial results from an experimental flight test of this developmental system will be presented. Specifically, the forward-looking operation of the system demonstrates the system's ability to produce high precision terrain mapping with obstacle detection and avoidance capability, showcasing the system's versatility in a true operational environment.

Computer Program Development Specification for Ada Integrated Environment: KAPSE (Kernel Ada Programming Support Environment)/Database, Type B5, B5-AIE(1).KAPSE(1).

DTIC Science & Technology

1982-11-12

File 1/0 Prgram Invocation Other Access M and Control Services KAPSE/Host Interface most Operating System Peripherals/ 01 su ?eetworks 6282318-2 Figure 3...3.2.4.3.8.5 Transitory Windows The TRANSITORY flag is used to prevent permanent dependence on temporary windows created simply for focusing on a part of the...KAPSE/Tool interfaces in terms of these low-level host-independent interfaces. In addition, the KAPSE/Host interface packages prevent the application

Evolution of a Patient Information Management System in a Local Area Network Environment at Loyola University of Chicago Medical Center

PubMed Central

Price, Ronald N; Chandrasekhar, Arcot J; Tamirisa, Balaji

1990-01-01

The Department of Medicine at Loyola University Medical Center (LUMC) of Chicago has implemented a local area network (LAN) based Patient Information Management System (PIMS) as part of its integrated departmental database management system. PIMS consists of related database applications encompassing demographic information, current medications, problem lists, clinical data, prior events, and on-line procedure results. Integration into the existing departmental database system permits PIMS to capture and manipulate data in other departmental applications. Standardization of clinical data is accomplished through three data tables that verify diagnosis codes, procedures codes and a standardized set of clinical data elements. The modularity of the system, coupled with standardized data formats, allowed the development of a Patient Information Protocol System (PIPS). PIPS, a userdefinable protocol processor, provides physicians with individualized data entry or review screens customized for their specific research protocols or practice habits. Physician feedback indicates that the PIMS/PIPS combination enhances their ability to collect and review specific patient information by filtering large amount of clinical data.

Oceanography Information System of Spanish Institute of Oceanography (IEO)

NASA Astrophysics Data System (ADS)

Tello, Olvido; Gómez, María; González, Sonsoles

2016-04-01

Since 1914, the Spanish Institute of Oceanography (IEO) performs multidisciplinary studies of the marine environment. In same case are systematic studies and in others are specific studies for special requirements (El Hierro submarine volcanic episode, spill Prestige, others.). Different methodologies and data acquisition techniques are used depending on studies aims. The acquired data are stored and presented in different formats. The information is organized into different databases according to the subject and the variables represented (geology, fisheries, aquaculture, pollution, habitats, etc.). Related to physical and chemical oceanography data, in 1964 was created the DATA CENTER of IEO (CEDO), in order to organize the data about physical and chemical variables, to standardize this information and to serve the international data network SeaDataNet. www.seadatanet.org. This database integrates data about temperature, salinity, nutrients, and tidal data. CEDO allows consult and download the data. http://indamar.ieo.es On the other hand, related to data about marine species in 1999 was developed SIRENO DATABASE. All data about species collected in oceanographic surveys carried out by researches of IEO, and data from observers on fishing vessels are incorporated in SIRENO database. In this database is stored catch data, biomass, abundance, etc. This system is based on architecture ORACLE. Due to the large amount of information collected over the 100 years of IEO history, there is a clear need to organize, standardize, integrate and relate the different databases and information, and to provide interoperability and access to the information. Consequently, in 2000 it emerged the first initiative to organize the IEO spatial information in an Oceanography Information System, based on a Geographical Information System (GIS). The GIS was consolidated as IEO institutional GIS and was created the Spatial Data Infrastructure of IEO (IDEO) following trend of INSPIRE. All data included in the GIS have their corresponding metadata about ISO19115 and INSPIRE. IDEO is based on Web services, Quality of Services, Open standards, ISO (OGC) and INSPIRE standards, and both provide access to the geographical marine information of IEO. The GIS allows the information to be organized, visualized, consulted and analyzed. The data from different IEO databases are integrated into a GIS corporate Geodatabase (Esri format). This tool is essential in the decision making of aspects like: - Protection of marine environment - Sustainable management of resources - Natural Hazards. - Marine spatial planning. Examples of the use of GIS as a spatial analysis tool are: - Mud volcanoes explored in LIFE-INDEMARES project. - Cartographic series about Spanish continental shelf, developed from data integrated in IEO marine GIS, acquired from oceanographic surveys in ESPACE project. - Cartography developed from the information gathered in Initial Assessment of Marine Strategy Framework Directive. - Studies of natural hazards related to submarine canyons in southeast region marine Spanish. Currently the IEO is participating in many European initiatives, especially in several lots of EMODNET. The IEO besides is working in consonance with INSPIRE, Growth Blue, Horizon 2020, etc., to contribute to, the knowledge of marine environment, its protection and its spatial planning are extremely relevant issues. In order to facilitate the access to the Spatial Data Infrastructure of IEO, the IEO Geoportal was developed in 2012. It mainly involves a metadata catalog, access to the data viewers and Web Services of IDEO. http://www.geo-ideo.ieo.es/geoportalideo/catalog/main/home.page

Performing private database queries in a real-world environment using a quantum protocol.

PubMed

Chan, Philip; Lucio-Martinez, Itzel; Mo, Xiaofan; Simon, Christoph; Tittel, Wolfgang

2014-06-10

In the well-studied cryptographic primitive 1-out-of-N oblivious transfer, a user retrieves a single element from a database of size N without the database learning which element was retrieved. While it has previously been shown that a secure implementation of 1-out-of-N oblivious transfer is impossible against arbitrarily powerful adversaries, recent research has revealed an interesting class of private query protocols based on quantum mechanics in a cheat sensitive model. Specifically, a practical protocol does not need to guarantee that the database provider cannot learn what element was retrieved if doing so carries the risk of detection. The latter is sufficient motivation to keep a database provider honest. However, none of the previously proposed protocols could cope with noisy channels. Here we present a fault-tolerant private query protocol, in which the novel error correction procedure is integral to the security of the protocol. Furthermore, we present a proof-of-concept demonstration of the protocol over a deployed fibre.

Performing private database queries in a real-world environment using a quantum protocol

PubMed Central

Chan, Philip; Lucio-Martinez, Itzel; Mo, Xiaofan; Simon, Christoph; Tittel, Wolfgang

2014-01-01

In the well-studied cryptographic primitive 1-out-of-N oblivious transfer, a user retrieves a single element from a database of size N without the database learning which element was retrieved. While it has previously been shown that a secure implementation of 1-out-of-N oblivious transfer is impossible against arbitrarily powerful adversaries, recent research has revealed an interesting class of private query protocols based on quantum mechanics in a cheat sensitive model. Specifically, a practical protocol does not need to guarantee that the database provider cannot learn what element was retrieved if doing so carries the risk of detection. The latter is sufficient motivation to keep a database provider honest. However, none of the previously proposed protocols could cope with noisy channels. Here we present a fault-tolerant private query protocol, in which the novel error correction procedure is integral to the security of the protocol. Furthermore, we present a proof-of-concept demonstration of the protocol over a deployed fibre. PMID:24913129

LIVIVO - the Vertical Search Engine for Life Sciences.

PubMed

Müller, Bernd; Poley, Christoph; Pössel, Jana; Hagelstein, Alexandra; Gübitz, Thomas

2017-01-01

The explosive growth of literature and data in the life sciences challenges researchers to keep track of current advancements in their disciplines. Novel approaches in the life science like the One Health paradigm require integrated methodologies in order to link and connect heterogeneous information from databases and literature resources. Current publications in the life sciences are increasingly characterized by the employment of trans-disciplinary methodologies comprising molecular and cell biology, genetics, genomic, epigenomic, transcriptional and proteomic high throughput technologies with data from humans, plants, and animals. The literature search engine LIVIVO empowers retrieval functionality by incorporating various literature resources from medicine, health, environment, agriculture and nutrition. LIVIVO is developed in-house by ZB MED - Information Centre for Life Sciences. It provides a user-friendly and usability-tested search interface with a corpus of 55 Million citations derived from 50 databases. Standardized application programming interfaces are available for data export and high throughput retrieval. The search functions allow for semantic retrieval with filtering options based on life science entities. The service oriented architecture of LIVIVO uses four different implementation layers to deliver search services. A Knowledge Environment is developed by ZB MED to deal with the heterogeneity of data as an integrative approach to model, store, and link semantic concepts within literature resources and databases. Future work will focus on the exploitation of life science ontologies and on the employment of NLP technologies in order to improve query expansion, filters in faceted search, and concept based relevancy rankings in LIVIVO.

A Spatial Analysis and Modeling System (SAMS) for environment management

NASA Technical Reports Server (NTRS)

Stetina, Fran; Hill, John; Chan, Paul; Jaske, Robert; Rochon, Gilbert

1993-01-01

This is a proposal to develop a uniform global environmental data gathering and distribution system to support the calibration and validation of remotely sensed data. SAMS is based on an enhanced version of FEMA's Integrated Emergency Management Information Systems and the Department of Defense's Air land Battlefield Environment Software Systems. This system consists of state-of-the-art graphics and visualization techniques, simulation models, database management and expert systems for conducting environmental and disaster preparedness studies. This software package will be integrated into various Landsat and UNEP-GRID stations which are planned to become direct readout stations during the EOS (Earth Observing System) timeframe. This system would be implemented as a pilot program to support the Tropical Rainfall Measuring Mission (TRMM). This will be a joint NASA-FEMA-University-Industry project.

A Spatial Analysis and Modeling System (SAMS) for environment management

NASA Technical Reports Server (NTRS)

Vermillion, Charles H.; Stetina, Fran; Hill, John; Chan, Paul; Jaske, Robert; Rochon, Gilbert

1992-01-01

This is a proposal to develop a uniform global environmental data gathering and distribution system to support the calibration and validation of remotely sensed data. SAMS is based on an enhanced version of FE MA's Integrated Emergency Management Information Systems and the Department of Defense's Air Land Battlefield Environment Software Systems. This system consists of state-of-the-art graphics and visualization techniques, simulation models, database management and expert systems for conducting environmental and disaster preparedness studies. This software package will be integrated into various Landsat and UNEP-GRID stations which are planned to become direct readout stations during the EOS timeframe. This system would be implemented as a pilot program to support the Tropical Rainfall Measuring Mission (TRMM). This will be a joint NASA-FEMA-University-Industry project.

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

PubMed Central

Gadelha, Luiz; Ribeiro-Alves, Marcelo; Porto, Fábio

2017-01-01

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 analyzed. The results are integrated into GeNNet-DB, a database about genes, clusters, experiments and their properties and relationships. The resulting graph database is explored with queries that demonstrate the expressiveness of this data model for reasoning about gene interaction networks. GeNNet is the first platform to integrate the analytical process of transcriptome data with graph databases. It provides a comprehensive set of tools that would otherwise be challenging for non-expert users to install and use. Developers can add new functionality to components of GeNNet. The derived data allows for testing previous hypotheses about an experiment and exploring new ones through the interactive graph database environment. It enables the analysis of different data on humans, rhesus, mice and rat coming from Affymetrix platforms. GeNNet is available as an open source platform at https://github.com/raquele/GeNNet and can be retrieved as a software container with the command docker pull quelopes/gennet. PMID:28695067

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

PubMed

Costa, Raquel L; Gadelha, Luiz; Ribeiro-Alves, Marcelo; Porto, Fábio

2017-01-01

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 analyzed. The results are integrated into GeNNet-DB, a database about genes, clusters, experiments and their properties and relationships. The resulting graph database is explored with queries that demonstrate the expressiveness of this data model for reasoning about gene interaction networks. GeNNet is the first platform to integrate the analytical process of transcriptome data with graph databases. It provides a comprehensive set of tools that would otherwise be challenging for non-expert users to install and use. Developers can add new functionality to components of GeNNet. The derived data allows for testing previous hypotheses about an experiment and exploring new ones through the interactive graph database environment. It enables the analysis of different data on humans, rhesus, mice and rat coming from Affymetrix platforms. GeNNet is available as an open source platform at https://github.com/raquele/GeNNet and can be retrieved as a software container with the command docker pull quelopes/gennet.

A probabilistic approach to information retrieval in heterogeneous databases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chatterjee, A.; Segev, A.

During the post decade, organizations have increased their scope and operations beyond their traditional geographic boundaries. At the same time, they have adopted heterogeneous and incompatible information systems independent of each other without a careful consideration that one day they may need to be integrated. As a result of this diversity, many important business applications today require access to data stored in multiple autonomous databases. This paper examines a problem of inter-database information retrieval in a heterogeneous environment, where conventional techniques are no longer efficient. To solve the problem, broader definitions for join, union, intersection and selection operators are proposed.more » Also, a probabilistic method to specify the selectivity of these operators is discussed. An algorithm to compute these probabilities is provided in pseudocode.« less

Human Connectome Project Informatics: quality control, database services, and data visualization

PubMed Central

Marcus, Daniel S.; Harms, Michael P.; Snyder, Abraham Z.; Jenkinson, Mark; Wilson, J Anthony; Glasser, Matthew F.; Barch, Deanna M.; Archie, Kevin A.; Burgess, Gregory C.; Ramaratnam, Mohana; Hodge, Michael; Horton, William; Herrick, Rick; Olsen, Timothy; McKay, Michael; House, Matthew; Hileman, Michael; Reid, Erin; Harwell, John; Coalson, Timothy; Schindler, Jon; Elam, Jennifer S.; Curtiss, Sandra W.; Van Essen, David C.

2013-01-01

The Human Connectome Project (HCP) has developed protocols, standard operating and quality control procedures, and a suite of informatics tools to enable high throughput data collection, data sharing, automated data processing and analysis, and data mining and visualization. Quality control procedures include methods to maintain data collection consistency over time, to measure head motion, and to establish quantitative modality-specific overall quality assessments. Database services developed as customizations of the XNAT imaging informatics platform support both internal daily operations and open access data sharing. The Connectome Workbench visualization environment enables user interaction with HCP data and is increasingly integrated with the HCP's database services. Here we describe the current state of these procedures and tools and their application in the ongoing HCP study. PMID:23707591

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes.

PubMed

Shao, Wei; Shan, Jigui; Kearney, Mary F; Wu, Xiaolin; Maldarelli, Frank; Mellors, John W; Luke, Brian; Coffin, John M; Hughes, Stephen H

2016-07-04

The NCI Retrovirus Integration Database is a MySql-based relational database created for storing and retrieving comprehensive information about retroviral integration sites, primarily, but not exclusively, HIV-1. The database is accessible to the public for submission or extraction of data originating from experiments aimed at collecting information related to retroviral integration sites including: the site of integration into the host genome, the virus family and subtype, the origin of the sample, gene exons/introns associated with integration, and proviral orientation. Information about the references from which the data were collected is also stored in the database. Tools are built into the website that can be used to map the integration sites to UCSC genome browser, to plot the integration site patterns on a chromosome, and to display provirus LTRs in their inserted genome sequence. The website is robust, user friendly, and allows users to query the database and analyze the data dynamically. https://rid.ncifcrf.gov ; or http://home.ncifcrf.gov/hivdrp/resources.htm .

Drug residues in urban water: A database for ecotoxicological risk management.

PubMed

Destrieux, Doriane; Laurent, François; Budzinski, Hélène; Pedelucq, Julie; Vervier, Philippe; Gerino, Magali

2017-12-31

Human-use drug residues (DR) are only partially eliminated by waste water treatment plants (WWTPs), so that residual amounts can reach natural waters and cause environmental hazards. In order to properly manage these hazards in the aquatic environment, a database is made available that integrates the concentration ranges for DR, which cause adverse effects for aquatic organisms, and the temporal variations of the ecotoxicological risks. To implement this database for the ecotoxicological risk assessment (ERA database), the required information for each DR is the predicted no effect concentrations (PNECs), along with the predicted environmental concentrations (PECs). The risk assessment is based on the ratio between the PNECs and the PECs. Adverse effect data or PNECs have been found in the publicly available literature for 45 substances. These ecotoxicity test data have been extracted from 125 different sources. This ERA database contains 1157 adverse effect data and 287 PNECs. The efficiency of this ERA database was tested with a data set coming from a simultaneous survey of WWTPs and the natural environment. In this data set, 26 DR were searched for in two WWTPs and in the river. On five sampling dates, concentrations measured in the river for 10 DR could pose environmental problems of which 7 were measured only downstream of WWTP outlets. From scientific literature and measurements, data implementation with unit homogenisation in a single database facilitates the actual ecotoxicological risk assessment, and may be useful for further risk coming from data arising from the future field survey. Moreover, the accumulation of a large ecotoxicity data set in a single database should not only improve knowledge of higher risk molecules but also supply an objective tool to help the rapid and efficient evaluation of the risk. Copyright © 2017 Elsevier B.V. All rights reserved.

Active in-database processing to support ambient assisted living systems.

PubMed

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.

Active In-Database Processing to Support Ambient Assisted Living Systems

PubMed Central

de Morais, Wagner O.; Lundström, Jens; Wickström, Nicholas

2014-01-01

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. PMID:25120164

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.

PubMed

Ortseifen, Vera; Stolze, Yvonne; Maus, Irena; Sczyrba, Alexander; Bremges, Andreas; Albaum, Stefan P; Jaenicke, Sebastian; Fracowiak, Jochen; Pühler, Alfred; Schlüter, Andreas

2016-08-10

To study the metaproteome of a biogas-producing microbial community, fermentation samples were taken from an agricultural biogas plant for microbial cell and protein extraction and corresponding metagenome analyses. Based on metagenome sequence data, taxonomic community profiling was performed to elucidate the composition of bacterial and archaeal sub-communities. The community's cytosolic metaproteome was represented in a 2D-PAGE approach. Metaproteome databases for protein identification were compiled based on the assembled metagenome sequence dataset for the biogas plant analyzed and non-corresponding biogas metagenomes. Protein identification results revealed that the corresponding biogas protein database facilitated the highest identification rate followed by other biogas-specific databases, whereas common public databases yielded insufficient identification rates. Proteins of the biogas microbiome identified as highly abundant were assigned to the pathways involved in methanogenesis, transport and carbon metabolism. Moreover, the integrated metagenome/-proteome approach enabled the examination of genetic-context information for genes encoding identified proteins by studying neighboring genes on the corresponding contig. Exemplarily, this approach led to the identification of a Methanoculleus sp. contig encoding 16 methanogenesis-related gene products, three of which were also detected as abundant proteins within the community's metaproteome. Thus, metagenome contigs provide additional information on the genetic environment of identified abundant proteins. Copyright © 2016 Elsevier B.V. All rights reserved.

BoreholeAR: A mobile tablet application for effective borehole database visualization using an augmented reality technology

NASA Astrophysics Data System (ADS)

Lee, Sangho; Suh, Jangwon; Park, Hyeong-Dong

2015-03-01

Boring logs are widely used in geological field studies since the data describes various attributes of underground and surface environments. However, it is difficult to manage multiple boring logs in the field as the conventional management and visualization methods are not suitable for integrating and combining large data sets. We developed an iPad application to enable its user to search the boring log rapidly and visualize them using the augmented reality (AR) technique. For the development of the application, a standard borehole database appropriate for a mobile-based borehole database management system was designed. The application consists of three modules: an AR module, a map module, and a database module. The AR module superimposes borehole data on camera imagery as viewed by the user and provides intuitive visualization of borehole locations. The map module shows the locations of corresponding borehole data on a 2D map with additional map layers. The database module provides data management functions for large borehole databases for other modules. Field survey was also carried out using more than 100,000 borehole data.

Active browsing using similarity pyramids

NASA Astrophysics Data System (ADS)

Chen, Jau-Yuen; Bouman, Charles A.; Dalton, John C.

1998-12-01

In this paper, we describe a new approach to managing large image databases, which we call active browsing. Active browsing integrates relevance feedback into the browsing environment, so that users can modify the database's organization to suit the desired task. Our method is based on a similarity pyramid data structure, which hierarchically organizes the database, so that it can be efficiently browsed. At coarse levels, the similarity pyramid allows users to view the database as large clusters of similar images. Alternatively, users can 'zoom into' finer levels to view individual images. We discuss relevance feedback for the browsing process, and argue that it is fundamentally different from relevance feedback for more traditional search-by-query tasks. We propose two fundamental operations for active browsing: pruning and reorganization. Both of these operations depend on a user-defined relevance set, which represents the image or set of images desired by the user. We present statistical methods for accurately pruning the database, and we propose a new 'worm hole' distance metric for reorganizing the database, so that members of the relevance set are grouped together.

Ontology based heterogeneous materials database integration and semantic query

NASA Astrophysics Data System (ADS)

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.

Generalized Database Management System Support for Numeric Database Environments.

ERIC Educational Resources Information Center

Dominick, Wayne D.; Weathers, Peggy G.

1982-01-01

This overview of potential for utilizing database management systems (DBMS) within numeric database environments highlights: (1) major features, functions, and characteristics of DBMS; (2) applicability to numeric database environment needs and user needs; (3) current applications of DBMS technology; and (4) research-oriented and…

Functional integration of automated system databases by means of artificial intelligence

NASA Astrophysics Data System (ADS)

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.

The Astrobiology Habitable Environments Database (AHED)

NASA Astrophysics Data System (ADS)

Lafuente, B.; Stone, N.; Downs, R. T.; Blake, D. F.; Bristow, T.; Fonda, M.; Pires, A.

2015-12-01

The Astrobiology Habitable Environments Database (AHED) is a central, high quality, long-term searchable repository for archiving and collaborative sharing of astrobiologically relevant data, including, morphological, textural and contextural images, chemical, biochemical, isotopic, sequencing, and mineralogical information. The aim of AHED is to foster long-term innovative research by supporting integration and analysis of diverse datasets in order to: 1) help understand and interpret planetary geology; 2) identify and characterize habitable environments and pre-biotic/biotic processes; 3) interpret returned data from present and past missions; 4) provide a citable database of NASA-funded published and unpublished data (after an agreed-upon embargo period). AHED uses the online open-source software "The Open Data Repository's Data Publisher" (ODR - http://www.opendatarepository.org) [1], which provides a user-friendly interface that research teams or individual scientists can use to design, populate and manage their own database according to the characteristics of their data and the need to share data with collaborators or the broader scientific community. This platform can be also used as a laboratory notebook. The database will have the capability to import and export in a variety of standard formats. Advanced graphics will be implemented including 3D graphing, multi-axis graphs, error bars, and similar scientific data functions together with advanced online tools for data analysis (e. g. the statistical package, R). A permissions system will be put in place so that as data are being actively collected and interpreted, they will remain proprietary. A citation system will allow research data to be used and appropriately referenced by other researchers after the data are made public. This project is supported by the Science-Enabling Research Activity (SERA) and NASA NNX11AP82A, Mars Science Laboratory Investigations. [1] Nate et al. (2015) AGU, submitted.

Techniques to Access Databases and Integrate Data for Hydrologic Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whelan, Gene; Tenney, Nathan D.; Pelton, Mitchell A.

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.more » 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 retrieve the required data, and their ability to integrate the data into environmental models using the FRAMES environment.« less

EPA Facility Registry Service (FRS): TRI

EPA Pesticide Factsheets

This web feature service contains location and facility identification information from EPA's Facility Registry Service (FRS) for the subset of facilities that link to the Toxic Release Inventory (TRI) System. TRI is a publicly available EPA database reported annually by certain covered industry groups, as well as federal facilities. It contains information about more than 650 toxic chemicals that are being used, manufactured, treated, transported, or released into the environment, and includes information about waste management and pollution prevention activities. FRS identifies and geospatially locates facilities, sites or places subject to environmental regulations or of environmental interest. Using vigorous verification and data management procedures, FRS integrates facility data from EPA's national program systems, other federal agencies, and State and tribal master facility records and provides EPA with a centrally managed, single source of comprehensive and authoritative information on facilities. This data set contains the subset of FRS integrated facilities that link to TRI facilities once the TRI data has been integrated into the FRS database. Additional information on FRS is available at the EPA website https://www.epa.gov/enviro/facility-registry-service-frs.

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

NASA Astrophysics Data System (ADS)

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.

Freva - Freie Univ Evaluation System Framework for Scientific Infrastructures in Earth System Modeling

NASA Astrophysics Data System (ADS)

Kadow, Christopher; Illing, Sebastian; Kunst, Oliver; Schartner, Thomas; Kirchner, Ingo; Rust, Henning W.; Cubasch, Ulrich; Ulbrich, Uwe

2016-04-01

The Freie Univ Evaluation System Framework (Freva - freva.met.fu-berlin.de) is a software infrastructure for standardized data and tool solutions in Earth system science. Freva runs on high performance computers to handle customizable evaluation systems of research projects, institutes or universities. It combines different software technologies into one common hybrid infrastructure, including all features present in the shell and web environment. The database interface satisfies the international standards provided by the Earth System Grid Federation (ESGF). Freva indexes different data projects into one common search environment by storing the meta data information of the self-describing model, reanalysis and observational data sets in a database. This implemented meta data system with its advanced but easy-to-handle search tool supports users, developers and their plugins to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitation of the provision and usage of tools and climate data automatically increases the number of scientists working with the data sets and identifying discrepancies. The integrated web-shell (shellinabox) adds a degree of freedom in the choice of the working environment and can be used as a gate to the research projects HPC. Plugins are able to integrate their e.g. post-processed results into the database of the user. This allows e.g. post-processing plugins to feed statistical analysis plugins, which fosters an active exchange between plugin developers of a research project. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a database. Configurations and results of the tools can be shared among scientists via shell or web system. Therefore, plugged-in tools benefit from transparency and reproducibility. Furthermore, if configurations match while starting an evaluation plugin, the system suggests to use results already produced by other users - saving CPU/h, I/O, disk space and time. The efficient interaction between different technologies improves the Earth system modeling science framed by Freva.

Freva - Freie Univ Evaluation System Framework for Scientific HPC Infrastructures in Earth System Modeling

NASA Astrophysics Data System (ADS)

Kadow, C.; Illing, S.; Schartner, T.; Grieger, J.; Kirchner, I.; Rust, H.; Cubasch, U.; Ulbrich, U.

2017-12-01

The Freie Univ Evaluation System Framework (Freva - freva.met.fu-berlin.de) is a software infrastructure for standardized data and tool solutions in Earth system science (e.g. www-miklip.dkrz.de, cmip-eval.dkrz.de). Freva runs on high performance computers to handle customizable evaluation systems of research projects, institutes or universities. It combines different software technologies into one common hybrid infrastructure, including all features present in the shell and web environment. The database interface satisfies the international standards provided by the Earth System Grid Federation (ESGF). Freva indexes different data projects into one common search environment by storing the meta data information of the self-describing model, reanalysis and observational data sets in a database. This implemented meta data system with its advanced but easy-to-handle search tool supports users, developers and their plugins to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. The integrated web-shell (shellinabox) adds a degree of freedom in the choice of the working environment and can be used as a gate to the research projects HPC. Plugins are able to integrate their e.g. post-processed results into the database of the user. This allows e.g. post-processing plugins to feed statistical analysis plugins, which fosters an active exchange between plugin developers of a research project. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a database. Configurations and results of the tools can be shared among scientists via shell or web system. Furthermore, if configurations match while starting an evaluation plugin, the system suggests to use results already produced by other users - saving CPU/h, I/O, disk space and time. The efficient interaction between different technologies improves the Earth system modeling science framed by Freva.

A Community Data Model for Hydrologic Observations

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Horsburgh, J. S.; Zaslavsky, I.; Maidment, D. R.; Valentine, D.; Jennings, B.

2006-12-01

The CUAHSI Hydrologic Information System project is developing information technology infrastructure to support hydrologic science. Hydrologic information science involves the description of hydrologic environments in a consistent way, using data models for information integration. This includes a hydrologic observations data model for the storage and retrieval of hydrologic observations in a relational database designed to facilitate data retrieval for integrated analysis of information collected by multiple investigators. It is intended to provide a standard format to facilitate the effective sharing of information between investigators and to facilitate analysis of information within a single study area or hydrologic observatory, or across hydrologic observatories and regions. The observations data model is designed to store hydrologic observations and sufficient ancillary information (metadata) about the observations to allow them to be unambiguously interpreted and used and provide traceable heritage from raw measurements to usable information. The design is based on the premise that a relational database at the single observation level is most effective for providing querying capability and cross dimension data retrieval and analysis. This premise is being tested through the implementation of a prototype hydrologic observations database, and the development of web services for the retrieval of data from and ingestion of data into the database. These web services hosted by the San Diego Supercomputer center make data in the database accessible both through a Hydrologic Data Access System portal and directly from applications software such as Excel, Matlab and ArcGIS that have Standard Object Access Protocol (SOAP) capability. This paper will (1) describe the data model; (2) demonstrate the capability for representing diverse data in the same database; (3) demonstrate the use of the database from applications software for the performance of hydrologic analysis across different observation types.

Towards the Interoperability of Web, Database, and Mass Storage Technologies for Petabyte Archives

NASA Technical Reports Server (NTRS)

Moore, Reagan; Marciano, Richard; Wan, Michael; Sherwin, Tom; Frost, Richard

1996-01-01

At the San Diego Supercomputer Center, a massive data analysis system (MDAS) is being developed to support data-intensive applications that manipulate terabyte sized data sets. The objective is to support scientific application access to data whether it is located at a Web site, stored as an object in a database, and/or storage in an archival storage system. We are developing a suite of demonstration programs which illustrate how Web, database (DBMS), and archival storage (mass storage) technologies can be integrated. An application presentation interface is being designed that integrates data access to all of these sources. We have developed a data movement interface between the Illustra object-relational database and the NSL UniTree archival storage system running in a production mode at the San Diego Supercomputer Center. With this interface, an Illustra client can transparently access data on UniTree under the control of the Illustr DBMS server. The current implementation is based on the creation of a new DBMS storage manager class, and a set of library functions that allow the manipulation and migration of data stored as Illustra 'large objects'. We have extended this interface to allow a Web client application to control data movement between its local disk, the Web server, the DBMS Illustra server, and the UniTree mass storage environment. This paper describes some of the current approaches successfully integrating these technologies. This framework is measured against a representative sample of environmental data extracted from the San Diego Ba Environmental Data Repository. Practical lessons are drawn and critical research areas are highlighted.

Model-Based Systems

NASA Technical Reports Server (NTRS)

Frisch, Harold P.

2007-01-01

Engineers, who design systems using text specification documents, focus their work upon the completed system to meet Performance, time and budget goals. Consistency and integrity is difficult to maintain within text documents for a single complex system and more difficult to maintain as several systems are combined into higher-level systems, are maintained over decades, and evolve technically and in performance through updates. This system design approach frequently results in major changes during the system integration and test phase, and in time and budget overruns. Engineers who build system specification documents within a model-based systems environment go a step further and aggregate all of the data. They interrelate all of the data to insure consistency and integrity. After the model is constructed, the various system specification documents are prepared, all from the same database. The consistency and integrity of the model is assured, therefore the consistency and integrity of the various specification documents is insured. This article attempts to define model-based systems relative to such an environment. The intent is to expose the complexity of the enabling problem by outlining what is needed, why it is needed and how needs are being addressed by international standards writing teams.

Best kept secrets ... First Coast Systems, Inc. (FCS).

PubMed

Andrew, W F

1991-04-01

The FCS/APaCS system is a viable option for small-to medium-size hospitals (up to 400 beds). The table-driven system takes full advantage of IBM AS/400 computer architecture. A comprehensive application set, provided in an integrated database environment, is adaptable to multi-facility environments. Price/performance appears to be competitive. Commitment to IBM AS/400 environment assures cost-effective hardware platforms backed by IBM support and resources. As an IBM Health Industry Business Partner, FCS (and its clients) benefits from IBM's well-known commitment to quality and service. Corporate emphasis on user involvement and satisfaction, along with a commitment to quality and service for the APaCS systems, assures clients of "leading edge" capabilities in this evolutionary healthcare delivery environment. FCS/APaCS will be a strong contender in selected marketing environments.

Distribution Grid Integration Unit Cost Database | Solar Research | NREL

Science.gov Websites

Unit Cost Database Distribution Grid Integration Unit Cost Database NREL's Distribution Grid Integration Unit Cost Database contains unit cost information for different components that may be used to associated with PV. It includes information from the California utility unit cost guides on traditional

The Development of Educational Environment Suited to the Japan-Specific Educational Service Using Requirements Engineering Techniques: Case Study of Running Sakai with PostgreSQL

ERIC Educational Resources Information Center

Terawaki, Yuki; Takahashi, Yuichi; Kodama, Yasushi; Yana, Kazuo

2011-01-01

This paper describes an integration of different Relational Database Management System (RDBMS) of two Course Management Systems (CMS) called Sakai and the Common Factory for Inspiration and Value in Education (CFIVE). First, when the service of CMS is provided campus-wide, the problems of user support, CMS operation and customization of CMS are…

Computational framework to support integration of biomolecular and clinical data within a translational approach.

PubMed

Miyoshi, Newton Shydeo Brandão; Pinheiro, Daniel Guariz; Silva, Wilson Araújo; Felipe, Joaquim Cezar

2013-06-06

The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. We have implemented an extension of Chado - the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different "omics" technologies with patient's clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans.

The approaches for the decision support in case natural hazards

NASA Astrophysics Data System (ADS)

Vyazilov, Evgeny; Chunyaev, Nikita

2013-04-01

In spite of using highly automated systems of measurement, collecting, storing, handling, prediction and delivery of information on the marine environment, including natural hazards, the amount of damage from natural phenomena increases. Because information on the marine environment delivered to the industrial facilities not effectively used. To such information pays little attention by individual decision-makers and not always perform preventive measures necessary for reduce and prevent damage. Automation of information support will improve the efficiency management of the marine activities. In Russia develops "The Unified system of the information about World ocean" (ESIMO, http://esimo.ru/), that integrates observation, analysis, prognostic and climate data. Necessary to create tools to automatic selection natural disasters through all integrated data; notification decision-makers about arising natural hazards - software agent; provision of information in a compact form for the decision-makers; assessment of possible damage and costs to the preventive measures; providing information on the impacts of environment on economic facilities and recommendations for decision-making; the use of maps, diagrams, tables for reporting. Tools for automatic selection designed for identification of natural phenomena based on the resources ESIMO and corresponding critical values of the indicators environment. The result of this module will be constantly updated database of critical situations of environment for each object or technological process. To operational notify and provide current information about natural hazards proposes using a software agent that is installed on the computer decision-makers, which is activated in case critical situations and provides a minimum of information. In the event of natural disaster software agent should be able to inform decision-makers about this, providing information on the current situation, and the possibility for more and detailed information about natural hazard. Software agent must be able to be configured by the user to a specific object: a specific station or a drilling rigs that region or area, regardless of the size of the object. And depending on the selected settings and parameters it needs to apply the values of critical indexes. There is a need for real-time display hydrometeorological information with compact scheme that reflects the environment indicators that affect industrial facility in the form of devices (thermometer, aneroid, footstock, speedometer, hygrometer, thermograph, barograph, rain gauge, wind vane, etc.) with the ability to display indicators exceed a critical value. This scheme is designed to provide maximum information in the shortest possible time reference that provides an intuitive interface (display by generally accepted standardized instruments). Analytical services ESIMO combined with geographic information service provides information about area or point to decision-makers of showing the dynamics of changes of parameters in the form of graphics, diagrams, maps, tables. If the data sources are updated, analytical services automatically provides the relevance of the data in the analytical views of the complex. Analytical services works with database of integrated data and used for the preparation and presentation of the consumers of the federal and regional level for the analysis of information on the World Oceans. The analytic services show a set of indicators about the situation in the World Ocean. The complex provides the processing, analysis of qualitative and quantitative characteristics (indexes) of the marine environment and maritime activities of the Russian Federation. To assess the need for preventive measures, decision-makers require information in the form of potential economic consequences of natural hazard, cost of preventive measures to prevent damage. We can use for that the economic and mathematical models. When making the decision decision-makers must understand the possible consequences of natural phenomena and rely on the advice that they receive from a decision support system. Such information about the impacts and recommendations are based on the knowledge base (rules of "if, then"), formed on the basis of experience gained in the past. This should take into account not only the critical values for each object and technological process, but also the type of information (observations, forecasting, climate, and after the phenomenon), the level of decision-making, the season of the year, the climate zone where the object is located. Within ESIMO created integrated database that containing the results of the monitoring of the marine environment. The database includes the observation, analysis, and forecasting and climate data. Operational data is updated automatically at specified intervals of a few minutes to a week, depending on the frequency of observations. Climatic data is updated as needed, for example, once a year or once every five years. Integrated database contains a set of indicators related to a specific object, and to a certain geographic area, according to the observations made and the data entered data. In addition to hydrometeorological parameters database contains socio-economic information. At present, was created the database of critical values and information about the impacts of and recommendations for the 30 natural hazards, developed the data structure and software is under development. The interaction of all components of an information support will reduce the economic damage from natural disaster on individual objects economy (ships, ports, etc.) and improve public safety through more prompt delivery of information to decision-makers and the public, besides receive more informative data (district with symptoms natural phenomena , assessment of possible damage, the impact of and recommendations).

Design research about coastal zone planning and management information system based on GIS and database technologies

NASA Astrophysics Data System (ADS)

Huang, Pei; Wu, Sangyun; Feng, Aiping; Guo, Yacheng

2008-10-01

As littoral areas in possession of concentrated population, abundant resources, developed industry and active economy, the coastal areas are bound to become the forward positions and supported regions for marine exploitation. In the 21st century, the pressure that coastal zones are faced with is as follows: growth of population and urbanization, rise of sea level and coastal erosion, shortage of freshwater resource and deterioration of water resource, and degradation of fishery resource and so on. So the resources of coastal zones should be programmed and used reasonably for the sustainable development of economy and environment. This paper proposes a design research on the construction of coastal zone planning and management information system based on GIS and database technologies. According to this system, the planning results of coastal zones could be queried and displayed expediently through the system interface. It is concluded that the integrated application of GIS and database technologies provides a new modern method for the management of coastal zone resources, and makes it possible to ensure the rational development and utilization of the coastal zone resources, along with the sustainable development of economy and environment.

Vector and Raster Data Storage Based on Morton Code

NASA Astrophysics Data System (ADS)

Zhou, G.; Pan, Q.; Yue, T.; Wang, Q.; Sha, H.; Huang, S.; Liu, X.

2018-05-01

Even though geomatique is so developed nowadays, the integration of spatial data in vector and raster formats is still a very tricky problem in geographic information system environment. And there is still not a proper way to solve the problem. This article proposes a method to interpret vector data and raster data. In this paper, we saved the image data and building vector data of Guilin University of Technology to Oracle database. Then we use ADO interface to connect database to Visual C++ and convert row and column numbers of raster data and X Y of vector data to Morton code in Visual C++ environment. This method stores vector and raster data to Oracle Database and uses Morton code instead of row and column and X Y to mark the position information of vector and raster data. Using Morton code to mark geographic information enables storage of data make full use of storage space, simultaneous analysis of vector and raster data more efficient and visualization of vector and raster more intuitive. This method is very helpful for some situations that need to analyse or display vector data and raster data at the same time.

MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution

PubMed Central

Boeuf, Dominique; Audic, Stéphane; Brillet-Guéguen, Loraine; Caron, Christophe; Jeanthon, Christian

2015-01-01

Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr. PMID:26286928

MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution.

PubMed

Boeuf, Dominique; Audic, Stéphane; Brillet-Guéguen, Loraine; Caron, Christophe; Jeanthon, Christian

2015-01-01

Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr. © The Author(s) 2015. Published by Oxford University Press.

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

PubMed

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.

BanTeC: a software tool for management of corneal transplantation.

PubMed

López-Alvarez, P; Caballero, F; Trias, J; Cortés, U; López-Navidad, A

2005-11-01

Until recently, all cornea information at our tissue bank was managed manually, no specific database or computer tool had been implemented to provide electronic versions of documents and medical reports. The main objective of the BanTeC project was therefore to create a computerized system to integrate and classify all the information and documents used in the center in order to facilitate management of retrieved, transplanted corneal tissues. We used the Windows platform to develop the project. Microsoft Access and Microsoft Jet Engine were used at the database level and Data Access Objects was the chosen data access technology. In short, the BanTeC software seeks to computerize the tissue bank. All the initial stages of the development have now been completed, from specification of needs, program design and implementation of the software components, to the total integration of the final result in the real production environment. BanTeC will allow the generation of statistical reports for analysis to improve our performance.

The NASA Program Management Tool: A New Vision in Business Intelligence

NASA Technical Reports Server (NTRS)

Maluf, David A.; Swanson, Keith; Putz, Peter; Bell, David G.; Gawdiak, Yuri

2006-01-01

This paper describes a novel approach to business intelligence and program management for large technology enterprises like the U.S. National Aeronautics and Space Administration (NASA). Two key distinctions of the approach are that 1) standard business documents are the user interface, and 2) a "schema-less" XML database enables flexible integration of technology information for use by both humans and machines in a highly dynamic environment. The implementation utilizes patent-pending NASA software called the NASA Program Management Tool (PMT) and its underlying "schema-less" XML database called Netmark. Initial benefits of PMT include elimination of discrepancies between business documents that use the same information and "paperwork reduction" for program and project management in the form of reducing the effort required to understand standard reporting requirements and to comply with those reporting requirements. We project that the underlying approach to business intelligence will enable significant benefits in the timeliness, integrity and depth of business information available to decision makers on all organizational levels.

The Pathway Tools software.

PubMed

Karp, Peter D; Paley, Suzanne; Romero, Pedro

2002-01-01

Bioinformatics requires reusable software tools for creating model-organism databases (MODs). The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users.

Basic level scene understanding: categories, attributes and structures

PubMed Central

Xiao, Jianxiong; Hays, James; Russell, Bryan C.; Patterson, Genevieve; Ehinger, Krista A.; Torralba, Antonio; Oliva, Aude

2013-01-01

A longstanding goal of computer vision is to build a system that can automatically understand a 3D scene from a single image. This requires extracting semantic concepts and 3D information from 2D images which can depict an enormous variety of environments that comprise our visual world. This paper summarizes our recent efforts toward these goals. First, we describe the richly annotated SUN database which is a collection of annotated images spanning 908 different scene categories with object, attribute, and geometric labels for many scenes. This database allows us to systematically study the space of scenes and to establish a benchmark for scene and object recognition. We augment the categorical SUN database with 102 scene attributes for every image and explore attribute recognition. Finally, we present an integrated system to extract the 3D structure of the scene and objects depicted in an image. PMID:24009590

Multidisciplinary analysis and design of printed wiring boards

NASA Astrophysics Data System (ADS)

Fulton, Robert E.; Hughes, Joseph L.; Scott, Waymond R., Jr.; Umeagukwu, Charles; Yeh, Chao-Pin

1991-04-01

Modern printed wiring board design depends on electronic prototyping using computer-based simulation and design tools. Existing electrical computer-aided design (ECAD) tools emphasize circuit connectivity with only rudimentary analysis capabilities. This paper describes a prototype integrated PWB design environment denoted Thermal Structural Electromagnetic Testability (TSET) being developed at Georgia Tech in collaboration with companies in the electronics industry. TSET provides design guidance based on enhanced electrical and mechanical CAD capabilities including electromagnetic modeling testability analysis thermal management and solid mechanics analysis. TSET development is based on a strong analytical and theoretical science base and incorporates an integrated information framework and a common database design based on a systematic structured methodology.

Automated mapping of pharmacy orders from two electronic health record systems to RxNorm within the STRIDE clinical data warehouse.

PubMed

Hernandez, Penni; Podchiyska, Tanya; Weber, Susan; Ferris, Todd; Lowe, Henry

2009-11-14

The Stanford Translational Research Integrated Database Environment (STRIDE) clinical data warehouse integrates medication information from two Stanford hospitals that use different drug representation systems. To merge this pharmacy data into a single, standards-based model supporting research we developed an algorithm to map HL7 pharmacy orders to RxNorm concepts. A formal evaluation of this algorithm on 1.5 million pharmacy orders showed that the system could accurately assign pharmacy orders in over 96% of cases. This paper describes the algorithm and discusses some of the causes of failures in mapping to RxNorm.

A Data Management System for International Space Station Simulation Tools

NASA Technical Reports Server (NTRS)

Betts, Bradley J.; DelMundo, Rommel; Elcott, Sharif; McIntosh, Dawn; Niehaus, Brian; Papasin, Richard; Mah, Robert W.; Clancy, Daniel (Technical Monitor)

2002-01-01

Groups associated with the design, operational, and training aspects of the International Space Station make extensive use of modeling and simulation tools. Users of these tools often need to access and manipulate large quantities of data associated with the station, ranging from design documents to wiring diagrams. Retrieving and manipulating this data directly within the simulation and modeling environment can provide substantial benefit to users. An approach for providing these kinds of data management services, including a database schema and class structure, is presented. Implementation details are also provided as a data management system is integrated into the Intelligent Virtual Station, a modeling and simulation tool developed by the NASA Ames Smart Systems Research Laboratory. One use of the Intelligent Virtual Station is generating station-related training procedures in a virtual environment, The data management component allows users to quickly and easily retrieve information related to objects on the station, enhancing their ability to generate accurate procedures. Users can associate new information with objects and have that information stored in a database.

Knowledge environments representing molecular entities for the virtual physiological human.

PubMed

Hofmann-Apitius, Martin; Fluck, Juliane; Furlong, Laura; Fornes, Oriol; Kolárik, Corinna; Hanser, Susanne; Boeker, Martin; Schulz, Stefan; Sanz, Ferran; Klinger, Roman; Mevissen, Theo; Gattermayer, Tobias; Oliva, Baldo; Friedrich, Christoph M

2008-09-13

In essence, the virtual physiological human (VPH) is a multiscale representation of human physiology spanning from the molecular level via cellular processes and multicellular organization of tissues to complex organ function. The different scales of the VPH deal with different entities, relationships and processes, and in consequence the models used to describe and simulate biological functions vary significantly. Here, we describe methods and strategies to generate knowledge environments representing molecular entities that can be used for modelling the molecular scale of the VPH. Our strategy to generate knowledge environments representing molecular entities is based on the combination of information extraction from scientific text and the integration of information from biomolecular databases. We introduce @neuLink, a first prototype of an automatically generated, disease-specific knowledge environment combining biomolecular, chemical, genetic and medical information. Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH.

Hospital Nurses' Work Environment Characteristics and Patient Safety Outcomes: A Literature Review.

PubMed

Lee, Seung Eun; Scott, Linda D

2018-01-01

This integrative literature review assesses the relationship between hospital nurses' work environment characteristics and patient safety outcomes and recommends directions for future research based on examination of the literature. Using an electronic search of five databases, 18 studies published in English between 1999 and 2016 were identified for review. All but one study used a cross-sectional design, and only four used a conceptual/theoretical framework to guide the research. No definition of work environment was provided in most studies. Differing variables and instruments were used to measure patient outcomes, and findings regarding the effects of work environment on patient outcomes were inconsistent. To clarify the relationship between nurses' work environment characteristics and patient safety outcomes, researchers should consider using a longitudinal study design, using a theoretical foundation, and providing clear operational definitions of concepts. Moreover, given the inconsistent findings of previous studies, they should choose their measurement methodologies with care.

The visual-landscape analysis during the integration of high-rise buildings within the historic urban environment

NASA Astrophysics Data System (ADS)

Akristiniy, Vera A.; Dikova, Elena A.

2018-03-01

The article is devoted to one of the types of urban planning studies - the visual-landscape analysis during the integration of high-rise buildings within the historic urban environment for the purposes of providing pre-design and design studies in terms of preserving the historical urban environment and the implementation of the reconstructional resource of the area. In the article formed and systematized the stages and methods of conducting the visual-landscape analysis taking into account the influence of high-rise buildings on objects of cultural heritage and valuable historical buildings of the city. Practical application of the visual-landscape analysis provides an opportunity to assess the influence of hypothetical location of high-rise buildings on the perception of a historically developed environment and optimal building parameters. The contents of the main stages in the conduct of the visual - landscape analysis and their key aspects, concerning the construction of predicted zones of visibility of the significant historically valuable urban development objects and hypothetically planned of the high-rise buildings are revealed. The obtained data are oriented to the successive development of the planning and typological structure of the city territory and preservation of the compositional influence of valuable fragments of the historical environment in the structure of the urban landscape. On their basis, an information database is formed to determine the permissible urban development parameters of the high-rise buildings for the preservation of the compositional integrity of the urban area.

Environmental geochemistry at the global scale

USGS Publications Warehouse

Plant, J.; Smith, D.; Smith, B.; Williams, L.

2000-01-01

Land degradation and pollution caused by population pressure and economic development pose a threat to the sustainability of the Earth's surface, especially in tropical regions where a long history of chemical weathering has made the surface environment particularly fragile. Systematic baseline geochemical data provide a means of monitoring the state of the environment and identifying problem areas. Regional surveys have already been carried out in some countries, and with increased national and international funding they can be extended to cover the rest of the land surface of the globe. Preparations have been made, under the auspices of the IUGS, for the establishment of just such an integrated global database.

Real-time speech gisting for ATC applications

NASA Astrophysics Data System (ADS)

Dunkelberger, Kirk A.

1995-06-01

Command and control within the ATC environment remains primarily voice-based. Hence, automatic real time, speaker independent, continuous speech recognition (CSR) has many obvious applications and implied benefits to the ATC community: automated target tagging, aircraft compliance monitoring, controller training, automatic alarm disabling, display management, and many others. However, while current state-of-the-art CSR systems provide upwards of 98% word accuracy in laboratory environments, recent low-intrusion experiments in the ATCT environments demonstrated less than 70% word accuracy in spite of significant investments in recognizer tuning. Acoustic channel irregularities and controller/pilot grammar verities impact current CSR algorithms at their weakest points. It will be shown herein, however, that real time context- and environment-sensitive gisting can provide key command phrase recognition rates of greater than 95% using the same low-intrusion approach. The combination of real time inexact syntactic pattern recognition techniques and a tight integration of CSR, gisting, and ATC database accessor system components is the key to these high phase recognition rates. A system concept for real time gisting in the ATC context is presented herein. After establishing an application context, discussion presents a minimal CSR technology context then focuses on the gisting mechanism, desirable interfaces into the ATCT database environment, and data and control flow within the prototype system. Results of recent tests for a subset of the functionality are presented together with suggestions for further research.

Social interaction in type 2 diabetes computer-mediated environments: How inherent features of the channels influence peer-to-peer interaction.

PubMed

Lewinski, Allison A; Fisher, Edwin B

2016-06-01

Interventions via the internet provide support to individuals managing chronic illness. The purpose of this integrative review was to determine how the features of a computer-mediated environment influence social interactions among individuals with type 2 diabetes. A combination of MeSH and keyword terms, based on the cognates of three broad groupings: social interaction, computer-mediated environments, and chronic illness, was used to search the PubMed, PsychInfo, Sociology Research Database, and Cumulative Index to Nursing and Allied Health Literature databases. Eleven articles met the inclusion criteria. Computer-mediated environments enhance an individual's ability to interact with peers while increasing the convenience of obtaining personalized support. A matrix, focused on social interaction among peers, identified themes across all articles, and five characteristics emerged: (1) the presence of synchronous and asynchronous communication, (2) the ability to connect with similar peers, (3) the presence or absence of a moderator, (4) personalization of feedback regarding individual progress and self-management, and (5) the ability of individuals to maintain choice during participation. Individuals interact with peers to obtain relevant, situation-specific information and knowledge about managing their own care. Computer-mediated environments facilitate the ability of individuals to exchange this information despite temporal or geographical barriers that may be present, thus improving T2D self-management. © The Author(s) 2015.

E-health and healthcare enterprise information system leveraging service-oriented architecture.

PubMed

Hsieh, Sung-Huai; Hsieh, Sheau-Ling; Cheng, Po-Hsun; Lai, Feipei

2012-04-01

To present the successful experiences of an integrated, collaborative, distributed, large-scale enterprise healthcare information system over a wired and wireless infrastructure in National Taiwan University Hospital (NTUH). In order to smoothly and sequentially transfer from the complex relations among the old (legacy) systems to the new-generation enterprise healthcare information system, we adopted the multitier framework based on service-oriented architecture to integrate the heterogeneous systems as well as to interoperate among many other components and multiple databases. We also present mechanisms of a logical layer reusability approach and data (message) exchange flow via Health Level 7 (HL7) middleware, DICOM standard, and the Integrating the Healthcare Enterprise workflow. The architecture and protocols of the NTUH enterprise healthcare information system, especially in the Inpatient Information System (IIS), are discussed in detail. The NTUH Inpatient Healthcare Information System is designed and deployed on service-oriented architecture middleware frameworks. The mechanisms of integration as well as interoperability among the components and the multiple databases apply the HL7 standards for data exchanges, which are embedded in XML formats, and Microsoft .NET Web services to integrate heterogeneous platforms. The preliminary performance of the current operation IIS is evaluated and analyzed to verify the efficiency and effectiveness of the designed architecture; it shows reliability and robustness in the highly demanding traffic environment of NTUH. The newly developed NTUH IIS provides an open and flexible environment not only to share medical information easily among other branch hospitals, but also to reduce the cost of maintenance. The HL7 message standard is widely adopted to cover all data exchanges in the system. All services are independent modules that enable the system to be deployed and configured to the highest degree of flexibility. Furthermore, we can conclude that the multitier Inpatient Healthcare Information System has been designed successfully and in a collaborative manner, based on the index of performance evaluations, central processing unit, and memory utilizations.

From Population Databases to Research and Informed Health Decisions and Policy.

PubMed

Machluf, Yossy; Tal, Orna; Navon, Amir; Chaiter, Yoram

2017-01-01

In the era of big data, the medical community is inspired to maximize the utilization and processing of the rapidly expanding medical datasets for clinical-related and policy-driven research. This requires a medical database that can be aggregated, interpreted, and integrated at both the individual and population levels. Policymakers seek data as a lever for wise, evidence-based decision-making and information-driven policy. Yet, bridging the gap between data collection, research, and policymaking, is a major challenge. To bridge this gap, we propose a four-step model: (A) creating a conjoined task force of all relevant parties to declare a national program to promote collaborations; (B) promoting a national digital records project, or at least a network of synchronized and integrated databases, in an accessible transparent manner; (C) creating an interoperative national research environment to enable the analysis of the organized and integrated data and to generate evidence; and (D) utilizing the evidence to improve decision-making, to support a wisely chosen national policy. For the latter purpose, we also developed a novel multidimensional set of criteria to illuminate insights and estimate the risk for future morbidity based on current medical conditions. Used by policymakers, providers of health plans, caregivers, and health organizations, we presume this model will assist transforming evidence generation to support the design of health policy and programs, as well as improved decision-making about health and health care, at all levels: individual, communal, organizational, and national.

A GIS-Enabled, Michigan-Specific, Hierarchical Groundwater Modeling and Visualization System

NASA Astrophysics Data System (ADS)

Liu, Q.; Li, S.; Mandle, R.; Simard, A.; Fisher, B.; Brown, E.; Ross, S.

2005-12-01

Efficient management of groundwater resources relies on a comprehensive database that represents the characteristics of the natural groundwater system as well as analysis and modeling tools to describe the impacts of decision alternatives. Many agencies in Michigan have spent several years compiling expensive and comprehensive surface water and groundwater inventories and other related spatial data that describe their respective areas of responsibility. However, most often this wealth of descriptive data has only been utilized for basic mapping purposes. The benefits from analyzing these data, using GIS analysis functions or externally developed analysis models or programs, has yet to be systematically realized. In this talk, we present a comprehensive software environment that allows Michigan groundwater resources managers and frontline professionals to make more effective use of the available data and improve their ability to manage and protect groundwater resources, address potential conflicts, design cleanup schemes, and prioritize investigation activities. In particular, we take advantage of the Interactive Ground Water (IGW) modeling system and convert it to a customized software environment specifically for analyzing, modeling, and visualizing the Michigan statewide groundwater database. The resulting Michigan IGW modeling system (IGW-M) is completely window-based, fully interactive, and seamlessly integrated with a GIS mapping engine. The system operates in real-time (on the fly) providing dynamic, hierarchical mapping, modeling, spatial analysis, and visualization. Specifically, IGW-M allows water resources and environmental professionals in Michigan to: * Access and utilize the extensive data from the statewide groundwater database, interactively manipulate GIS objects, and display and query the associated data and attributes; * Analyze and model the statewide groundwater database, interactively convert GIS objects into numerical model features, automatically extract data and attributes, and simulate unsteady groundwater flow and contaminant transport in response to water and land management decisions; * Visualize and map model simulations and predictions with data from the statewide groundwater database in a seamless interactive environment. IGW-M has the potential to significantly improve the productivity of Michigan groundwater management investigations. It changes the role of engineers and scientists in modeling and analyzing the statewide groundwater database from heavily physical to cognitive problem-solving and decision-making tasks. The seamless real-time integration, real-time visual interaction, and real-time processing capability allows a user to focus on critical management issues, conflicts, and constraints, to quickly and iteratively examine conceptual approximations, management and planning scenarios, and site characterization assumptions, to identify dominant processes, to evaluate data worth and sensitivity, and to guide further data-collection activities. We illustrate the power and effectiveness of the M-IGW modeling and visualization system with a real case study and a real-time, live demonstration.

Development of a geophysical data fusion system for assessment and remediation studies of polluted groundwater aquifers. Scientific report No. 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murphy, J.R.; O`Neill, D.C.; Barker, B.W.

1994-10-01

The research described in this report is directed toward the development of a workstation-based data management, analysis and visualization system which can be used to improve the Air Force`s capability to evaluate site specific environmental hazards. The initial prototype system described in this report is directed toward a specific application to the Massachusetts Military Reservation (formerly Otis Air Force Base) on Cape Cod, Massachusetts. This system integrates a comprehensive, on-line environmental database for the site together with a map-based graphical user interface which facilitates analyst access to the databases and analysis tools needed to characterize the subsurface geologic and hydrologicmore » environments at the site.« less

Microvax-based data management and reduction system for the regional planetary image facilities

NASA Technical Reports Server (NTRS)

Arvidson, R.; Guinness, E.; Slavney, S.; Weiss, B.

1987-01-01

Presented is a progress report for the Regional Planetary Image Facilities (RPIF) prototype image data management and reduction system being jointly implemented by Washington University and the USGS, Flagstaff. The system will consist of a MicroVAX with a high capacity (approx 300 megabyte) disk drive, a compact disk player, an image display buffer, a videodisk player, USGS image processing software, and SYSTEM 1032 - a commercial relational database management package. The USGS, Flagstaff, will transfer their image processing software including radiometric and geometric calibration routines, to the MicroVAX environment. Washington University will have primary responsibility for developing the database management aspects of the system and for integrating the various aspects into a working system.

WebVR: an interactive web browser for virtual environments

NASA Astrophysics Data System (ADS)

Barsoum, Emad; Kuester, Falko

2005-03-01

The pervasive nature of web-based content has lead to the development of applications and user interfaces that port between a broad range of operating systems and databases, while providing intuitive access to static and time-varying information. However, the integration of this vast resource into virtual environments has remained elusive. In this paper we present an implementation of a 3D Web Browser (WebVR) that enables the user to search the internet for arbitrary information and to seamlessly augment this information into virtual environments. WebVR provides access to the standard data input and query mechanisms offered by conventional web browsers, with the difference that it generates active texture-skins of the web contents that can be mapped onto arbitrary surfaces within the environment. Once mapped, the corresponding texture functions as a fully integrated web-browser that will respond to traditional events such as the selection of links or text input. As a result, any surface within the environment can be turned into a web-enabled resource that provides access to user-definable data. In order to leverage from the continuous advancement of browser technology and to support both static as well as streamed content, WebVR uses ActiveX controls to extract the desired texture skin from industry strength browsers, providing a unique mechanism for data fusion and extensibility.

Automation of Shuttle Tile Inspection - Engineering methodology for Space Station

NASA Technical Reports Server (NTRS)

Wiskerchen, M. J.; Mollakarimi, C.

1987-01-01

The Space Systems Integration and Operations Research Applications (SIORA) Program was initiated in late 1986 as a cooperative applications research effort between Stanford University, NASA Kennedy Space Center, and Lockheed Space Operations Company. One of the major initial SIORA tasks was the application of automation and robotics technology to all aspects of the Shuttle tile processing and inspection system. This effort has adopted a systems engineering approach consisting of an integrated set of rapid prototyping testbeds in which a government/university/industry team of users, technologists, and engineers test and evaluate new concepts and technologies within the operational world of Shuttle. These integrated testbeds include speech recognition and synthesis, laser imaging inspection systems, distributed Ada programming environments, distributed relational database architectures, distributed computer network architectures, multimedia workbenches, and human factors considerations.

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Po-E; Lo, Chien -Chi; Anderson, Joseph J.

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the easemore » of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. As a result, this bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.« less

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

PubMed Central

Li, Po-E; Lo, Chien-Chi; Anderson, Joseph J.; Davenport, Karen W.; Bishop-Lilly, Kimberly A.; Xu, Yan; Ahmed, Sanaa; Feng, Shihai; Mokashi, Vishwesh P.; Chain, Patrick S.G.

2017-01-01

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research. PMID:27899609

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

DOE PAGES

Li, Po-E; Lo, Chien -Chi; Anderson, Joseph J.; ...

2016-11-24

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the easemore » of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. As a result, this bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.« less

Integrated Primary Care Information Database (IPCI)

Cancer.gov

The Integrated Primary Care Information Database is a longitudinal observational database that was created specifically for pharmacoepidemiological and pharmacoeconomic studies, inlcuding data from computer-based patient records supplied voluntarily by general practitioners.

Mass spectrometry-based protein identification by integrating de novo sequencing with database searching.

PubMed

Wang, Penghao; Wilson, Susan R

2013-01-01

Mass spectrometry-based protein identification is a very challenging task. The main identification approaches include de novo sequencing and database searching. Both approaches have shortcomings, so an integrative approach has been developed. The integrative approach firstly infers partial peptide sequences, known as tags, directly from tandem spectra through de novo sequencing, and then puts these sequences into a database search to see if a close peptide match can be found. However the current implementation of this integrative approach has several limitations. Firstly, simplistic de novo sequencing is applied and only very short sequence tags are used. Secondly, most integrative methods apply an algorithm similar to BLAST to search for exact sequence matches and do not accommodate sequence errors well. Thirdly, by applying these methods the integrated de novo sequencing makes a limited contribution to the scoring model which is still largely based on database searching. We have developed a new integrative protein identification method which can integrate de novo sequencing more efficiently into database searching. Evaluated on large real datasets, our method outperforms popular identification methods.

Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences

PubMed Central

Lam, Hugo Y.K.; Marenco, Luis; Shepherd, Gordon M.; Miller, Perry L.; Cheung, Kei-Hoi

2006-01-01

Integrative neuroscience involves the integration and analysis of diverse types of neuroscience data involving many different experimental techniques. This data will increasingly be distributed across many heterogeneous databases that are web-accessible. Currently, these databases do not expose their schemas (database structures) and their contents to web applications/agents in a standardized, machine-friendly way. This limits database interoperation. To address this problem, we describe a pilot project that illustrates how neuroscience databases can be expressed using the Web Ontology Language, which is a semantically-rich ontological language, as a common data representation language to facilitate complex cross-database queries. In this pilot project, an existing tool called “D2RQ” was used to translate two neuroscience databases (NeuronDB and CoCoDat) into OWL, and the resulting OWL ontologies were then merged. An OWL-based reasoner (Racer) was then used to provide a sophisticated query language (nRQL) to perform integrated queries across the two databases based on the merged ontology. This pilot project is one step toward exploring the use of semantic web technologies in the neurosciences. PMID:17238384

Specification and Enforcement of Semantic Integrity Constraints in Microsoft Access

ERIC Educational Resources Information Center

Dadashzadeh, Mohammad

2007-01-01

Semantic integrity constraints are business-specific rules that limit the permissible values in a database. For example, a university rule dictating that an "incomplete" grade cannot be changed to an A constrains the possible states of the database. To maintain database integrity, business rules should be identified in the course of database…

DataHub: Knowledge-based data management for data discovery

NASA Astrophysics Data System (ADS)

Handley, Thomas H.; Li, Y. Philip

1993-08-01

Currently available database technology is largely designed for business data-processing applications, and seems inadequate for scientific applications. The research described in this paper, the DataHub, will address the issues associated with this shortfall in technology utilization and development. The DataHub development is addressing the key issues in scientific data management of scientific database models and resource sharing in a geographically distributed, multi-disciplinary, science research environment. Thus, the DataHub will be a server between the data suppliers and data consumers to facilitate data exchanges, to assist science data analysis, and to provide as systematic approach for science data management. More specifically, the DataHub's objectives are to provide support for (1) exploratory data analysis (i.e., data driven analysis); (2) data transformations; (3) data semantics capture and usage; analysis-related knowledge capture and usage; and (5) data discovery, ingestion, and extraction. Applying technologies that vary from deductive databases, semantic data models, data discovery, knowledge representation and inferencing, exploratory data analysis techniques and modern man-machine interfaces, DataHub will provide a prototype, integrated environement to support research scientists' needs in multiple disciplines (i.e. oceanography, geology, and atmospheric) while addressing the more general science data management issues. Additionally, the DataHub will provide data management services to exploratory data analysis applications such as LinkWinds and NCSA's XIMAGE.

From LDEF to a national Space Environment and Effects (SEE) program: A natural progression

NASA Technical Reports Server (NTRS)

Bowles, David E.; Calloway, Robert L.; Funk, Joan G.; Kinard, William H.; Levine, Arlene S.

1995-01-01

As the LDEF program draws to a close, it leaves in place the fundamental building blocks for a Space Environment and Effects (SEE) program. Results from LDEF data analyses and investigations now form a substantial core of knowledge on the long term effects of the space environment on materials, system and structures. In addition, these investigations form the basic structure of a critically-needed SEE archive and database system. An agency-wide effort is required to capture all elements of a SEE program to provide a more comprehensive and focused approach to understanding the space environment, determining the best techniques for both flight and ground-based experimentation, updating the models which predict both the environments and those effects on subsystems and spacecraft, and, finally, ensuring that this multitudinous information is properly maintained, and inserted into spacecraft design programs. Many parts and pieces of a SEE program already exist at various locations to fulfill specific needs. The primary purpose of this program, under the direction of the Office of Advanced Concepts and Technology (OACT) in NASA Headquarters, is to take advantage of these parts; apply synergisms where possible; identify and when possible fill-in gaps; coordinate and advocate a comprehensive SEE program. The SEE program must coordinate and support the efforts of well-established technical communities wherein the bulk of the work will continue to be done. The SEE program will consist of a NASA-led SEE Steering Committee, consisting of government and industry users, with the responsibility for coordination between technology developers and NASA customers; and Technical Working Groups with primary responsibility for program technical content in response to user needs. The Technical Working Groups are as follows: Materials and Processes; Plasma and Fields; Ionizing Radiation; Meteoroids and Orbital Debris; Neutral External Contamination; Thermosphere, Thermal, and Solar Conditions; Electromagnetic Effects; Integrated Assessments and Databases. Specific technology development tasks will be solicited through a NASA Research Announcement to be released in May of 1994. The areas in which tasks are solicited include: (1) engineering environment definitions, (2) environments and effects design guidelines, (3) environments and effects assessment models and databases, and (4) flight/ground simulation/technology assessment data.

From LDEF to a national Space Environment and Effects (SEE) program: A natural progression

NASA Astrophysics Data System (ADS)

Bowles, David E.; Calloway, Robert L.; Funk, Joan G.; Kinard, William H.; Levine, Arlene S.

1995-02-01

As the LDEF program draws to a close, it leaves in place the fundamental building blocks for a Space Environment and Effects (SEE) program. Results from LDEF data analyses and investigations now form a substantial core of knowledge on the long term effects of the space environment on materials, system and structures. In addition, these investigations form the basic structure of a critically-needed SEE archive and database system. An agency-wide effort is required to capture all elements of a SEE program to provide a more comprehensive and focused approach to understanding the space environment, determining the best techniques for both flight and ground-based experimentation, updating the models which predict both the environments and those effects on subsystems and spacecraft, and, finally, ensuring that this multitudinous information is properly maintained, and inserted into spacecraft design programs. Many parts and pieces of a SEE program already exist at various locations to fulfill specific needs. The primary purpose of this program, under the direction of the Office of Advanced Concepts and Technology (OACT) in NASA Headquarters, is to take advantage of these parts; apply synergisms where possible; identify and when possible fill-in gaps; coordinate and advocate a comprehensive SEE program. The SEE program must coordinate and support the efforts of well-established technical communities wherein the bulk of the work will continue to be done. The SEE program will consist of a NASA-led SEE Steering Committee, consisting of government and industry users, with the responsibility for coordination between technology developers and NASA customers; and Technical Working Groups with primary responsibility for program technical content in response to user needs. The Technical Working Groups are as follows: Materials and Processes; Plasma and Fields; Ionizing Radiation; Meteoroids and Orbital Debris; Neutral External Contamination; Thermosphere, Thermal, and Solar Conditions; Electromagnetic Effects; Integrated Assessments and Databases. Specific technology development tasks will be solicited through a NASA Research Announcement to be released in May of 1994. The areas in which tasks are solicited include: (1) engineering environment definitions, (2) environments and effects design guidelines, (3) environments and effects assessment models and databases, and (4) flight/ground simulation/technology assessment data.

Chemical Informatics and the Drug Discovery Knowledge Pyramid

PubMed Central

Lushington, Gerald H.; Dong, Yinghua; Theertham, Bhargav

2012-01-01

The magnitude of the challenges in preclinical drug discovery is evident in the large amount of capital invested in such efforts in pursuit of a small static number of eventually successful marketable therapeutics. An explosion in the availability of potentially drug-like compounds and chemical biology data on these molecules can provide us with the means to improve the eventual success rates for compounds being considered at the preclinical level, but only if the community is able to access available information in an efficient and meaningful way. Thus, chemical database resources are critical to any serious drug discovery effort. This paper explores the basic principles underlying the development and implementation of chemical databases, and examines key issues of how molecular information may be encoded within these databases so as to enhance the likelihood that users will be able to extract meaningful information from data queries. In addition to a broad survey of conventional data representation and query strategies, key enabling technologies such as new context-sensitive chemical similarity measures and chemical cartridges are examined, with recommendations on how such resources may be integrated into a practical database environment. PMID:23782037

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

NASA Astrophysics Data System (ADS)

Sushko, Iurii; Novotarskyi, Sergii; Körner, Robert; Pandey, Anil Kumar; Rupp, Matthias; Teetz, Wolfram; Brandmaier, Stefan; Abdelaziz, Ahmed; Prokopenko, Volodymyr V.; Tanchuk, Vsevolod Y.; Todeschini, Roberto; Varnek, Alexandre; Marcou, Gilles; Ertl, Peter; Potemkin, Vladimir; Grishina, Maria; Gasteiger, Johann; Schwab, Christof; Baskin, Igor I.; Palyulin, Vladimir A.; Radchenko, Eugene V.; Welsh, William J.; Kholodovych, Vladyslav; Chekmarev, Dmitriy; Cherkasov, Artem; Aires-de-Sousa, Joao; Zhang, Qing-You; Bender, Andreas; Nigsch, Florian; Patiny, Luc; Williams, Antony; Tkachenko, Valery; Tetko, Igor V.

2011-06-01

The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.

[Development of fixed-base full task space flight training simulator].

PubMed

Xue, Liang; Chen, Shan-quang; Chang, Tian-chun; Yang, Hong; Chao, Jian-gang; Li, Zhi-peng

2003-01-01

Fixed-base full task flight training simulator is a very critical and important integrated training facility. It is mostly used in training of integrated skills and tasks, such as running the flight program of manned space flight, dealing with faults, operating and controlling spacecraft flight, communicating information between spacecraft and ground. This simulator was made up of several subentries including spacecraft simulation, simulating cabin, sight image, acoustics, main controlling computer, instructor and assistant support. It has implemented many simulation functions, such as spacecraft environment, spacecraft movement, communicating information between spacecraft and ground, typical faults, manual control and operating training, training control, training monitor, training database management, training data recording, system detecting and so on.

[Offshore work and the work of nurses on board: an integrative review].

PubMed

Antoniolli, Silvana Aline Cordeiro; Emmel, Suzel Vaz; Ferreira, Gímerson Erick; Paz, Potiguara de Oliveira; Kaiser, Dagmar Elaine

2015-08-01

To know the production of theoretical approaches on issues related to offshore work and the work of offshore nurses. Integrative literature review conducted in the databases of LILACS, BDENF, MEDLINE, SciELO and Index PSI. We selected 33 studies published in national and international journals between 1997 and 2014. The thematic analysis corpus resulted in four central themes: offshore work environment; amid work adversities, an escape; structuring of offshore health and safety services; in search of safe practices. This study contributes to the offshore work of nurses in relation to the nature of work, acting amid adversities and the restless search for safe practices in the open sea.

[Integrated DNA barcoding database for identifying Chinese animal medicine].

PubMed

Shi, Lin-Chun; Yao, Hui; Xie, Li-Fang; Zhu, Ying-Jie; Song, Jing-Yuan; Zhang, Hui; Chen, Shi-Lin

2014-06-01

In order to construct an integrated DNA barcoding database for identifying Chinese animal medicine, the authors and their cooperators have completed a lot of researches for identifying Chinese animal medicines using DNA barcoding technology. Sequences from GenBank have been analyzed simultaneously. Three different methods, BLAST, barcoding gap and Tree building, have been used to confirm the reliabilities of barcode records in the database. The integrated DNA barcoding database for identifying Chinese animal medicine has been constructed using three different parts: specimen, sequence and literature information. This database contained about 800 animal medicines and the adulterants and closely related species. Unknown specimens can be identified by pasting their sequence record into the window on the ID page of species identification system for traditional Chinese medicine (www. tcmbarcode. cn). The integrated DNA barcoding database for identifying Chinese animal medicine is significantly important for animal species identification, rare and endangered species conservation and sustainable utilization of animal resources.

geophylobuilder 1.0: an arcgis extension for creating 'geophylogenies'.

PubMed

Kidd, David M; Liu, Xianhua

2008-01-01

Evolution is inherently a spatiotemporal process; however, despite this, phylogenetic and geographical data and models remain largely isolated from one another. Geographical information systems provide a ready-made spatial modelling, analysis and dissemination environment within which phylogenetic models can be explicitly linked with their associated spatial data and subsequently integrated with other georeferenced data sets describing the biotic and abiotic environment. geophylobuilder 1.0 is an extension for the arcgis geographical information system that builds a 'geophylogenetic' data model from a phylogenetic tree and associated geographical data. Geophylogenetic database objects can subsequently be queried, spatially analysed and visualized in both 2D and 3D within a geographical information systems. © 2007 The Authors.

Navigation system for autonomous mapper robots

NASA Astrophysics Data System (ADS)

Halbach, Marc; Baudoin, Yvan

1993-05-01

This paper describes the conception and realization of a fast, robust, and general navigation system for a mobile (wheeled or legged) robot. A database, representing a high level map of the environment is generated and continuously updated. The first part describes the legged target vehicle and the hexapod robot being developed. The second section deals with spatial and temporal sensor fusion for dynamic environment modeling within an obstacle/free space probabilistic classification grid. Ultrasonic sensors are used, others are suspected to be integrated, and a-priori knowledge is treated. US sensors are controlled by the path planning module. The third part concerns path planning and a simulation of a wheeled robot is also presented.

E-MSD: an integrated data resource for bioinformatics.

PubMed

Velankar, S; McNeil, P; Mittard-Runte, V; Suarez, A; Barrell, D; Apweiler, R; Henrick, K

2005-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

Proactive Response to Potential Material Shortages Arising from Environmental Restrictions Using Automatic Discovery and Extraction of Information from Technical Documents

DTIC Science & Technology

2012-12-21

material data and other key information in a UIMA environment. In the course of this project, the tools and methods developed were used to extract and...Architecture ( UIMA ) library from the Apache Software Foundation. Using this architecture, a given document is run through several “annotators” to...material taxonomy developed for the XSB, Inc. Coherent View™ database. In order to integrate this technology into the Java-based UIMA annotation

A sensor simulation framework for the testing and evaluation of external hazard monitors and integrated alerting and notification functions

NASA Astrophysics Data System (ADS)

Uijt de Haag, Maarten; Venable, Kyle; Bezawada, Rajesh; Adami, Tony; Vadlamani, Ananth K.

2009-05-01

This paper discusses a sensor simulator/synthesizer framework that can be used to test and evaluate various sensor integration strategies for the implementation of an External Hazard Monitor (EHM) and Integrated Alerting and Notification (IAN) function as part of NASA's Integrated Intelligent Flight Deck (IIFD) project. The IIFD project under the NASA's Aviation Safety program "pursues technologies related to the flight deck that ensure crew workload and situational awareness are both safely optimized and adapted to the future operational environment as envisioned by NextGen." Within the simulation framework, various inputs to the IIFD and its subsystems, the EHM and IAN, are simulated, synthesized from actual collected data, or played back from actual flight test sensor data. Sensors and avionics included in this framework are TCAS, ADS-B, Forward-Looking Infrared, Vision cameras, GPS, Inertial navigators, EGPWS, Laser Detection and Ranging sensors, altimeters, communication links with ATC, and weather radar. The framework is implemented in Simulink, a modeling language developed by The Mathworks. This modeling language allows for test and evaluation of various sensor and communication link configurations as well as the inclusion of feedback from the pilot on the performance of the aircraft. Specifically, this paper addresses the architecture of the simulator, the sensor model interfaces, the timing and database (environment) aspects of the sensor models, the user interface of the modeling environment, and the various avionics implementations.

Ecoregions and ecodistricts: Ecological regionalizations for the Netherlands' environmental policy

NASA Astrophysics Data System (ADS)

Klijn, Frans; de Waal, Rein W.; Oude Voshaar, Jan H.

1995-11-01

For communicating data on the state of the environment to policy makers, various integrative frameworks are used, including regional integration. For this kind of integration we have developed two related ecological regionalizations, ecoregions and ecodistricts, which are two levels in a series of classifications for hierarchically nested ecosystems at different spatial scale levels. We explain the compilation of the maps from existing geographical data, demonstrating the relatively holistic, a priori integrated approach. The resulting maps are submitted to discriminant analysis to test the consistancy of the use of mapping characteristics, using data on individual abiotic ecosystem components from a national database on a 1-km2 grid. This reveals that the spatial patterns of soil, groundwater, and geomorphology correspond with the ecoregion and ecodistrict maps. Differences between the original maps and maps formed by automatically reclassifying 1-km2 cells with these discriminant components are found to be few. These differences are discussed against the background of the principal dilemma between deductive, a priori integrated, and inductive, a posteriori, classification.

SIDD: A Semantically Integrated Database towards a Global View of Human Disease

PubMed Central

Cheng, Liang; Wang, Guohua; Li, Jie; Zhang, Tianjiao; Xu, Peigang; Wang, Yadong

2013-01-01

Background A number of databases have been developed to collect disease-related molecular, phenotypic and environmental features (DR-MPEs), such as genes, non-coding RNAs, genetic variations, drugs, phenotypes and environmental factors. However, each of current databases focused on only one or two DR-MPEs. There is an urgent demand to develop an integrated database, which can establish semantic associations among disease-related databases and link them to provide a global view of human disease at the biological level. This database, once developed, will facilitate researchers to query various DR-MPEs through disease, and investigate disease mechanisms from different types of data. Methodology To establish an integrated disease-associated database, disease vocabularies used in different databases are mapped to Disease Ontology (DO) through semantic match. 4,284 and 4,186 disease terms from Medical Subject Headings (MeSH) and Online Mendelian Inheritance in Man (OMIM) respectively are mapped to DO. Then, the relationships between DR-MPEs and diseases are extracted and merged from different source databases for reducing the data redundancy. Conclusions A semantically integrated disease-associated database (SIDD) is developed, which integrates 18 disease-associated databases, for researchers to browse multiple types of DR-MPEs in a view. A web interface allows easy navigation for querying information through browsing a disease ontology tree or searching a disease term. Furthermore, a network visualization tool using Cytoscape Web plugin has been implemented in SIDD. It enhances the SIDD usage when viewing the relationships between diseases and DR-MPEs. The current version of SIDD (Jul 2013) documents 4,465,131 entries relating to 139,365 DR-MPEs, and to 3,824 human diseases. The database can be freely accessed from: http://mlg.hit.edu.cn/SIDD. PMID:24146757

Cardiological database management system as a mediator to clinical decision support.

PubMed

Pappas, C; Mavromatis, A; Maglaveras, N; Tsikotis, A; Pangalos, G; Ambrosiadou, V

1996-03-01

An object-oriented medical database management system is presented for a typical cardiologic center, facilitating epidemiological trials. Object-oriented analysis and design were used for the system design, offering advantages for the integrity and extendibility of medical information systems. The system was developed using object-oriented design and programming methodology, the C++ language and the Borland Paradox Relational Data Base Management System on an MS-Windows NT environment. Particular attention was paid to system compatibility, portability, the ease of use, and the suitable design of the patient record so as to support the decisions of medical personnel in cardiovascular centers. The system was designed to accept complex, heterogeneous, distributed data in various formats and from different kinds of examinations such as Holter, Doppler and electrocardiography.

Andromeda: a peptide search engine integrated into the MaxQuant environment.

PubMed

Cox, Jürgen; Neuhauser, Nadin; Michalski, Annette; Scheltema, Richard A; Olsen, Jesper V; Mann, Matthias

2011-04-01

A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. Furthermore, it can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. The algorithms of Andromeda are provided. Andromeda can function independently or as an integrated search engine of the widely used MaxQuant computational proteomics platform and both are freely available at www.maxquant.org. The combination enables analysis of large data sets in a simple analysis workflow on a desktop computer. For searching individual spectra Andromeda is also accessible via a web server. We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides.

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

PubMed Central

Paley, Suzanne M.; Krummenacker, Markus; Latendresse, Mario; Dale, Joseph M.; Lee, Thomas J.; Kaipa, Pallavi; Gilham, Fred; Spaulding, Aaron; Popescu, Liviu; Altman, Tomer; Paulsen, Ian; Keseler, Ingrid M.; Caspi, Ron

2010-01-01

Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry. PMID:19955237

Customer and household matching: resolving entity identity in data warehouses

NASA Astrophysics Data System (ADS)

Berndt, Donald J.; Satterfield, Ronald K.

2000-04-01

The data preparation and cleansing tasks necessary to ensure high quality data are among the most difficult challenges faced in data warehousing and data mining projects. The extraction of source data, transformation into new forms, and loading into a data warehouse environment are all time consuming tasks that can be supported by methodologies and tools. This paper focuses on the problem of record linkage or entity matching, tasks that can be very important in providing high quality data. Merging two or more large databases into a single integrated system is a difficult problem in many industries, especially in the wake of acquisitions. For example, managing customer lists can be challenging when duplicate entries, data entry problems, and changing information conspire to make data quality an elusive target. Common tasks with regard to customer lists include customer matching to reduce duplicate entries and household matching to group customers. These often O(n2) problems can consume significant resources, both in computing infrastructure and human oversight, and the goal of high accuracy in the final integrated database can be difficult to assure. This paper distinguishes between attribute corruption and entity corruption, discussing the various impacts on quality. A metajoin operator is proposed and used to organize past and current entity matching techniques. Finally, a logistic regression approach to implementing the metajoin operator is discussed and illustrated with an example. The metajoin can be used to determine whether two records match, don't match, or require further evaluation by human experts. Properly implemented, the metajoin operator could allow the integration of individual databases with greater accuracy and lower cost.

Specifications of insilicoML 1.0: a multilevel biophysical model description language.

PubMed

Asai, Yoshiyuki; Suzuki, Yasuyuki; Kido, Yoshiyuki; Oka, Hideki; Heien, Eric; Nakanishi, Masao; Urai, Takahito; Hagihara, Kenichi; Kurachi, Yoshihisa; Nomura, Taishin

2008-12-01

An extensible markup language format, insilicoML (ISML), version 0.1, describing multi-level biophysical models has been developed and available in the public domain. ISML is fully compatible with CellML 1.0, a model description standard developed by the IUPS Physiome Project, for enhancing knowledge integration and model sharing. This article illustrates the new specifications of ISML 1.0 that largely extend the capability of ISML 0.1. ISML 1.0 can describe various types of mathematical models, including ordinary/partial differential/difference equations representing the dynamics of physiological functions and the geometry of living organisms underlying the functions. ISML 1.0 describes a model using a set of functional elements (modules) each of which can specify mathematical expressions of the functions. Structural and logical relationships between any two modules are specified by edges, which allow modular, hierarchical, and/or network representations of the model. The role of edge-relationships is enriched by key words in order for use in constructing a physiological ontology. The ontology is further improved by the traceability of history of the model's development and by linking between different ISML models stored in the model's database using meta-information. ISML 1.0 is designed to operate with a model database and integrated environments for model development and simulations for knowledge integration and discovery.

Emission & Generation Resource Integrated Database (eGRID)

EPA Pesticide Factsheets

The Emissions & Generation Resource Integrated Database (eGRID) is an integrated source of data on environmental characteristics of electric power generation. Twelve federal databases are represented by eGRID, which provides air emission and resource mix information for thousands of power plants and generating companies. eGRID allows direct comparison of the environmental attributes of electricity from different plants, companies, States, or regions of the power grid.

The Computing and Data Grid Approach: Infrastructure for Distributed Science Applications

NASA Technical Reports Server (NTRS)

Johnston, William E.

2002-01-01

With the advent of Grids - infrastructure for using and managing widely distributed computing and data resources in the science environment - there is now an opportunity to provide a standard, large-scale, computing, data, instrument, and collaboration environment for science that spans many different projects and provides the required infrastructure and services in a relatively uniform and supportable way. Grid technology has evolved over the past several years to provide the services and infrastructure needed for building 'virtual' systems and organizations. We argue that Grid technology provides an excellent basis for the creation of the integrated environments that can combine the resources needed to support the large- scale science projects located at multiple laboratories and universities. We present some science case studies that indicate that a paradigm shift in the process of science will come about as a result of Grids providing transparent and secure access to advanced and integrated information and technologies infrastructure: powerful computing systems, large-scale data archives, scientific instruments, and collaboration tools. These changes will be in the form of services that can be integrated with the user's work environment, and that enable uniform and highly capable access to these computers, data, and instruments, regardless of the location or exact nature of these resources. These services will integrate transient-use resources like computing systems, scientific instruments, and data caches (e.g., as they are needed to perform a simulation or analyze data from a single experiment); persistent-use resources. such as databases, data catalogues, and archives, and; collaborators, whose involvement will continue for the lifetime of a project or longer. While we largely address large-scale science in this paper, Grids, particularly when combined with Web Services, will address a broad spectrum of science scenarios. both large and small scale.

How innovative ICT tools can enhance understanding of interactions between societal, hydrological and environmental changes

NASA Astrophysics Data System (ADS)

Foglia, L.; Borsi, I.; Cannata, M.; De Filippis, G.; Criollo, R.; Mehl, S.; Rossetto, R.

2017-12-01

The interaction of environmental, physical, and socioeconomic processes alter and are altered by water and by how human can affect water use. For example, a warming climate increases the chance of warm temperatures and lack of precipitation, and when combined with growing population requires understanding of impact on water resources and on all the processes related to the water budget including evapotranspiration. On this foundation, humans add engineered and social systems to control, manage, utilize, and alter our water environment for a variety of uses and through a variety of organizational and individual decisions. Some engineered systems have mixed consequences, for example groundwater helped sustain agriculture during drought periods, but then groundwater levels critically decrease with no chances to recover in some parts of the world. Innovative ICT tools have been demonstrated as a helpful tool for enhancing human understanding of the effect that societal, economical, and policy-based decisions have on the water resources and on the environment in general. Here we apply the new FREEWAT platform to demonstrate the importance of developing ad-hoc database and hydrological models to simulate different scenarios using a participatory approach. Stakeholders have been involved in data collection, database design and model development during the entire project period and discussion between researcher and stakeholders have been fostered during Focus Groups and workshops organized in many countries in Europe and beyond (including case studies in Ukraine and Africa). FREEWAT is an open source and public domain GIS integrated modelling environment for simulation of water quantity and quality in surface water and groundwater with an integrated water management and planning module. FREEWAT aims at promoting water resource management by simplifying the application of the Water Framework Directive and related Directives. Fourteen case studies have been considered and database and models have been developed and discussed with the local stakeholders. Here a summary of the drawbacks and successes of this approach will be presented using careful analysis of the case study implemented within the project.

Integration of a synthetic vision system with airborne laser range scanner-based terrain referenced navigation for precision approach guidance

NASA Astrophysics Data System (ADS)

Uijt de Haag, Maarten; Campbell, Jacob; van Graas, Frank

2005-05-01

Synthetic Vision Systems (SVS) provide pilots with a virtual visual depiction of the external environment. When using SVS for aircraft precision approach guidance systems accurate positioning relative to the runway with a high level of integrity is required. Precision approach guidance systems in use today require ground-based electronic navigation components with at least one installation at each airport, and in many cases multiple installations to service approaches to all qualifying runways. A terrain-referenced approach guidance system is envisioned to provide precision guidance to an aircraft without the use of ground-based electronic navigation components installed at the airport. This autonomy makes it a good candidate for integration with an SVS. At the Ohio University Avionics Engineering Center (AEC), work has been underway in the development of such a terrain referenced navigation system. When used in conjunction with an Inertial Measurement Unit (IMU) and a high accuracy/resolution terrain database, this terrain referenced navigation system can provide navigation and guidance information to the pilot on a SVS or conventional instruments. The terrain referenced navigation system, under development at AEC, operates on similar principles as other terrain navigation systems: a ground sensing sensor (in this case an airborne laser scanner) gathers range measurements to the terrain; this data is then matched in some fashion with an onboard terrain database to find the most likely position solution and used to update an inertial sensor-based navigator. AEC's system design differs from today's common terrain navigators in its use of a high resolution terrain database (~1 meter post spacing) in conjunction with an airborne laser scanner which is capable of providing tens of thousands independent terrain elevation measurements per second with centimeter-level accuracies. When combined with data from an inertial navigator the high resolution terrain database and laser scanner system is capable of providing near meter-level horizontal and vertical position estimates. Furthermore, the system under development capitalizes on 1) The position and integrity benefits provided by the Wide Area Augmentation System (WAAS) to reduce the initial search space size and; 2) The availability of high accuracy/resolution databases. This paper presents results from flight tests where the terrain reference navigator is used to provide guidance cues for a precision approach.

Student outcomes of distance learning in nursing education: an integrative review.

PubMed

Patterson, Barbara J; Krouse, Anne M; Roy, Linda

2012-09-01

Distance learning offers a distinctive environment to educate nursing students. While there is a significant body of evidence in the literature related to course, program, and faculty outcomes of distance education, little attention has been given by researchers to evaluate student outcomes, with the exception of student satisfaction. There is a need to evaluate and translate findings related to student outcomes in distance learning into educational practice. Integrative reviews offer one strategy to contribute to evidence-based teaching practice initiatives. A search of available published qualitative and quantitative research on student outcomes of distance learning from 1999 to 2009 was conducted using a number of databases. Astin's Input-Environment-Output conceptual model provided a framework for this review. Thirty-three studies met the inclusion criteria. Bothcognitive and affective student outcomes emerged. The cognitive outcomes were student learning, learning process, and technology proficiency. Affective outcomes included personal and professional growth, satisfaction, and connectedness. Implications, recommendations, and future research are discussed.

An efficient 3D R-tree spatial index method for virtual geographic environments

NASA Astrophysics Data System (ADS)

Zhu, Qing; Gong, Jun; Zhang, Yeting

A three-dimensional (3D) spatial index is required for real time applications of integrated organization and management in virtual geographic environments of above ground, underground, indoor and outdoor objects. Being one of the most promising methods, the R-tree spatial index has been paid increasing attention in 3D geospatial database management. Since the existing R-tree methods are usually limited by their weakness of low efficiency, due to the critical overlap of sibling nodes and the uneven size of nodes, this paper introduces the k-means clustering method and employs the 3D overlap volume, 3D coverage volume and the minimum bounding box shape value of nodes as the integrative grouping criteria. A new spatial cluster grouping algorithm and R-tree insertion algorithm is then proposed. Experimental analysis on comparative performance of spatial indexing shows that by the new method the overlap of R-tree sibling nodes is minimized drastically and a balance in the volumes of the nodes is maintained.

GIS Application System Design Applied to Information Monitoring

NASA Astrophysics Data System (ADS)

Qun, Zhou; Yujin, Yuan; Yuena, Kang

Natural environment information management system involves on-line instrument monitoring, data communications, database establishment, information management software development and so on. Its core lies in collecting effective and reliable environmental information, increasing utilization rate and sharing degree of environment information by advanced information technology, and maximizingly providing timely and scientific foundation for environmental monitoring and management. This thesis adopts C# plug-in application development and uses a set of complete embedded GIS component libraries and tools libraries provided by GIS Engine to finish the core of plug-in GIS application framework, namely, the design and implementation of framework host program and each functional plug-in, as well as the design and implementation of plug-in GIS application framework platform. This thesis adopts the advantages of development technique of dynamic plug-in loading configuration, quickly establishes GIS application by visualized component collaborative modeling and realizes GIS application integration. The developed platform is applicable to any application integration related to GIS application (ESRI platform) and can be as basis development platform of GIS application development.

Heterogeneous database integration in biomedicine.

PubMed

Sujansky, W

2001-08-01

The rapid expansion of biomedical knowledge, reduction in computing costs, and spread of internet access have created an ocean of electronic data. The decentralized nature of our scientific community and healthcare system, however, has resulted in a patchwork of diverse, or heterogeneous, database implementations, making access to and aggregation of data across databases very difficult. The database heterogeneity problem applies equally to clinical data describing individual patients and biological data characterizing our genome. Specifically, databases are highly heterogeneous with respect to the data models they employ, the data schemas they specify, the query languages they support, and the terminologies they recognize. Heterogeneous database systems attempt to unify disparate databases by providing uniform conceptual schemas that resolve representational heterogeneities, and by providing querying capabilities that aggregate and integrate distributed data. Research in this area has applied a variety of database and knowledge-based techniques, including semantic data modeling, ontology definition, query translation, query optimization, and terminology mapping. Existing systems have addressed heterogeneous database integration in the realms of molecular biology, hospital information systems, and application portability.

HNS-MS : Improving Member States preparedness to face an HNS pollution of the Marine System

NASA Astrophysics Data System (ADS)

Legrand, Sebastien; Le Floch, Stéphane; Aprin, Laurent; Parthenay, Valérie; Donnay, Eric; Parmentier, Koen; Ovidio, Fabrice; Schallier, Ronny; Poncet, Florence; Chataing, Sophie; Poupon, Emmanuelle; Hellouvry, Yann-Hervé

2016-04-01

When dealing with a HNS pollution incident, one of the priority requirements is the identification of the hazard and an assessment of the risk posed to the public and responder safety, the environment and socioeconomic assets upon which a state or coastal community depend. The primary factors which determine the safety, environmental and socioeconomic impact of the released substance(s) relate to their physico-chemical properties and fate in the environment. Until now, preparedness actions at various levels have primarily aimed at classifying the general environmental or public health hazard of an HNS, or at performing a risk analysis of HNS transported in European marine regions. Operational datasheets have been (MIDSIS-TROCS) or are being (MAR-CIS) developed collating detailed, substance-specific information for responders and covering information needs at the first stage of an incident. However, contrary to oil pollution preparedness and response tools, only few decision-support tools used by Member State authorities (Coastguard agencies or other) integrate 3D models that are able to simulate the drift, fate and behaviour of HNS spills in the marine environment. When they do, they usually consider simplified or steady-state environmental conditions. Moreover, the above-mentioned available HNS information is currently not sufficiently detailed or not suitably classified to be used as an input for an advanced HNS support decision tool. HNS-MS aims at developing a 'one-stop shop' integrated HNS decision-support tool that is able to predict the drift, behaviour and Fate of HNS spills under realistic environmental conditions and at providing key product information - drawing upon and in complement to existing studies and databases - to improve the understanding and evaluation of a HNS spill situation in the field and the environmental and safety-related issues at stake. The 3D HNS drift and fate model and decision-support tool will also be useful at the preparedness stage. The expected results will be an operational HNS decision-support tool (prototype) for the Bonn Agreement area that can also be viewed as a demonstrator tool for other European marine regions. The developed tool will have a similar operational level as OSERIT, the Belgian oil spill drift model. The HNS decision-support tool will integrate the following features: 1. A database containing the physico-chemical parameters needed to compute the behaviour in the marine environment of 100+ relevant HNS; 2. A database of environmental and socioeconomic HNS-sensitive features; 3. A three dimensional HNS spill drift and fate model able to simulate HNS behaviour in the marine environment (including floaters, sinkers, evaporators and dissolvers). 4. A user-friendly web-based interface allowing Coastguard stations to launch a HNS drift simulation and visualize post-processed results in support of an incident evaluation and decision-making process. In this contribution, we will present the methodology followed to develop these four features.

A network identity authentication system based on Fingerprint identification technology

NASA Astrophysics Data System (ADS)

Xia, Hong-Bin; Xu, Wen-Bo; Liu, Yuan

2005-10-01

Fingerprint verification is one of the most reliable personal identification methods. However, most of the automatic fingerprint identification system (AFIS) is not run via Internet/Intranet environment to meet today's increasing Electric commerce requirements. This paper describes the design and implementation of the archetype system of identity authentication based on fingerprint biometrics technology, and the system can run via Internet environment. And in our system the COM and ASP technology are used to integrate Fingerprint technology with Web database technology, The Fingerprint image preprocessing algorithms are programmed into COM, which deployed on the internet information server. The system's design and structure are proposed, and the key points are discussed. The prototype system of identity authentication based on Fingerprint have been successfully tested and evaluated on our university's distant education applications in an internet environment.

A Computational framework for telemedicine.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foster, I.; von Laszewski, G.; Thiruvathukal, G. K.

1998-07-01

Emerging telemedicine applications require the ability to exploit diverse and geographically distributed resources. Highspeed networks are used to integrate advanced visualization devices, sophisticated instruments, large databases, archival storage devices, PCs, workstations, and supercomputers. This form of telemedical environment is similar to networked virtual supercomputers, also known as metacomputers. Metacomputers are already being used in many scientific application areas. In this article, we analyze requirements necessary for a telemedical computing infrastructure and compare them with requirements found in a typical metacomputing environment. We will show that metacomputing environments can be used to enable a more powerful and unified computational infrastructure formore » telemedicine. The Globus metacomputing toolkit can provide the necessary low level mechanisms to enable a large scale telemedical infrastructure. The Globus toolkit components are designed in a modular fashion and can be extended to support the specific requirements for telemedicine.« less

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models.

PubMed

Ye, Chao; Xu, Nan; Dong, Chuan; Ye, Yuannong; Zou, Xuan; Chen, Xiulai; Guo, Fengbiao; Liu, Liming

2017-04-07

Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.

Monitoring Wildlife Interactions with Their Environment: An Interdisciplinary Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Charles-Smith, Lauren E.; Domnguez, Ignacio X.; Fornaro, Robert J.

In a rapidly changing world, wildlife ecologists strive to correctly model and predict complex relationships between animals and their environment, which facilitates management decisions impacting public policy to conserve and protect delicate ecosystems. Recent advances in monitoring systems span scientific domains, including animal and weather monitoring devices and landscape classification mapping techniques. The current challenge is how to combine and use detailed output from various sources to address questions spanning multiple disciplines. WolfScout wildlife and weather tracking system is a software tool capable of filling this niche. WolfScout automates integration of the latest technological advances in wildlife GPS collars, weathermore » stations, drought conditions, and severe weather reports, and animal demographic information. The WolfScout database stores a variety of classified landscape maps including natural and manmade features. Additionally, WolfScout’s spatial database management system allows users to calculate distances between animals’ location and landscape characteristics, which are linked to the best approximation of environmental conditions at the animal’s location during the interaction. Through a secure website, data are exported in formats compatible with multiple software programs including R and ArcGIS. The WolfScout design promotes interoperability in data, between researchers, and software applications while standardizing analyses of animal interactions with their environment.« less

E-MSD: an integrated data resource for bioinformatics

PubMed Central

Velankar, S.; McNeil, P.; Mittard-Runte, V.; Suarez, A.; Barrell, D.; Apweiler, R.; Henrick, K.

2005-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the ‘Structure Integration with Function, Taxonomy and Sequences (SIFTS)’ initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group. PMID:15608192

Probabilistic Models for Solar Particle Events

NASA Technical Reports Server (NTRS)

Adams, James H., Jr.; Dietrich, W. F.; Xapsos, M. A.; Welton, A. M.

2009-01-01

Probabilistic Models of Solar Particle Events (SPEs) are used in space mission design studies to provide a description of the worst-case radiation environment that the mission must be designed to tolerate.The models determine the worst-case environment using a description of the mission and a user-specified confidence level that the provided environment will not be exceeded. This poster will focus on completing the existing suite of models by developing models for peak flux and event-integrated fluence elemental spectra for the Z>2 elements. It will also discuss methods to take into account uncertainties in the data base and the uncertainties resulting from the limited number of solar particle events in the database. These new probabilistic models are based on an extensive survey of SPE measurements of peak and event-integrated elemental differential energy spectra. Attempts are made to fit the measured spectra with eight different published models. The model giving the best fit to each spectrum is chosen and used to represent that spectrum for any energy in the energy range covered by the measurements. The set of all such spectral representations for each element is then used to determine the worst case spectrum as a function of confidence level. The spectral representation that best fits these worst case spectra is found and its dependence on confidence level is parameterized. This procedure creates probabilistic models for the peak and event-integrated spectra.

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

NASA Technical Reports Server (NTRS)

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.

Data Sharing in Astrobiology: the Astrobiology Habitable Environments Database (AHED)

NASA Astrophysics Data System (ADS)

Bristow, T.; Lafuente Valverde, B.; Keller, R.; Stone, N.; Downs, R. T.; Blake, D. F.; Fonda, M.; Pires, A.

2016-12-01

Astrobiology is a multidisciplinary area of scientific research focused on studying the origins of life on Earth and the conditions under which life might have emerged elsewhere in the universe. The understanding of complex questions in astrobiology requires integration and analysis of data spanning a range of disciplines including biology, chemistry, geology, astronomy and planetary science. However, the lack of a centralized repository makes it difficult for astrobiology teams to share data and benefit from resultant synergies. Moreover, in recent years, federal agencies are requiring that results of any federally funded scientific research must be available and useful for the public and the science community. Astrobiology, as any other scientific discipline, needs to respond to these mandates. The Astrobiology Habitable Environments Database (AHED) is a central, high quality, long-term searchable repository designed to help the community by promoting the integration and sharing of all the data generated by these diverse disciplines. AHED provides public and open-access to astrobiology-related research data through a user-managed web portal implemented using the open-source software The Open Data Repository's (ODR) Data Publisher [1]. ODR-DP provides a user-friendly interface that research teams or individual scientists can use to design, populate and manage their own databases or laboratory notebooks according to the characteristics of their data. AHED is then a collection of databases housed in the ODR framework that store information about samples, along with associated measurements, analyses, and contextual information about field sites where samples were collected, the instruments or equipment used for analysis, and people and institutions involved in their collection. Advanced graphics are implemented together with advanced online tools for data analysis (e.g. R, MATLAB, Project Jupyter-http://jupyter.org). A permissions system will be put in place so that as data are being actively collected and interpreted, they will remain proprietary. A citation system will allow research data to be used and appropriately referenced by other researchers after the data are made public. This project is supported by SERA and NASA NNX11AP82A, MSL. [1] Stone et al. (2016) AGU, submitted.

PTGBase: an integrated database to study tandem duplicated genes in plants.

PubMed

Yu, Jingyin; Ke, Tao; Tehrim, Sadia; Sun, Fengming; Liao, Boshou; Hua, Wei

2015-01-01

Tandem duplication is a wide-spread phenomenon in plant genomes and plays significant roles in evolution and adaptation to changing environments. Tandem duplicated genes related to certain functions will lead to the expansion of gene families and bring increase of gene dosage in the form of gene cluster arrays. Many tandem duplication events have been studied in plant genomes; yet, there is a surprising shortage of efforts to systematically present the integration of large amounts of information about publicly deposited tandem duplicated gene data across the plant kingdom. To address this shortcoming, we developed the first plant tandem duplicated genes database, PTGBase. It delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly sequenced species alike. Across these genomes, 54 130 tandem duplicated gene clusters (129 652 genes) are presented in the database. Each tandem array, as well as its member genes, is characterized in complete detail. Tandem duplicated genes in PTGBase can be explored through browsing or searching by identifiers or keywords of functional annotation and sequence similarity. Users can download tandem duplicated gene arrays easily to any scale, up to the complete annotation data set for an entire plant genome. PTGBase will be updated regularly with newly sequenced plant species as they become available. © The Author(s) 2015. Published by Oxford University Press.

MV-OPES: Multivalued-Order Preserving Encryption Scheme: A Novel Scheme for Encrypting Integer Value to Many Different Values

NASA Astrophysics Data System (ADS)

Kadhem, Hasan; Amagasa, Toshiyuki; Kitagawa, Hiroyuki

Encryption can provide strong security for sensitive data against inside and outside attacks. This is especially true in the “Database as Service” model, where confidentiality and privacy are important issues for the client. In fact, existing encryption approaches are vulnerable to a statistical attack because each value is encrypted to another fixed value. This paper presents a novel database encryption scheme called MV-OPES (Multivalued — Order Preserving Encryption Scheme), which allows privacy-preserving queries over encrypted databases with an improved security level. Our idea is to encrypt a value to different multiple values to prevent statistical attacks. At the same time, MV-OPES preserves the order of the integer values to allow comparison operations to be directly applied on encrypted data. Using calculated distance (range), we propose a novel method that allows a join query between relations based on inequality over encrypted values. We also present techniques to offload query execution load to a database server as much as possible, thereby making a better use of server resources in a database outsourcing environment. Our scheme can easily be integrated with current database systems as it is designed to work with existing indexing structures. It is robust against statistical attack and the estimation of true values. MV-OPES experiments show that security for sensitive data can be achieved with reasonable overhead, establishing the practicability of the scheme.

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform.

PubMed

Li, Po-E; Lo, Chien-Chi; Anderson, Joseph J; Davenport, Karen W; Bishop-Lilly, Kimberly A; Xu, Yan; Ahmed, Sanaa; Feng, Shihai; Mokashi, Vishwesh P; Chain, Patrick S G

2017-01-09

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Review article: Staff perception of the emergency department working environment: Integrative review of the literature

PubMed Central

Abraham, Louisa; Greenslade, Jaimi; Thom, Ogilvie; Carlstrom, Eric; Wallis, Marianne; Crilly, Julia

2016-01-01

Abstract Employees in EDs report increasing role overload because of critical staff shortages, budgetary cuts and increased patient numbers and acuity. Such overload could compromise staff satisfaction with their working environment. This integrative review identifies, synthesises and evaluates current research around staff perceptions of the working conditions in EDs. A systematic search of relevant databases, using MeSH descriptors ED/EDs, Emergency room/s, ER/s, or A&E coupled with (and) working environment, working condition/s, staff perception/s, as well as reference chaining was conducted. We identified 31 key studies that were evaluated using the mixed methods assessment tool (MMAT). These comprised 24 quantitative‐descriptive studies, four mixed descriptive/comparative (non‐randomised controlled trial) studies and three qualitative studies. Studies included varied widely in quality with MMAT scores ranging from 0% to 100%. A key finding was that perceptions of working environment varied across clinical staff and study location, but that high levels of autonomy and teamwork offset stress around high pressure and high volume workloads. The large range of tools used to assess staff perception of working environment limits the comparability of the studies. A dearth of intervention studies around enhancing working environments in EDs limits the capacity to recommend evidence‐based interventions to improve staff morale. © 2016 The Authors. Emergency Medicine Australasia published by John Wiley & Sons Australia, Ltd on behalf of Australasian College for Emergency Medicine and Australasian Society for Emergency Medicine PMID:26784282

Representation and Integration of Scientific Information

NASA Technical Reports Server (NTRS)

1998-01-01

The objective of this Joint Research Interchange with NASA-Ames was to investigate how the Tsimmis technology could be used to represent and integrate scientific information. The main goal of the Tsimmis project is to allow a decision maker to find information of interest from such sources, fuse it, and process it (e.g., summarize it, visualize it, discover trends). Another important goal is the easy incorporation of new sources, as well the ability to deal with sources whose structure or services evolve. During the Interchange we had research meetings approximately every month or two. The funds provided by NASA supported work that lead to the following two papers: Fusion Queries over Internet Databases; Efficient Query Subscription Processing in a Multicast Environment.

CryoTran user's manual, version 1.0

NASA Technical Reports Server (NTRS)

Cowgill, Glenn R.; Chato, David J.; Saad, Ehab

1989-01-01

The development of cryogenic fluid management systems for space operation is a major portion of the efforts of the Cryogenic Fluids Technology Office (CFTO) at the NASA Lewis Research Center. Analytical models are a necessary part of experimental programs which are used to verify the results of experiments and are also used as a predictor for parametric studies. The CryoTran computer program is a bridge to obtain analytical results. The object of CryoTran is to coordinate these separate analyses into an integrated framework with a user-friendly interface and a common cryogenic property database. CryoTran is an integrated software system designed to help solve a diverse set of problems involving cryogenic fluid storage and transfer in both ground and low-g environments.

BioWarehouse: a bioinformatics database warehouse toolkit

PubMed Central

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

2006-01-01

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 database integration problem for bioinformatics. PMID:16556315

BioWarehouse: a bioinformatics database warehouse toolkit.

PubMed

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.

Towards G2G: Systems of Technology Database Systems

NASA Technical Reports Server (NTRS)

Maluf, David A.; Bell, David

2005-01-01

We present an approach and methodology for developing Government-to-Government (G2G) Systems of Technology Database Systems. G2G will deliver technologies for distributed and remote integration of technology data for internal use in analysis and planning as well as for external communications. G2G enables NASA managers, engineers, operational teams and information systems to "compose" technology roadmaps and plans by selecting, combining, extending, specializing and modifying components of technology database systems. G2G will interoperate information and knowledge that is distributed across organizational entities involved that is ideal for NASA future Exploration Enterprise. Key contributions of the G2G system will include the creation of an integrated approach to sustain effective management of technology investments that supports the ability of various technology database systems to be independently managed. The integration technology will comply with emerging open standards. Applications can thus be customized for local needs while enabling an integrated management of technology approach that serves the global needs of NASA. The G2G capabilities will use NASA s breakthrough in database "composition" and integration technology, will use and advance emerging open standards, and will use commercial information technologies to enable effective System of Technology Database systems.

Building a multi-scaled geospatial temporal ecology database from disparate data sources: fostering open science and data reuse.

PubMed

Soranno, Patricia A; Bissell, Edward G; Cheruvelil, Kendra S; Christel, Samuel T; Collins, Sarah M; Fergus, C Emi; Filstrup, Christopher T; Lapierre, Jean-Francois; Lottig, Noah R; Oliver, Samantha K; Scott, Caren E; Smith, Nicole J; Stopyak, Scott; Yuan, Shuai; Bremigan, Mary Tate; Downing, John A; Gries, Corinna; Henry, Emily N; Skaff, Nick K; Stanley, Emily H; Stow, Craig A; Tan, Pang-Ning; Wagner, Tyler; Webster, Katherine E

2015-01-01

Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km(2)). LAGOS includes two modules: LAGOSGEO, with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOSLIMNO, with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.

Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science through data reuse

USGS Publications Warehouse

Soranno, Patricia A.; Bissell, E.G.; Cheruvelil, Kendra S.; Christel, Samuel T.; Collins, Sarah M.; Fergus, C. Emi; Filstrup, Christopher T.; Lapierre, Jean-Francois; Lotting, Noah R.; Oliver, Samantha K.; Scott, Caren E.; Smith, Nicole J.; Stopyak, Scott; Yuan, Shuai; Bremigan, Mary Tate; Downing, John A.; Gries, Corinna; Henry, Emily N.; Skaff, Nick K.; Stanley, Emily H.; Stow, Craig A.; Tan, Pang-Ning; Wagner, Tyler; Webster, Katherine E.

2015-01-01

Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km2). LAGOS includes two modules: LAGOSGEO, with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOSLIMNO, with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.

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

PubMed

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.

Consistent Query Answering of Conjunctive Queries under Primary Key Constraints

ERIC Educational Resources Information Center

Pema, Enela

2014-01-01

An inconsistent database is a database that violates one or more of its integrity constraints. In reality, violations of integrity constraints arise frequently under several different circumstances. Inconsistent databases have long posed the challenge to develop suitable tools for meaningful query answering. A principled approach for querying…

Enhancing Knowledge Integration: An Information System Capstone Project

ERIC Educational Resources Information Center

Steiger, David M.

2009-01-01

This database project focuses on learning through knowledge integration; i.e., sharing and applying specialized (database) knowledge within a group, and combining it with other business knowledge to create new knowledge. Specifically, the Tiny Tots, Inc. project described below requires students to design, build, and instantiate a database system…

Measurement and Characterization of Space Shuttle Solid Rocket Motor Plume Acoustics

NASA Technical Reports Server (NTRS)

Kenny, Jeremy; Hobbs, Chris; Plotkin, Ken; Pilkey, Debbie

2009-01-01

Lift-off acoustic environments generated by the future Ares I launch vehicle are assessed by the NASA Marshall Space Flight Center (MSFC) acoustics team using several prediction tools. This acoustic environment is directly caused by the Ares I First Stage booster, powered by the five-segment Reusable Solid Rocket Motor (RSRMV). The RSRMV is a larger-thrust derivative design from the currently used Space Shuttle solid rocket motor, the Reusable Solid Rocket Motor (RSRM). Lift-off acoustics is an integral part of the composite launch vibration environment affecting the Ares launch vehicle and must be assessed to help generate hardware qualification levels and ensure structural integrity of the vehicle during launch and lift-off. Available prediction tools that use free field noise source spectrums as a starting point for generation of lift-off acoustic environments are described in the monograph NASA SP-8072: "Acoustic Loads Generated by the Propulsion System." This monograph uses a reference database for free field noise source spectrums which consist of subscale rocket motor firings, oriented in horizontal static configurations. The phrase "subscale" is appropriate, since the thrust levels of rockets in the reference database are orders of magnitude lower than the current design thrust for the Ares launch family. Thus, extrapolation is needed to extend the various reference curves to match Ares-scale acoustic levels. This extrapolation process yields a subsequent amount of uncertainty added upon the acoustic environment predictions. As the Ares launch vehicle design schedule progresses, it is important to take every opportunity to lower prediction uncertainty and subsequently increase prediction accuracy. Never before in NASA s history has plume acoustics been measured for large scale solid rocket motors. Approximately twice a year, the RSRM prime vendor, ATK Launch Systems, static fires an assembled RSRM motor in a horizontal configuration at their test facility in Utah. The remaining RSRM static firings will take place on elevated terrain, with the nozzle exit plume being mostly undeflected and the landscape allowing placement of microphones within direct line of sight to the exhaust plume. These measurements will help assess the current extrapolation process by direct comparison between subscale and full scale solid rocket motor data.

Construction of a linked health and social care database resource--lessons on process, content and culture.

PubMed

Witham, Miles D; Frost, Helen; McMurdo, Marion; Donnan, Peter T; McGilchrist, Mark

2015-01-01

Combining routinely collected health and social care data on older people is essential to advance both service delivery and research for this client group. Little data is available on how to combine health and social care data; this article provides an overview of a successful data linkage process and discusses potential barriers to executing such projects. We successfully obtained and linked data on older people within Dundee from three sources: Dundee Social Work Department database (30,000 individuals aged 65 years and over), healthcare data held on NHS Tayside patients by the Health Informatics Centre (400,000 individuals), Dundee, and the Dundee of Medicine for the Elderly rehabilitation database (4300 individuals). Data were linked, anonymized and transferred to a Safe Haven environment to ensuring confidentiality and strict access control. Challenges were faced around workflows, culture and documentation. Exploiting the resultant data set raises further challenges centered on database documentation, understanding the way data were collected, dealing with missing data, data validity and collection at different time periods. Routinely collected health and social care data sets can be linked, but significant process barriers must be overcome to allow successful linkage and integration of data and its full exploitation.

Attributes of clinical leadership in contemporary nursing: an integrative review.

PubMed

Mannix, Judy; Wilkes, Lesley; Daly, John

2013-08-01

Effective clinical leadership is offered as the key to healthy, functional and supportive work environments for nurses and other health professionals. However, as a concept it lacks a standard definition and is poorly understood. This paper reports on an integrative review undertaken to uncover current understandings of defining attributes of contemporary clinical leadership in nursing. Data collection involved a search of relevant electronic databases for a 10-year period. Keywords for the search were 'clinical leadership' and 'nursing'. Ten research papers met the inclusion criteria for the integrative review. Analysis of these studies indicated clinical leadership attributes had a clinical focus, a follower/team focus or a personal qualities focus; attributes necessary to sustain supportive workplaces and build the capacity and resilience of nursing workforces. The small number of research-based studies yielded for the review indicates the need for further research in the area of clinical leadership.

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

PubMed

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.

An integrated biomedical telemetry system for sleep monitoring employing a portable body area network of sensors (SENSATION).

PubMed

Astaras, Alexander; Arvanitidou, Marina; Chouvarda, Ioanna; Kilintzis, Vassilis; Koutkias, Vassilis; Sanchez, Eduardo Monton; Stalidis, George; Triantafyllidis, Andreas; Maglaveras, Nicos

2008-01-01

A flexible, scaleable and cost-effective medical telemetry system is described for monitoring sleep-related disorders in the home environment. The system was designed and built for real-time data acquisition and processing, allowing for additional use in intensive care unit scenarios where rapid medical response is required in case of emergency. It comprises a wearable body area network of Zigbee-compatible wireless sensors worn by the subject, a central database repository residing in the medical centre and thin client workstations located at the subject's home and in the clinician's office. The system supports heterogeneous setup configurations, involving a variety of data acquisition sensors to suit several medical applications. All telemetry data is securely transferred and stored in the central database under the clinicians' ownership and control.

Virtual Manufacturing Techniques Designed and Applied to Manufacturing Activities in the Manufacturing Integration and Technology Branch

NASA Technical Reports Server (NTRS)

Shearrow, Charles A.

1999-01-01

One of the identified goals of EM3 is to implement virtual manufacturing by the time the year 2000 has ended. To realize this goal of a true virtual manufacturing enterprise the initial development of a machinability database and the infrastructure must be completed. This will consist of the containment of the existing EM-NET problems and developing machine, tooling, and common materials databases. To integrate the virtual manufacturing enterprise with normal day to day operations the development of a parallel virtual manufacturing machinability database, virtual manufacturing database, virtual manufacturing paradigm, implementation/integration procedure, and testable verification models must be constructed. Common and virtual machinability databases will include the four distinct areas of machine tools, available tooling, common machine tool loads, and a materials database. The machine tools database will include the machine envelope, special machine attachments, tooling capacity, location within NASA-JSC or with a contractor, and availability/scheduling. The tooling database will include available standard tooling, custom in-house tooling, tool properties, and availability. The common materials database will include materials thickness ranges, strengths, types, and their availability. The virtual manufacturing databases will consist of virtual machines and virtual tooling directly related to the common and machinability databases. The items to be completed are the design and construction of the machinability databases, virtual manufacturing paradigm for NASA-JSC, implementation timeline, VNC model of one bridge mill and troubleshoot existing software and hardware problems with EN4NET. The final step of this virtual manufacturing project will be to integrate other production sites into the databases bringing JSC's EM3 into a position of becoming a clearing house for NASA's digital manufacturing needs creating a true virtual manufacturing enterprise.

Cross-correlation between the controlled collision environment and real-world motor vehicle collisions: Evaluating the protection of the thoracic side airbag.

PubMed

Gaylor, Luke; Junge, Mirko; Abanteriba, Sylvester

2018-05-19

Thoracic side airbags (tSABs) were integrated into the vehicle fleet to attenuate and distribute forces on the occupant's chest and abdomen, dissipate the impact energy, and move the occupant away from the intruding structure, all of which reduce the risk of injury. This research piece investigates and evaluates the safety performance of the airbag unit by cross-correlating data from a controlled collision environment with field data. We focus exclusively on vehicle-vehicle lateral impacts from the NHTSA's Vehicle Crash Test Database and NASS-CDS database, which are replicated in the controlled environment by the (crabbed) barrier impact. Similar collisions with and without seat-embedded tSABs are matched to each other and the injury risks are compared. Results indicated that dummy-based thoracic injury metrics were significantly lower with tSAB exposure (P <.001). Yet, when the controlled collision environment data were cross-correlated with NASS-CDS collisions, deployment of the tSAB indicated no association with thoracic injury (tho. MAIS 2+ unadjusted relative risk [RR] = 1.14; 90% confidence interval [CI], 0.80-1.62; tho. MAIS 3+ unadjusted RR = 1.12; 90% CI, 0.76-1.65). The data from the controlled collision environment indicated an unequivocal benefit provided by the thoracic side airbag for the crash dummy; however, the real-world collisions demonstrate that no benefit is provided to the occupant. This has resulted from a noncorrelation between the crash test/dummy-based design taking the abstracting process too far to represent the real-world collision scenario.

Designing a low cost bedside workstation for intensive care units.

PubMed Central

Michel, A.; Zörb, L.; Dudeck, J.

1996-01-01

The paper describes the design and implementation of a software architecture for a low cost bedside workstation for intensive care units. The development is fully integrated into the information infrastructure of the existing hospital information system (HIS) at the University Hospital of Giessen. It provides cost efficient and reliable access for data entry and review from the HIS database from within patient rooms, even in very space limited environments. The architecture further supports automatical data input from medical devices. First results from three different intensive care units are reported. PMID:8947771

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

PubMed Central

2010-01-01

Background Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api. PMID:21083943

Neural networks to classify speaker independent isolated words recorded in radio car environments

NASA Astrophysics Data System (ADS)

Alippi, C.; Simeoni, M.; Torri, V.

1993-02-01

Many applications, in particular the ones requiring nonlinear signal processing, have proved Artificial Neural Networks (ANN's) to be invaluable tools for model free estimation. The classifying abilities of ANN's are addressed by testing their performance in a speaker independent word recognition application. A real world case requiring implementation of compact integrated devices is taken into account: the classification of isolated words in radio car environment. A multispeaker database of isolated words was recorded in different environments. Data were first processed to determinate the boundaries of each word and then to extract speech features, the latter accomplished by using cepstral coefficient representation, log area ratios and filters bank techniques. Multilayered perceptron and adaptive vector quantization neural paradigms were tested to find a reasonable compromise between performances and network simplicity, fundamental requirement for the implementation of compact real time running neural devices.

[Integrated use of data bases to map manufacturing processes involving exposure to carcinogens in the Piedmont Region: the example of formaldehyde].

PubMed

Falcone, U; Gilardi, Luisella; Pasqualini, O; Santoro, S; Coffano, Elena

2010-01-01

Exposure to carcinogens is still widespread in working environments. For the purpose of defining priority of interventions, it is necessary to estimate the number and the geographic distribution of workers potentially exposed to carcinogens. It could therefore be useful to test the use of tools and information sources already available in order to map the distribution of exposure to carcinogens. Formaldehyde is suggested as an example of an occupational carcinogen in this study. The study aimed at verifying and investigating the potential of 3 integrated databases: MATline, CAREX, and company databases resulting from occupational accident and disease claims (INAIL), in order to estimate the number of workers exposed to formaldehyde and map their distribution in the Piedmont Region. The list of manufacturing processes involving exposure to formaldehyde was sorted by MIATline; for each process the number of firms and employees were obtained from the INAIL archives. By applying the prevalence of exposed workers obtained with CAREX, an estimate of exposure for each process was determined. A map of the distribution of employees associated with a specific process was produced using ArcView GIS software. It was estimated that more than 13,000 employees are exposed to formaldehyde in the Piedmont Region. The manufacture of furniture was identified as the process with the highest number of workers exposed to formaldehyde (3,130),followed by metal workers (2,301 exposed) and synthetic resin processing (1,391 exposed). The results obtained from the integrated use of databases provide a basis for defining priority of preventive interventions required in the industrial processes involving exposure to carcinogens in the Piedmont Region.

The Application of Lidar to Synthetic Vision System Integrity

NASA Technical Reports Server (NTRS)

Campbell, Jacob L.; UijtdeHaag, Maarten; Vadlamani, Ananth; Young, Steve

2003-01-01

One goal in the development of a Synthetic Vision System (SVS) is to create a system that can be certified by the Federal Aviation Administration (FAA) for use at various flight criticality levels. As part of NASA s Aviation Safety Program, Ohio University and NASA Langley have been involved in the research and development of real-time terrain database integrity monitors for SVS. Integrity monitors based on a consistency check with onboard sensors may be required if the inherent terrain database integrity is not sufficient for a particular operation. Sensors such as the radar altimeter and weather radar, which are available on most commercial aircraft, are currently being investigated for use in a real-time terrain database integrity monitor. This paper introduces the concept of using a Light Detection And Ranging (LiDAR) sensor as part of a real-time terrain database integrity monitor. A LiDAR system consists of a scanning laser ranger, an inertial measurement unit (IMU), and a Global Positioning System (GPS) receiver. Information from these three sensors can be combined to generate synthesized terrain models (profiles), which can then be compared to the stored SVS terrain model. This paper discusses an initial performance evaluation of the LiDAR-based terrain database integrity monitor using LiDAR data collected over Reno, Nevada. The paper will address the consistency checking mechanism and test statistic, sensitivity to position errors, and a comparison of the LiDAR-based integrity monitor to a radar altimeter-based integrity monitor.

Integration of Information Retrieval and Database Management Systems.

ERIC Educational Resources Information Center

Deogun, Jitender S.; Raghavan, Vijay V.

1988-01-01

Discusses the motivation for integrating information retrieval and database management systems, and proposes a probabilistic retrieval model in which records in a file may be composed of attributes (formatted data items) and descriptors (content indicators). The details and resolutions of difficulties involved in integrating such systems are…

Microplastics in the marine environment: Current trends and future perspectives.

PubMed

Barboza, Luís Gabriel Antão; Gimenez, Barbara Carolina Garcia

2015-08-15

Over the last decade, the presence of microplastics on marine environments has become an important environmental concern and focus of interest of many researches. Thus, to provide a more integrated view of the research trends regarding this topic, we use a scientometric approach to systematically assess and quantify advances in knowledge related to microplastics in the marine environment. The papers that we used for our assessment were obtained from the database Thomson Reuters (ISI Web of Science), between 2004 and 2014. Our results reveal the overall research performance in the study area of microplastics present in the marine environment over the past decade as a newly developed research field. It has been recognized that there are several important issues that should be investigated. Toward that end, based on the suggested directions on all papers reviewed, we point out areas/topics of interest that may guide future work in the coming years. Copyright © 2015 Elsevier Ltd. All rights reserved.

The NCBI BioSystems database.

PubMed

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.

The Chemical Aquatic Fate and Effects database (CAFE), a tool that supports assessments of chemical spills in aquatic environments.

PubMed

Bejarano, Adriana C; Farr, James K; Jenne, Polly; Chu, Valerie; Hielscher, Al

2016-06-01

The Chemical Aquatic Fate and Effects (CAFE) database is a centralized repository that allows for rapid and unrestricted access to data. Information in CAFE is integrated into a user-friendly tool with modules containing fate and effects data for 32 377 and 4498 chemicals, respectively. Toxicity data are summarized in the form of species sensitivity distributions (SSDs) with associated 1st and 5th percentile hazard concentrations (HCs). An assessment of data availability relative to reported chemical incidents showed that CAFE had fate and toxicity data for 32 and 20 chemicals, respectively, of 55 chemicals reported in the US National Response Center database (2000-2014), and fate and toxicity data for 86 and 103, respectively, of 205 chemicals reported by the National Oceanic and Atmospheric Administration (2003-2014). Modeled environmental concentrations of 2 hypothetical spills (acrylonitrile, 625 barrels; and denatured ethanol, 857 barrels) were used to demonstrate CAFE's practical application. Most species in the 24-h SSD could be potentially impacted by acrylonitrile and denatured ethanol during the first 35 min and 15 h post spill, respectively, with concentrations falling below their HC5s (17 mg/L and 2676 mg/L) at 45 min and 60 h post spill, respectively. Comparisons of CAFE-based versus published HC5 values for 100 chemicals showed that nearly half of values were within a 2-fold difference, with a relatively small number of comparisons exceeding a 10-fold difference. The development of CAFE facilitates access to relevant environmental information, with potential uses likely expanding beyond those related to assessment of spills in aquatic environments. Environ Toxicol Chem 2016;35:1576-1586. © 2015 SETAC. © 2015 SETAC.

Rapid HIS, RIS, PACS Integration Using Graphical CASE Tools

NASA Astrophysics Data System (ADS)

Taira, Ricky K.; Breant, Claudine M.; Stepczyk, Frank M.; Kho, Hwa T.; Valentino, Daniel J.; Tashima, Gregory H.; Materna, Anthony T.

1994-05-01

We describe the clinical requirements of the integrated federation of databases and present our client-mediator-server design. The main body of the paper describes five important aspects of integrating information systems: (1) global schema design, (2) establishing sessions with remote database servers, (3) development of schema translators, (4) integration of global system triggers, and (5) development of job workflow scripts.

A Model of Object-Identities and Values

DTIC Science & Technology

1990-02-23

integrity constraints in its construct, which provides the natural integration of the logical database model and the object-oriented database model. 20...portions are integrated by a simple commutative diagram of modeling functions. The formalism includes the expression of integrity constraints in its ...38 .5.2.2 The (Concept Model and Its Semantics .. .. .. .. ... .... ... .. 40 5.2.3 Two K%.inds of Predicates

Navigation integrity monitoring and obstacle detection for enhanced-vision systems

NASA Astrophysics Data System (ADS)

Korn, Bernd; Doehler, Hans-Ullrich; Hecker, Peter

2001-08-01

Typically, Enhanced Vision (EV) systems consist of two main parts, sensor vision and synthetic vision. Synthetic vision usually generates a virtual out-the-window view using databases and accurate navigation data, e. g. provided by differential GPS (DGPS). The reliability of the synthetic vision highly depends on both, the accuracy of the used database and the integrity of the navigation data. But especially in GPS based systems, the integrity of the navigation can't be guaranteed. Furthermore, only objects that are stored in the database can be displayed to the pilot. Consequently, unexpected obstacles are invisible and this might cause severe problems. Therefore, additional information has to be extracted from sensor data to overcome these problems. In particular, the sensor data analysis has to identify obstacles and has to monitor the integrity of databases and navigation. Furthermore, if a lack of integrity arises, navigation data, e.g. the relative position of runway and aircraft, has to be extracted directly from the sensor data. The main contribution of this paper is about the realization of these three sensor data analysis tasks within our EV system, which uses the HiVision 35 GHz MMW radar of EADS, Ulm as the primary EV sensor. For the integrity monitoring, objects extracted from radar images are registered with both database objects and objects (e. g. other aircrafts) transmitted via data link. This results in a classification into known and unknown radar image objects and consequently, in a validation of the integrity of database and navigation. Furthermore, special runway structures are searched for in the radar image where they should appear. The outcome of this runway check contributes to the integrity analysis, too. Concurrent to this investigation a radar image based navigation is performed without using neither precision navigation nor detailed database information to determine the aircraft's position relative to the runway. The performance of our approach is demonstrated with real data acquired during extensive flight tests to several airports in Northern Germany.

A national environmental monitoring system to support the Moroccan sustainable development strategy

NASA Astrophysics Data System (ADS)

Mourhir, A.; Rachidi, T.

2010-12-01

Morocco is a mountainous country, subject to both marine and Saharan influences. The increase in population has led to an increase of the gross domestic product (GDP), which accentuated by inadequate resource management, has been accompanied by the degradation of the environment. The annual cost of environmental damage has been estimated at nearly eight percent of Morocco’s GDP. Morocco is a country that has scarce natural resources, especially arable land and water. In recent years, intensive agricultural production, large-scale irrigation schemes, industrialization, and urbanization have been creating serious problems. The country has faced severe air, water and soil pollution, environmental health problems, deforestation and soil erosion. The country is very vulnerable to impacts of global climate change. Morocco’s approach to sustainable development (SD) is mainly environmental. The two main documents for Morocco’s SD strategy are the National Strategy for the Protection of the Environment and Sustainable Development (SNPEDD), 1995, and the National Plan of Action for the Environment (PANE), 1998. SNPEDD’s main objective is the integration and strengthening of environmental concerns in economic development activities. The activities for the formulation and implementation of the strategy include: a) studies on the state of the Moroccan environment; b) formulation of the PANE; c) preparation of a sensitization program on environmental issues and the implementation of a database and information system on the environment; (d) preparation of regional and local environmental monographies. The aim of the current work is to create an information system as an approach to complex sustainability analyses at the national level using GIS technologies. This information system includes the following: 1.Development of a database of SD indicators and historical data. Morocco has been involved in the working framework of the Mediterranean Commission for Sustainable Development to set up an indicator system (IDD) specific to Morocco. The National Committee for Sustainable Development Indicators was set up to create a program to test and validate the IDD. A number of indicators have been chosen and the Moroccan government’s Environment Department has made the database available through a publication and via the internet, which will be updated regularly. The database will be organized to facilitate ad hoc query and analysis. 2.Development of a GIS structure to help map plans for achieving successful management strategies that are sustainable both at the regional and national levels. 3.Visualization and analysis tools for spatial and temporal changes of environmental indicators to help manage growth and change.

Integration of Irma tactical scene generator into directed-energy weapon system simulation

NASA Astrophysics Data System (ADS)

Owens, Monte A.; Cole, Madison B., III; Laine, Mark R.

2003-08-01

Integrated high-fidelity physics-based simulations that include engagement models, image generation, electro-optical hardware models and control system algorithms have previously been developed by Boeing-SVS for various tracking and pointing systems. These simulations, however, had always used images with featureless or random backgrounds and simple target geometries. With the requirement to engage tactical ground targets in the presence of cluttered backgrounds, a new type of scene generation tool was required to fully evaluate system performance in this challenging environment. To answer this need, Irma was integrated into the existing suite of Boeing-SVS simulation tools, allowing scene generation capabilities with unprecedented realism. Irma is a US Air Force research tool used for high-resolution rendering and prediction of target and background signatures. The MATLAB/Simulink-based simulation achieves closed-loop tracking by running track algorithms on the Irma-generated images, processing the track errors through optical control algorithms, and moving simulated electro-optical elements. The geometry of these elements determines the sensor orientation with respect to the Irma database containing the three-dimensional background and target models. This orientation is dynamically passed to Irma through a Simulink S-function to generate the next image. This integrated simulation provides a test-bed for development and evaluation of tracking and control algorithms against representative images including complex background environments and realistic targets calibrated using field measurements.

Secondary Use of Claims Data from the Austrian Health Insurance System with i2b2: A Pilot Study.

PubMed

Endel, Florian; Duftschmid, Georg

2016-01-01

In conformity with increasing international efforts to reuse routine health data for scientific purposes, the Main Association of Austrian Social Security Organisations provides pseudonymized claims data of the Austrian health care system for clinical research. We aimed to examine, whether an integration of the corresponding database into i2b2 would be possible and provide benefits. We applied docker-based software containers and data transformations to set up the system. To assess the benefits of i2b2 we plan to reenact the task of cohort formation of an earlier research project. The claims database was successfully integrated into i2b2. The docker-based installation approach will be published as git repository. The assessment of i2b2's benefits is currently work in progress and will be presented at the conference. Docker enables a flexible, reproducible, and resource-efficient installation of i2b2 within the restricted environment implied by our highly secured target system. First preliminary tests indicated several potential benefits of i2b2 compared to the methods applied during the earlier research project.

Save medical personnel's time by improved user interfaces.

PubMed

Kindler, H

1997-01-01

Common objectives in the industrial countries are the improvement of quality of care, clinical effectiveness, and cost control. Cost control, in particular, has been addressed through the introduction of case mix systems for reimbursement by social-security institutions. More data is required to enable quality improvement, increases in clinical effectiveness and for juridical reasons. At first glance, this documentation effort is contradictory to cost reduction. However, integrated services for resource management based on better documentation should help to reduce costs. The clerical effort for documentation should be decreased by providing a co-operative working environment for healthcare professionals applying sophisticated human-computer interface technology. Additional services, e.g., automatic report generation, increase the efficiency of healthcare personnel. Modelling the medical work flow forms an essential prerequisite for integrated resource management services and for co-operative user interfaces. A user interface aware of the work flow provides intelligent assistance by offering the appropriate tools at the right moment. Nowadays there is a trend to client/server systems with relational databases or object-oriented databases as repository. The work flows used for controlling purposes and to steer the user interfaces must be represented in the repository.

Power system modeling and optimization methods vis-a-vis integrated resource planning (IRP)

NASA Astrophysics Data System (ADS)

Arsali, Mohammad H.

1998-12-01

The state-of-the-art restructuring of power industries is changing the fundamental nature of retail electricity business. As a result, the so-called Integrated Resource Planning (IRP) strategies implemented on electric utilities are also undergoing modifications. Such modifications evolve from the imminent considerations to minimize the revenue requirements and maximize electrical system reliability vis-a-vis capacity-additions (viewed as potential investments). IRP modifications also provide service-design bases to meet the customer needs towards profitability. The purpose of this research as deliberated in this dissertation is to propose procedures for optimal IRP intended to expand generation facilities of a power system over a stretched period of time. Relevant topics addressed in this research towards IRP optimization are as follows: (1) Historical prospective and evolutionary aspects of power system production-costing models and optimization techniques; (2) A survey of major U.S. electric utilities adopting IRP under changing socioeconomic environment; (3) A new technique designated as the Segmentation Method for production-costing via IRP optimization; (4) Construction of a fuzzy relational database of a typical electric power utility system for IRP purposes; (5) A genetic algorithm based approach for IRP optimization using the fuzzy relational database.

Airport databases for 3D synthetic-vision flight-guidance displays: database design, quality assessment, and data generation

NASA Astrophysics Data System (ADS)

Friedrich, Axel; Raabe, Helmut; Schiefele, Jens; Doerr, Kai Uwe

1999-07-01

In future aircraft cockpit designs SVS (Synthetic Vision System) databases will be used to display 3D physical and virtual information to pilots. In contrast to pure warning systems (TAWS, MSAW, EGPWS) SVS serve to enhance pilot spatial awareness by 3-dimensional perspective views of the objects in the environment. Therefore all kind of aeronautical relevant data has to be integrated into the SVS-database: Navigation- data, terrain-data, obstacles and airport-Data. For the integration of all these data the concept of a GIS (Geographical Information System) based HQDB (High-Quality- Database) has been created at the TUD (Technical University Darmstadt). To enable database certification, quality- assessment procedures according to ICAO Annex 4, 11, 14 and 15 and RTCA DO-200A/EUROCAE ED76 were established in the concept. They can be differentiated in object-related quality- assessment-methods following the keywords accuracy, resolution, timeliness, traceability, assurance-level, completeness, format and GIS-related quality assessment methods with the keywords system-tolerances, logical consistence and visual quality assessment. An airport database is integrated in the concept as part of the High-Quality- Database. The contents of the HQDB are chosen so that they support both Flight-Guidance-SVS and other aeronautical applications like SMGCS (Surface Movement and Guidance Systems) and flight simulation as well. Most airport data are not available. Even though data for runways, threshold, taxilines and parking positions were to be generated by the end of 1997 (ICAO Annex 11 and 15) only a few countries fulfilled these requirements. For that reason methods of creating and certifying airport data have to be found. Remote sensing and digital photogrammetry serve as means to acquire large amounts of airport objects with high spatial resolution and accuracy in much shorter time than with classical surveying methods. Remotely sensed images can be acquired from satellite-platforms or aircraft-platforms. To achieve the highest horizontal accuracy requirements stated in ICAO Annex 14 for runway centerlines (0.50 meters), at the present moment only images acquired from aircraft based sensors can be used as source data. Still, ground reference by GCP (Ground Control-points) is obligatory. A DEM (Digital Elevation Model) can be created automatically in the photogrammetric process. It can be used as highly accurate elevation model for the airport area. The final verification of airport data is accomplished by independent surveyed runway- and taxiway- control-points. The concept of generation airport-data by means of remote sensing and photogrammetry was tested with the Stuttgart/Germany airport. The results proved that the final accuracy was within the accuracy specification defined by ICAO Annex 14.

Neuroimaging Study Designs, Computational Analyses and Data Provenance Using the LONI Pipeline

PubMed Central

Dinov, Ivo; Lozev, Kamen; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Pierce, Jonathan; Zamanyan, Alen; Chakrapani, Shruthi; Van Horn, John; Parker, D. Stott; Magsipoc, Rico; Leung, Kelvin; Gutman, Boris; Woods, Roger; Toga, Arthur

2010-01-01

Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges—management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu. PMID:20927408

The NCBI BioSystems database

PubMed Central

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. PMID:19854944

The integrated web service and genome database for agricultural plants with biotechnology information.

PubMed

Kim, Changkug; Park, Dongsuk; Seol, Youngjoo; Hahn, Jangho

2011-01-01

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a Web based relational database for agricultural plants with biotechnology information. The NABIC has concentrated on functional genomics of major agricultural plants, building an integrated biotechnology database for agro-biotech information that focuses on genomics of major agricultural resources. This genome database provides annotated genome information from 1,039,823 records mapped to rice, Arabidopsis, and Chinese cabbage.

Comprehensive Environmental Informatics System (CEIS) Integrating Crew and Vehicle Environmental Health

NASA Technical Reports Server (NTRS)

Nall, Mark E.

2006-01-01

Integrated Vehicle Health Management (IVHM) systems have been pursued as highly integrated systems that include smart sensors, diagnostic and prognostics software for assessments of real-time and life-cycle vehicle health information. Inclusive to such a system is the requirement to monitor the environmental health within the vehicle and the occupants of the vehicle. In this regard an enterprise approach to informatics is used to develop a methodology entitled, Comprehensive Environmental Informatics System (CEIS). The hardware and software technologies integrated into this system will be embedded in the vehicle subsystems, and maintenance operations, to provide both real-time and life-cycle health information of the environment within the vehicle cabin and of its occupants. This comprehensive information database will enable informed decision making and logistics management. One key element of the CEIS is interoperability for data acquisition and archive between environment and human system monitoring. With comprehensive components the data acquired in this system will use model based reasoning systems for subsystem and system level managers, advanced on-board and ground-based mission and maintenance planners to assess system functionality. Knowledge databases of the vehicle health state will be continuously updated and reported for critical failure modes, and routinely updated and reported for life cycle condition trending. Sufficient intelligence, including evidence-based engineering practices which are analogous to evidencebased medicine practices, will be included in the CEIS to result in more rapid recognition of off-nominal operation to enable quicker corrective actions. This will result from better information (rather than just data) for improved crew/operator situational awareness, which will produce significant vehicle and crew safety improvements, as well as increasing the chance for mission success, future mission planning as well as training. Other benefits include improved reliability, increase safety in operations and cost of operations. The cost benefits stem from significantly reduced processing and operations manpower, predictive maintenance for systems and subjects. The improvements in vehicle functionality and cost will result from increased prognostic and diagnostic capability due to the detailed total human exploration system health knowledge from CEIS. A collateral benefit is that there will be closer observations of the vehicle occupants as wrist watch sized devices are worn for continuous health monitoring. Additional database acquisition will stem from activities in countermeasure practices to ensure peak performance capability by occupants of the vehicle. The CEIS will provide data from advanced sensing technologies and informatics modeling which will be useful in problem troubleshooting, and improving NASA s awareness of systems during operation.

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

PubMed

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.

Object Recognition and Localization: The Role of Tactile Sensors

PubMed Central

Aggarwal, Achint; Kirchner, Frank

2014-01-01

Tactile sensors, because of their intrinsic insensitivity to lighting conditions and water turbidity, provide promising opportunities for augmenting the capabilities of vision sensors in applications involving object recognition and localization. This paper presents two approaches for haptic object recognition and localization for ground and underwater environments. The first approach called Batch Ransac and Iterative Closest Point augmented Particle Filter (BRICPPF) is based on an innovative combination of particle filters, Iterative-Closest-Point algorithm, and a feature-based Random Sampling and Consensus (RANSAC) algorithm for database matching. It can handle a large database of 3D-objects of complex shapes and performs a complete six-degree-of-freedom localization of static objects. The algorithms are validated by experimentation in ground and underwater environments using real hardware. To our knowledge this is the first instance of haptic object recognition and localization in underwater environments. The second approach is biologically inspired, and provides a close integration between exploration and recognition. An edge following exploration strategy is developed that receives feedback from the current state of recognition. A recognition by parts approach is developed which uses the BRICPPF for object sub-part recognition. Object exploration is either directed to explore a part until it is successfully recognized, or is directed towards new parts to endorse the current recognition belief. This approach is validated by simulation experiments. PMID:24553087

Parameterization of the ACRU model for estimating biophysical and climatological change impacts, Beaver Creek, Alberta

NASA Astrophysics Data System (ADS)

Forbes, K. A.; Kienzle, S. W.; Coburn, C. A.; Byrne, J. M.

2006-12-01

Multiple threats, including intensification of agricultural production, non-renewable resource extraction and climate change, are threatening Southern Alberta's water supply. The objective of this research is to calibrate/evaluate the Agricultural Catchments Research Unit (ACRU) agrohydrological model; with the end goal of forecasting the impacts of a changing environment on water quantity. The strength of this model is the intensive multi-layered soil water budgeting routine that integrates water movement between the surface and atmosphere. The ACRU model was parameterized using data from Environment Canada's climate database for a twenty year period (1984-2004) and was used to simulate streamflow for Beaver Creek. The simulated streamflow was compared to Environment Canada's historical streamflow database to validate the model output. The Beaver Creek Watershed, located in the Porcupine Hills southwestern Alberta, Canada contains a heterogeneous cover of deciduous, coniferous, native prairie grasslands and forage crops. In a catchment with highly diversified land cover, canopy architecture cannot be overlooked in rainfall interception parameterization. Preliminary testing of ACRU suggests that streamflows were sensitive to varied levels of leaf area index (LAI), a representative fraction of canopy foliage. Further testing using remotely sensed LAI's will provide a more accurate representation of canopy foliage and ultimately best represent this important element of the hydrological cycle and the associated processes which govern the natural hydrology of the Beaver Creek watershed.

NiCd cell reliability in the mission environment

NASA Technical Reports Server (NTRS)

Denson, William K.; Klein, Glenn C.

1993-01-01

This paper summarizes an effort by Gates Aerospace Batteries (GAB) and the Reliability Analysis Center (RAC) to analyze survivability data for both General Electric and GAB NiCd cells utilized in various spacecraft. For simplicity sake, all mission environments are described as either low Earth orbital (LEO) or geosynchronous Earth orbit (GEO). 'Extreme value statistical methods' are applied to this database because of the longevity of the numerous missions while encountering relatively few failures. Every attempt was made to include all known instances of cell-induced-failures of the battery and to exclude battery-induced-failures of the cell. While this distinction may be somewhat limited due to availability of in-flight data, we have accepted the learned opinion of the specific customer contacts to ensure integrity of the common databases. This paper advances the preliminary analysis reported upon at the 1991 NASA Battery Workshop. That prior analysis was concerned with an estimated 278 million cell-hours of operation encompassing 183 satellites. The paper also cited 'no reported failures to date.' This analysis reports on 428 million cell hours of operation emcompassing 212 satellites. This analysis also reports on seven 'cell-induced-failures.'

Data Sharing in Astrobiology: The Astrobiology Habitable Environments Database (AHED)

NASA Technical Reports Server (NTRS)

Lafuente, B.; Bristow, T.; Stone, N.; Pires, A.; Keller, R.; Downs, Robert; Blake, D.; Fonda, M.

2017-01-01

Astrobiology is a multidisciplinary area of scientific research focused on studying the origins of life on Earth and the conditions under which life might have emerged elsewhere in the universe. NASA uses the results of Astrobiology research to help define targets for future missions that are searching for life elsewhere in the universe. The understanding of complex questions in Astrobiology requires integration and analysis of data spanning a range of disciplines including biology, chemistry, geology, astronomy and planetary science. However, the lack of a centralized repository makes it difficult for Astrobiology teams to share data and benefit from resultant synergies. Moreover, in recent years, federal agencies are requiring that results of any federally funded scientific research must be available and useful for the public and the science community. The Astrobiology Habitable Environments Database (AHED), developed with a consolidated group of astrobiologists from different active research teams at NASA Ames Research Center, is designed to help to address these issues. AHED is a central, high-quality, long-term data repository for mineralogical, textural, morphological, inorganic and organic chemical, isotopic and other information pertinent to the advancement of the field of Astrobiology.

Data Sharing in Astrobiology: the Astrobiology Habitable Environments Database (AHED)

NASA Technical Reports Server (NTRS)

Lafuente, B.; Bristow, T.; Stone, N.; Pires, A.; Keller, R. M.; Downs, R. T.; Blake, D.; Fonda, M.

2017-01-01

Astrobiology is a multidisciplinary area of scientific research focused on studying the origins of life on Earth and the conditions under which life might have emerged elsewhere in the universe. NASA uses the results of Astrobiology research to help define targets for future missions that are searching for life elsewhere in the universe. The understanding of complex questions in Astrobiology requires integration and analysis of data spanning a range of disciplines including biology, chemistry, geology, astronomy and planetary science. However, the lack of a centralized repository makes it difficult for Astrobiology teams to share data and benefit from resultant synergies. Moreover, in recent years, federal agencies are requiring that results of any federally funded scientific research must be available and useful for the public and the science community. The Astrobiology Habitable Environments Database (AHED), developed with a consolidated group of astrobiologists from different active research teams at NASA Ames Research Center, is designed to help to address these issues. AHED is a central, high-quality, long-term data repository for mineralogical, textural, morphological, inorganic and organic chemical, isotopic and other information pertinent to the advancement of the field of Astrobiology.

An approach for access differentiation design in medical distributed applications built on databases.

PubMed

Shoukourian, S K; Vasilyan, A M; Avagyan, A A; Shukurian, A K

1999-01-01

A formalized "top to bottom" design approach was described in [1] for distributed applications built on databases, which were considered as a medium between virtual and real user environments for a specific medical application. Merging different components within a unified distributed application posits new essential problems for software. Particularly protection tools, which are sufficient separately, become deficient during the integration due to specific additional links and relationships not considered formerly. E.g., it is impossible to protect a shared object in the virtual operating room using only DBMS protection tools, if the object is stored as a record in DB tables. The solution of the problem should be found only within the more general application framework. Appropriate tools are absent or unavailable. The present paper suggests a detailed outline of a design and testing toolset for access differentiation systems (ADS) in distributed medical applications which use databases. The appropriate formal model as well as tools for its mapping to a DMBS are suggested. Remote users connected via global networks are considered too.

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

PubMed

Wang, L; Rodriguez-Tomé, P; Redaschi, N; McNeil, P; Robinson, A; Lijnzaad, P

2000-01-01

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

Accessing and distributing EMBL data using CORBA (common object request broker architecture)

PubMed Central

Wang, Lichun; Rodriguez-Tomé, Patricia; Redaschi, Nicole; McNeil, Phil; Robinson, Alan; Lijnzaad, Philip

2000-01-01

Background: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. Results: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. Conclusions: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems. PMID:11178259

Space Suit Portable Life Support System (PLSS) 2.0 Unmanned Vacuum Environment Testing

NASA Technical Reports Server (NTRS)

Watts, Carly; Vogel, Matthew

2016-01-01

For the first time in more than 30 years, an advanced space suit Portable Life Support System (PLSS) design was operated inside a vacuum chamber representative of the flight operating environment. The test article, PLSS 2.0, was the second system-level integrated prototype of the advanced PLSS design, following the PLSS 1.0 Breadboard that was developed and tested throughout 2011. Whereas PLSS 1.0 included five technology development components with the balance the system simulated using commercial-off-the-shelf items, PLSS 2.0 featured first generation or later prototypes for all components less instrumentation, tubing and fittings. Developed throughout 2012, PLSS 2.0 was the first attempt to package the system into a flight-like representative volume. PLSS 2.0 testing included an extensive functional evaluation known as Pre-Installation Acceptance (PIA) testing, Human-in-the-Loop testing in which the PLSS 2.0 prototype was integrated via umbilicals to a manned prototype space suit for 19 two-hour simulated EVAs, and unmanned vacuum environment testing. Unmanned vacuum environment testing took place from 1/9/15-7/9/15 with PLSS 2.0 located inside a vacuum chamber. Test sequences included performance mapping of several components, carbon dioxide removal evaluations at simulated intravehicular activity (IVA) conditions, a regulator pressure schedule assessment, and culminated with 25 simulated extravehicular activities (EVAs). During the unmanned vacuum environment test series, PLSS 2.0 accumulated 378 hours of integrated testing including 291 hours of operation in a vacuum environment and 199 hours of simulated EVA time. The PLSS prototype performed nominally throughout the test series, with two notable exceptions including a pump failure and a Spacesuit Water Membrane Evaporator (SWME) leak, for which post-test failure investigations were performed. In addition to generating an extensive database of PLSS 2.0 performance data, achievements included requirements and operational concepts verification, as well as demonstration of vehicular interfaces, consumables sizing and recharge, and water quality control.

Cyberinfrastructure for the Unified Study of Earth Structure and Earthquake Sources in Complex Geologic Environments

NASA Astrophysics Data System (ADS)

Zhao, L.; Chen, P.; Jordan, T. H.; Olsen, K. B.; Maechling, P.; Faerman, M.

2004-12-01

The Southern California Earthquake Center (SCEC) is developing a Community Modeling Environment (CME) to facilitate the computational pathways of physics-based seismic hazard analysis (Maechling et al., this meeting). Major goals are to facilitate the forward modeling of seismic wavefields in complex geologic environments, including the strong ground motions that cause earthquake damage, and the inversion of observed waveform data for improved models of Earth structure and fault rupture. Here we report on a unified approach to these coupled inverse problems that is based on the ability to generate and manipulate wavefields in densely gridded 3D Earth models. A main element of this approach is a database of receiver Green tensors (RGT) for the seismic stations, which comprises all of the spatial-temporal displacement fields produced by the three orthogonal unit impulsive point forces acting at each of the station locations. Once the RGT database is established, synthetic seismograms for any earthquake can be simply calculated by extracting a small, source-centered volume of the RGT from the database and applying the reciprocity principle. The partial derivatives needed for point- and finite-source inversions can be generated in the same way. Moreover, the RGT database can be employed in full-wave tomographic inversions launched from a 3D starting model, because the sensitivity (Fréchet) kernels for travel-time and amplitude anomalies observed at seismic stations in the database can be computed by convolving the earthquake-induced displacement field with the station RGTs. We illustrate all elements of this unified analysis with an RGT database for 33 stations of the California Integrated Seismic Network in and around the Los Angeles Basin, which we computed for the 3D SCEC Community Velocity Model (SCEC CVM3.0) using a fourth-order staggered-grid finite-difference code. For a spatial grid spacing of 200 m and a time resolution of 10 ms, the calculations took ~19,000 node-hours on the Linux cluster at USC's High-Performance Computing Center. The 33-station database with a volume of ~23.5 TB was archived in the SCEC digital library at the San Diego Supercomputer Center using the Storage Resource Broker (SRB). From a laptop, anyone with access to this SRB collection can compute synthetic seismograms for an arbitrary source in the CVM in a matter of minutes. Efficient approaches have been implemented to use this RGT database in the inversions of waveforms for centroid and finite moment tensors and tomographic inversions to improve the CVM. Our experience with these large problems suggests areas where the cyberinfrastructure currently available for geoscience computation needs to be improved.

Environmental geochemistry at the global scale

USGS Publications Warehouse

Plant, J.; Smith, D.; Smith, B.; Williams, L.

2001-01-01

Land degradation and pollution caused by population pressure and economic development pose a threat to the sustainability of the earth's surface, especially in tropical regions where a long history of chemical weathering has made the surface environment particularly fragile. Systematic baseline geochemical data provide a means of monitoring the state of the environment and identifying problem areas. Regional surveys have already been carried out in some countries, and with increased national and international funding they can be extended to cover the rest of the land surface of the globe. Preparations have been made, under the auspices of the International Union of Geological Surveys (IUGS) and the International Association of Geochemistry and Cosmochemistry (IAGC) for the establishment of just such an integrated global database. ?? 2001 NERC. Published by Elsevier Science Ltd.

Connection of European particle therapy centers and generation of a common particle database system within the European ULICE-framework

PubMed Central

2012-01-01

Background To establish a common database on particle therapy for the evaluation of clinical studies integrating a large variety of voluminous datasets, different documentation styles, and various information systems, especially in the field of radiation oncology. Methods We developed a web-based documentation system for transnational and multicenter clinical studies in particle therapy. 560 patients have been treated from November 2009 to September 2011. Protons, carbon ions or a combination of both, as well as a combination with photons were applied. To date, 12 studies have been initiated and more are in preparation. Results It is possible to immediately access all patient information and exchange, store, process, and visualize text data, any DICOM images and multimedia data. Accessing the system and submitting clinical data is possible for internal and external users. Integrated into the hospital environment, data is imported both manually and automatically. Security and privacy protection as well as data validation and verification are ensured. Studies can be designed to fit individual needs. Conclusions The described database provides a basis for documentation of large patient groups with specific and specialized questions to be answered. Having recently begun electronic documentation, it has become apparent that the benefits lie in the user-friendly and timely workflow for documentation. The ultimate goal is a simplification of research work, better study analyses quality and eventually, the improvement of treatment concepts by evaluating the effectiveness of particle therapy. PMID:22828013

Loopedia, a database for loop integrals

NASA Astrophysics Data System (ADS)

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.

Assessing the Nexus of Built, Natural, and Social Environments and Public Health Outcomes

NASA Astrophysics Data System (ADS)

Archer, R.; Alexander, S.; Douglas, J.

2017-12-01

This study investigates community-related environmental justice concerns and chemical and non-chemical health stressors from built, natural, and social environments in Southeast Los Angeles (SELA) County and East Oakland, California. The geographical distribution of health outcomes is related to the built and natural environments, as well as impacts from the social environment. A holistic systems view is important in assessing healthy behaviors within a community, because they do not occur in isolation. Geospatial analysis will be performed to integrate a total environment framework and explore the spatial patterns of exposure to chemical and non-chemical stressors and access to health-promoting environments. Geographic Information Systems (GIS) analysis using primary and secondary existing data will be performed to determine how social environments impact exposure to chemical health stressors and access to health-promoting built and natural environments. This project will develop a comprehensive list of health-promoting built and natural environments (e.g., parks and community gardens) and polluting sites (e.g., shipping ports and sources of pollution not included in federal regulatory databases) in East Oakland and SELA. California Department of Public Health and U.S. Decennial Census data will also be included for geospatial analysis to overlay the distribution of air pollution-related morbidities (e.g. asthma, diabetes, and cancer) and access to health-promoting built and natural environments and related community assets, exposure to polluting industries, social disorganization, and public health outcomes in the target areas. This research will help identify the spatial and temporal distribution and cumulative impacts of critical pollution hotspots causing community environmental health impacts. The research team will also map how social environments impact exposure to chemical health stressors and access to health-promoting built and natural environments. The process and outcomes of this research should empower communities and aid decision-makers to integrate environmental justice considerations into public health policies.

Geodiametris: an integrated geoinformatic approach for monitoring land pollution from the disposal of olive oil mill wastes

NASA Astrophysics Data System (ADS)

Alexakis, Dimitrios D.; Sarris, Apostolos; Papadopoulos, Nikos; Soupios, Pantelis; Doula, Maria; Cavvadias, Victor

2014-08-01

The olive-oil industry is one of the most important sectors of agricultural production in Greece, which is the third in olive-oil production country worldwide. Olive oil mill wastes (OOMW) constitute a major factor in pollution in olivegrowing regions and an important problem to be solved for the agricultural industry. The olive-oil mill wastes are normally deposited at tanks, or directly in the soil or even on adjacent torrents, rivers and lakes posing a high risk to the environmental pollution and the community health. GEODIAMETRIS project aspires to develop integrated geoinformatic methodologies for performing monitoring of land pollution from the disposal of OOMW in the island of Crete -Greece. These methodologies integrate GPS surveys, satellite remote sensing and risk assessment analysis in GIS environment, application of in situ and laboratory geophysical methodologies as well as soil and water physicochemical analysis. Concerning project's preliminary results, all the operating OOMW areas located in Crete have been already registered through extensive GPS field campaigns. Their spatial and attribute information has been stored in an integrated GIS database and an overall OOMW spectral signature database has been constructed through the analysis of multi-temporal Landsat-8 OLI satellite images. In addition, a specific OOMW area located in Alikianos village (Chania-Crete) has been selected as one of the main case study areas. Various geophysical methodologies, such as Electrical Resistivity Tomography, Induced Polarization, multifrequency electromagnetic, Self Potential measurements and Ground Penetrating Radar have been already implemented. Soil as well as liquid samples have been collected for performing physico-chemical analysis. The preliminary results have already contributed to the gradual development of an integrated environmental monitoring tool for studying and understanding environmental degradation from the disposal of OOMW.

Nonbibliographic Databases in a Corporate Health, Safety, and Environment Organization.

ERIC Educational Resources Information Center

Cubillas, Mary M.

1981-01-01

Summarizes the characteristics of TOXIN, CHEMFILE, and the Product Profile Information System (PPIS), nonbibliographic databases used by Shell Oil Company's Health, Safety, and Environment Organization. (FM)

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

PubMed

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.

The PartnerWeb Project: a component-based approach to enterprise-wide information integration and dissemination.

PubMed Central

Karson, T. H.; Perkins, C.; Dixon, C.; Ehresman, J. P.; Mammone, G. L.; Sato, L.; Schaffer, J. L.; Greenes, R. A.

1997-01-01

A component-based health information resource, delivered on an intranet and the Internet, utilizing World Wide Web (WWW) technology, has been built to meet the needs of a large integrated delivery network (IDN). Called PartnerWeb, this resource is intended to provide a variety of health care and reference information to both practitioners and consumers/patients. The initial target audience has been providers. Content management for the numerous departments, divisions, and other organizational entities within the IDN is accomplished by a distributed authoring and editing environment. Structured entry using a set of form tools into databases facilitates consistency of information presentation, while empowering designated authors and editors in the various entities to be responsible for their own materials, but not requiring them to be technically skilled. Each form tool manages an encapsulated component. The output of each component can be a dynamically generated display on WWW platforms, or an appropriate interface to other presentation environments. The PartnerWeb project lays the foundation for both an internal and external communication infrastructure for the enterprise that can facilitate information dissemination. PMID:9357648

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

USGS Publications Warehouse

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.

The EBI SRS server-new features.

PubMed

Zdobnov, Evgeny M; Lopez, Rodrigo; Apweiler, Rolf; Etzold, Thure

2002-08-01

Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. The new additions include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in 'Nice views', SRSQuickSearch bookmarklets. SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration.

Computational toxicology using the OpenTox application programming interface and Bioclipse

PubMed Central

2011-01-01

Background Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications. Findings This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources. Conclusions A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers. PMID:22075173

Building An Integrated Neurodegenerative Disease Database At An Academic Health Center

PubMed Central

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.

2010-01-01

Background 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 (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration (FTLD). These comparative studies rely on powerful database tools to quickly generate data sets which match diverse and complementary criteria set by the studies. Methods In this paper, we present a novel Integrated NeuroDegenerative Disease (INDD) database developed at the University of Pennsylvania (Penn) through a consortium of Penn investigators. Since these investigators work on AD, PD, ALS and FTLD, this allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used Microsoft SQL Server as the platform with built-in “backwards” functionality to provide Access as a front-end client to interface with the database. We used PHP hypertext Preprocessor to create the “front end” web interface and then integrated individual neurodegenerative disease databases using a master lookup table. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Results We compare the results of a biomarker study using the INDD database to those using an alternative approach by querying individual database separately. Conclusions 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 across several neurodegenerative diseases. PMID:21784346

DBGC: A Database of Human Gastric Cancer

PubMed Central

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

The integrated web service and genome database for agricultural plants with biotechnology information

PubMed Central

Kim, ChangKug; Park, DongSuk; Seol, YoungJoo; Hahn, JangHo

2011-01-01

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a Web based relational database for agricultural plants with biotechnology information. The NABIC has concentrated on functional genomics of major agricultural plants, building an integrated biotechnology database for agro-biotech information that focuses on genomics of major agricultural resources. This genome database provides annotated genome information from 1,039,823 records mapped to rice, Arabidopsis, and Chinese cabbage. PMID:21887015

The Comprehensive Antibiotic Resistance Database

PubMed Central

McArthur, Andrew G.; Waglechner, Nicholas; Nizam, Fazmin; Yan, Austin; Azad, Marisa A.; Baylay, Alison J.; Bhullar, Kirandeep; Canova, Marc J.; De Pascale, Gianfranco; Ejim, Linda; Kalan, Lindsay; King, Andrew M.; Koteva, Kalinka; Morar, Mariya; Mulvey, Michael R.; O'Brien, Jonathan S.; Pawlowski, Andrew C.; Piddock, Laura J. V.; Spanogiannopoulos, Peter; Sutherland, Arlene D.; Tang, Irene; Taylor, Patricia L.; Thaker, Maulik; Wang, Wenliang; Yan, Marie; Yu, Tennison

2013-01-01

The field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few specialized bioinformatic tools developed to mine the growing amount of genomic data associated with pathogens. In particular, there are few tools to study the genetics and genomics of antibiotic resistance and how it impacts bacterial populations, ecology, and the clinic. We have initiated development of such tools in the form of the Comprehensive Antibiotic Research Database (CARD; http://arpcard.mcmaster.ca). The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture, and the environment. PMID:23650175

An Integrated Korean Biodiversity and Genetic Information Retrieval System

PubMed Central

Lim, Jeongheui; Bhak, Jong; Oh, Hee-Mock; Kim, Chang-Bae; Park, Yong-Ha; Paek, Woon Kee

2008-01-01

Background On-line biodiversity information databases are growing quickly and being integrated into general bioinformatics systems due to the advances of fast gene sequencing technologies and the Internet. These can reduce the cost and effort of performing biodiversity surveys and genetic searches, which allows scientists to spend more time researching and less time collecting and maintaining data. This will cause an increased rate of knowledge build-up and improve conservations. The biodiversity databases in Korea have been scattered among several institutes and local natural history museums with incompatible data types. Therefore, a comprehensive database and a nation wide web portal for biodiversity information is necessary in order to integrate diverse information resources, including molecular and genomic databases. Results The Korean Natural History Research Information System (NARIS) was built and serviced as the central biodiversity information system to collect and integrate the biodiversity data of various institutes and natural history museums in Korea. This database aims to be an integrated resource that contains additional biological information, such as genome sequences and molecular level diversity. Currently, twelve institutes and museums in Korea are integrated by the DiGIR (Distributed Generic Information Retrieval) protocol, with Darwin Core2.0 format as its metadata standard for data exchange. Data quality control and statistical analysis functions have been implemented. In particular, integrating molecular and genetic information from the National Center for Biotechnology Information (NCBI) databases with NARIS was recently accomplished. NARIS can also be extended to accommodate other institutes abroad, and the whole system can be exported to establish local biodiversity management servers. Conclusion A Korean data portal, NARIS, has been developed to efficiently manage and utilize biodiversity data, which includes genetic resources. NARIS aims to be integral in maximizing bio-resource utilization for conservation, management, research, education, industrial applications, and integration with other bioinformation data resources. It can be found at . PMID:19091024

PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology

PubMed Central

Gioutlakis, Aris; Klapa, Maria I.

2017-01-01

It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primary datasets, presenting the PPIs at various genetic reference levels. Existing PPI meta-databases perform integration via normalization; namely, PPIs are merged after converted to a certain target level. Hence, the node set of the integrated network depends each time on the number and type of the combined datasets. Moreover, the irreversible a priori normalization process hinders the identification of normalization artifacts in the integrated network, which originate from the nonlinearity characterizing the genetic information flow. PICKLE (Protein InteraCtion KnowLedgebasE) 2.0 implements a new architecture for this recently introduced human PPI meta-database. Its main novel feature over the existing meta-databases is its approach to primary PPI dataset integration via genetic information ontology. Building upon the PICKLE principles of using the reviewed human complete proteome (RHCP) of UniProtKB/Swiss-Prot as the reference protein interactor set, and filtering out protein interactions with low probability of being direct based on the available evidence, PICKLE 2.0 first assembles the RHCP genetic information ontology network by connecting the corresponding genes, nucleotide sequences (mRNAs) and proteins (UniProt entries) and then integrates PPI datasets by superimposing them on the ontology network without any a priori transformations. Importantly, this process allows the resulting heterogeneous integrated network to be reversibly normalized to any level of genetic reference without loss of the original information, the latter being used for identification of normalization biases, and enables the appraisal of potential false positive interactions through PPI source database cross-checking. The PICKLE web-based interface (www.pickle.gr) allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein (UniProt) or the gene level, at three PPI filtering modes. PMID:29023571

SPIRE: Systematic protein investigative research environment.

PubMed

Kolker, Eugene; Higdon, Roger; Morgan, Phil; Sedensky, Margaret; Welch, Dean; Bauman, Andrew; Stewart, Elizabeth; Haynes, Winston; Broomall, William; Kolker, Natali

2011-12-10

The SPIRE (Systematic Protein Investigative Research Environment) provides web-based experiment-specific mass spectrometry (MS) proteomics analysis (https://www.proteinspire.org). Its emphasis is on usability and integration of the best analytic tools. SPIRE provides an easy to use web-interface and generates results in both interactive and simple data formats. In contrast to run-based approaches, SPIRE conducts the analysis based on the experimental design. It employs novel methods to generate false discovery rates and local false discovery rates (FDR, LFDR) and integrates the best and complementary open-source search and data analysis methods. The SPIRE approach of integrating X!Tandem, OMSSA and SpectraST can produce an increase in protein IDs (52-88%) over current combinations of scoring and single search engines while also providing accurate multi-faceted error estimation. One of SPIRE's primary assets is combining the results with data on protein function, pathways and protein expression from model organisms. We demonstrate some of SPIRE's capabilities by analyzing mitochondrial proteins from the wild type and 3 mutants of C. elegans. SPIRE also connects results to publically available proteomics data through its Model Organism Protein Expression Database (MOPED). SPIRE can also provide analysis and annotation for user supplied protein ID and expression data. Copyright © 2011. Published by Elsevier B.V.

Context-aware access control for pervasive access to process-based healthcare systems.

PubMed

Koufi, Vassiliki; Vassilacopoulos, George

2008-01-01

Healthcare is an increasingly collaborative enterprise involving a broad range of healthcare services provided by many individuals and organizations. Grid technology has been widely recognized as a means for integrating disparate computing resources in the healthcare field. Moreover, Grid portal applications can be developed on a wireless and mobile infrastructure to execute healthcare processes which, in turn, can provide remote access to Grid database services. Such an environment provides ubiquitous and pervasive access to integrated healthcare services at the point of care, thus improving healthcare quality. In such environments, the ability to provide an effective access control mechanism that meets the requirement of the least privilege principle is essential. Adherence to the least privilege principle requires continuous adjustments of user permissions in order to adapt to the current situation. This paper presents a context-aware access control mechanism for HDGPortal, a Grid portal application which provides access to workflow-based healthcare processes using wireless Personal Digital Assistants. The proposed mechanism builds upon and enhances security mechanisms provided by the Grid Security Infrastructure. It provides tight, just-in-time permissions so that authorized users get access to specific objects according to the current context. These permissions are subject to continuous adjustments triggered by the changing context. Thus, the risk of compromising information integrity during task executions is reduced.

An integrative review of literature on determinants of nurses' organizational commitment.

PubMed

Vagharseyyedin, Seyyed Abolfazl

2016-01-01

This integrative review was aimed to examine in literature and integrate the determinants of nurses' organizational commitment in hospital settings. In this study, an integrative review of the literature was used. The search strategy began with six electronic databases (e.g. CINAHL and Medline). Considering the inclusion criteria, published studies that examined the factors influencing nurses' organizational commitment in the timeframe of 2000 through 2013 were chosen. Data extraction and analysis were completed on all included studies. The final sample for this integrative review comprised 33 studies. Based on common meanings and central issues, 63 different factors contributing to nurses' organizational commitment were integrated and grouped into four main categories: Personal characteristics and traits of nurses, leadership and management style and behavior, perception of organizational context, and characteristics of job and work environment. In general, categories emerged in this study could be useful for formulating initiatives to stimulate nurses' OC. However, little is known about the relative significance of each identified factor among nurses working in different countries. Qualitative research is recommended for narrowing this gap. Future research should be directed to examine the psychometric properties of the organizational scales for nurses in different cultures.

A pilot GIS database of active faults of Mt. Etna (Sicily): A tool for integrated hazard evaluation

NASA Astrophysics Data System (ADS)

Barreca, Giovanni; Bonforte, Alessandro; Neri, Marco

2013-02-01

A pilot GIS-based system has been implemented for the assessment and analysis of hazard related to active faults affecting the eastern and southern flanks of Mt. Etna. The system structure was developed in ArcGis® environment and consists of different thematic datasets that include spatially-referenced arc-features and associated database. Arc-type features, georeferenced into WGS84 Ellipsoid UTM zone 33 Projection, represent the five main fault systems that develop in the analysed region. The backbone of the GIS-based system is constituted by the large amount of information which was collected from the literature and then stored and properly geocoded in a digital database. This consists of thirty five alpha-numeric fields which include all fault parameters available from literature such us location, kinematics, landform, slip rate, etc. Although the system has been implemented according to the most common procedures used by GIS developer, the architecture and content of the database represent a pilot backbone for digital storing of fault parameters, providing a powerful tool in modelling hazard related to the active tectonics of Mt. Etna. The database collects, organises and shares all scientific currently available information about the active faults of the volcano. Furthermore, thanks to the strong effort spent on defining the fields of the database, the structure proposed in this paper is open to the collection of further data coming from future improvements in the knowledge of the fault systems. By layering additional user-specific geographic information and managing the proposed database (topological querying) a great diversity of hazard and vulnerability maps can be produced by the user. This is a proposal of a backbone for a comprehensive geographical database of fault systems, universally applicable to other sites.

Space Situational Awareness Data Processing Scalability Utilizing Google Cloud Services

NASA Astrophysics Data System (ADS)

Greenly, D.; Duncan, M.; Wysack, J.; Flores, F.

Space Situational Awareness (SSA) is a fundamental and critical component of current space operations. The term SSA encompasses the awareness, understanding and predictability of all objects in space. As the population of orbital space objects and debris increases, the number of collision avoidance maneuvers grows and prompts the need for accurate and timely process measures. The SSA mission continually evolves to near real-time assessment and analysis demanding the need for higher processing capabilities. By conventional methods, meeting these demands requires the integration of new hardware to keep pace with the growing complexity of maneuver planning algorithms. SpaceNav has implemented a highly scalable architecture that will track satellites and debris by utilizing powerful virtual machines on the Google Cloud Platform. SpaceNav algorithms for processing CDMs outpace conventional means. A robust processing environment for tracking data, collision avoidance maneuvers and various other aspects of SSA can be created and deleted on demand. Migrating SpaceNav tools and algorithms into the Google Cloud Platform will be discussed and the trials and tribulations involved. Information will be shared on how and why certain cloud products were used as well as integration techniques that were implemented. Key items to be presented are: 1.Scientific algorithms and SpaceNav tools integrated into a scalable architecture a) Maneuver Planning b) Parallel Processing c) Monte Carlo Simulations d) Optimization Algorithms e) SW Application Development/Integration into the Google Cloud Platform 2. Compute Engine Processing a) Application Engine Automated Processing b) Performance testing and Performance Scalability c) Cloud MySQL databases and Database Scalability d) Cloud Data Storage e) Redundancy and Availability

A natural language interface plug-in for cooperative query answering in biological databases.

PubMed

Jamil, Hasan M

2012-06-11

One of the many unique features of biological databases is that the mere existence of a ground data item is not always a precondition for a query response. It may be argued that from a biologist's standpoint, queries are not always best posed using a structured language. By this we mean that approximate and flexible responses to natural language like queries are well suited for this domain. This is partly due to biologists' tendency to seek simpler interfaces and partly due to the fact that questions in biology involve high level concepts that are open to interpretations computed using sophisticated tools. In such highly interpretive environments, rigidly structured databases do not always perform well. In this paper, our goal is to propose a semantic correspondence plug-in to aid natural language query processing over arbitrary biological database schema with an aim to providing cooperative responses to queries tailored to users' interpretations. Natural language interfaces for databases are generally effective when they are tuned to the underlying database schema and its semantics. Therefore, changes in database schema become impossible to support, or a substantial reorganization cost must be absorbed to reflect any change. We leverage developments in natural language parsing, rule languages and ontologies, and data integration technologies to assemble a prototype query processor that is able to transform a natural language query into a semantically equivalent structured query over the database. We allow knowledge rules and their frequent modifications as part of the underlying database schema. The approach we adopt in our plug-in overcomes some of the serious limitations of many contemporary natural language interfaces, including support for schema modifications and independence from underlying database schema. The plug-in introduced in this paper is generic and facilitates connecting user selected natural language interfaces to arbitrary databases using a semantic description of the intended application. We demonstrate the feasibility of our approach with a practical example.

Climatic Data Integration and Analysis - Regional Approaches to Climate Change for Pacific Northwest Agriculture (REACCH PNA)

NASA Astrophysics Data System (ADS)

Seamon, E.; Gessler, P. E.; Flathers, E.; Sheneman, L.; Gollberg, G.

2013-12-01

The Regional Approaches to Climate Change for Pacific Northwest Agriculture (REACCH PNA) is a five-year USDA/NIFA-funded coordinated agriculture project to examine the sustainability of cereal crop production systems in the Pacific Northwest, in relationship to ongoing climate change. As part of this effort, an extensive data management system has been developed to enable researchers, students, and the public, to upload, manage, and analyze various data. The REACCH PNA data management team has developed three core systems to encompass cyberinfrastructure and data management needs: 1) the reacchpna.org portal (https://www.reacchpna.org) is the entry point for all public and secure information, with secure access by REACCH PNA members for data analysis, uploading, and informational review; 2) the REACCH PNA Data Repository is a replicated, redundant database server environment that allows for file and database storage and access to all core data; and 3) the REACCH PNA Libraries which are functional groupings of data for REACCH PNA members and the public, based on their access level. These libraries are accessible thru our https://www.reacchpna.org portal. The developed system is structured in a virtual server environment (data, applications, web) that includes a geospatial database/geospatial web server for web mapping services (ArcGIS Server), use of ESRI's Geoportal Server for data discovery and metadata management (under the ISO 19115-2 standard), Thematic Realtime Environmental Distributed Data Services (THREDDS) for data cataloging, and Interactive Python notebook server (IPython) technology for data analysis. REACCH systems are housed and maintained by the Northwest Knowledge Network project (www.northwestknowledge.net), which provides data management services to support research. Initial project data harvesting and meta-tagging efforts have resulted in the interrogation and loading of over 10 terabytes of climate model output, regional entomological data, agricultural and atmospheric information, as well as imagery, publications, videos, and other soft content. In addition, the outlined data management approach has focused on the integration and interconnection of hard data (raw data output) with associated publications, presentations, or other narrative documentation - through metadata lineage associations. This harvest-and-consume data management methodology could additionally be applied to other research team environments that involve large and divergent data.

The Perfect Marriage: Integrated Word Processing and Data Base Management Programs.

ERIC Educational Resources Information Center

Pogrow, Stanley

1983-01-01

Discussion of database integration and how it operates includes recommendations on compatible brand name word processing and database management programs, and a checklist for evaluating essential and desirable features of the available programs. (MBR)

Integration of air traffic databases : a case study

DOT National Transportation Integrated Search

1995-03-01

This report describes a case study to show the benefits from maximum utilization of existing air traffic databases. The study demonstrates the utility of integrating available data through developing and demonstrating a methodology addressing the iss...

SUPERSITES INTEGRATED RELATIONAL DATABASE (SIRD)

EPA Science Inventory

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

Enabling a systems biology knowledgebase with gaggle and firegoose

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baliga, Nitin S.

The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is anmore » open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and improve the integration within different environments, and we have created a new tools pipeline for generating EGRIN2 models in a largely automated way.« less

A Web-based tool for UV irradiance data: predictions for European and Southeast Asian sites.

PubMed

Kift, Richard; Webb, Ann R; Page, John; Rimmer, John; Janjai, Serm

2006-01-01

There are a range of UV models available, but one needs significant pre-existing knowledge and experience in order to be able to use them. In this article a comparatively simple Web-based model developed for the SoDa (Integration and Exploitation of Networked Solar Radiation Databases for Environment Monitoring) project is presented. This is a clear-sky model with modifications for cloud effects. To determine if the model produces realistic UV data the output is compared with 1 year sets of hourly measurements at sites in the United Kingdom and Thailand. The accuracy of the output depends on the input, but reasonable results were obtained with the use of the default database inputs and improved when pyranometer instead of modeled data provided the global radiation input needed to estimate the UV. The average modeled values of UV for the UK site were found to be within 10% of measurements. For the tropical sites in Thailand the average modeled values were within 1120% of measurements for the four sites with the use of the default SoDa database values. These results improved when pyranometer data and TOMS ozone data from 2002 replaced the standard SoDa database values, reducing the error range for all four sites to less than 15%.

Development of a web-based video management and application processing system

NASA Astrophysics Data System (ADS)

Chan, Shermann S.; Wu, Yi; Li, Qing; Zhuang, Yueting

2001-07-01

How to facilitate efficient video manipulation and access in a web-based environment is becoming a popular trend for video applications. In this paper, we present a web-oriented video management and application processing system, based on our previous work on multimedia database and content-based retrieval. In particular, we extend the VideoMAP architecture with specific web-oriented mechanisms, which include: (1) Concurrency control facilities for the editing of video data among different types of users, such as Video Administrator, Video Producer, Video Editor, and Video Query Client; different users are assigned various priority levels for different operations on the database. (2) Versatile video retrieval mechanism which employs a hybrid approach by integrating a query-based (database) mechanism with content- based retrieval (CBR) functions; its specific language (CAROL/ST with CBR) supports spatio-temporal semantics of video objects, and also offers an improved mechanism to describe visual content of videos by content-based analysis method. (3) Query profiling database which records the `histories' of various clients' query activities; such profiles can be used to provide the default query template when a similar query is encountered by the same kind of users. An experimental prototype system is being developed based on the existing VideoMAP prototype system, using Java and VC++ on the PC platform.

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

PubMed Central

Attimonelli, M.; Altamura, N.; Benne, R.; Brennicke, A.; Cooper, J. M.; D’Elia, D.; Montalvo, A. de; Pinto, B. de; 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. V.; 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 cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl . The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme. PMID:10592207

Integrated Functional and Executional Modelling of Software Using Web-Based Databases

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Marietta, Roberta

1998-01-01

NASA's software subsystems undergo extensive modification and updates over the operational lifetimes. It is imperative that modified software should satisfy safety goals. This report discusses the difficulties encountered in doing so and discusses a solution based on integrated modelling of software, use of automatic information extraction tools, web technology and databases. To appear in an article of Journal of Database Management.

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

PubMed

Yang, Jin Ok; Hwang, Sohyun; Oh, Jeongsu; Bhak, Jong; Sohn, Tae-Kwon

2008-12-12

Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases. To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS) for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC) and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page http://diseasome.kobic.re.kr/, and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes. Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for evaluation in both epidemiological and molecular biological approaches to diseases-gene association studies. Furthermore, researchers then can decide semi-automatically the data set for association studies while considering the relationships between genetic variation and diseases. The database can also be economical for disease-association studies, as well as to facilitate an understanding of the processes which cause disease. Currently, the database contains 14,674 SNP records and 109,715 gene records associated with human diseases and it is updated at regular intervals.

Extraction, integration and analysis of alternative splicing and protein structure distributed information

PubMed Central

D'Antonio, Matteo; Masseroli, Marco

2009-01-01

Background Alternative splicing has been demonstrated to affect most of human genes; different isoforms from the same gene encode for proteins which differ for a limited number of residues, thus yielding similar structures. This suggests possible correlations between alternative splicing and protein structure. In order to support the investigation of such relationships, we have developed the Alternative Splicing and Protein Structure Scrutinizer (PASS), a Web application to automatically extract, integrate and analyze human alternative splicing and protein structure data sparsely available in the Alternative Splicing Database, Ensembl databank and Protein Data Bank. Primary data from these databases have been integrated and analyzed using the Protein Identifier Cross-Reference, BLAST, CLUSTALW and FeatureMap3D software tools. Results A database has been developed to store the considered primary data and the results from their analysis; a system of Perl scripts has been implemented to automatically create and update the database and analyze the integrated data; a Web interface has been implemented to make the analyses easily accessible; a database has been created to manage user accesses to the PASS Web application and store user's data and searches. Conclusion PASS automatically integrates data from the Alternative Splicing Database with protein structure data from the Protein Data Bank. Additionally, it comprehensively analyzes the integrated data with publicly available well-known bioinformatics tools in order to generate structural information of isoform pairs. Further analysis of such valuable information might reveal interesting relationships between alternative splicing and protein structure differences, which may be significantly associated with different functions. PMID:19828075

KaBOB: ontology-based semantic integration of biomedical databases.

PubMed

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 formal reasoning over a wealth of integrated biomedical data.

Heterogeneous Biomedical Database Integration Using a Hybrid Strategy: A p53 Cantcer Research Database

PubMed Central

Bichutskiy, Vadim Y.; Colman, Richard; Brachmann, Rainer K.; Lathrop, Richard H.

2006-01-01

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.) PMID:19458771

Network-based drug discovery by integrating systems biology and computational technologies

PubMed Central

Leung, Elaine L.; Cao, Zhi-Wei; Jiang, Zhi-Hong; Zhou, Hua

2013-01-01

Network-based intervention has been a trend of curing systemic diseases, but it relies on regimen optimization and valid multi-target actions of the drugs. The complex multi-component nature of medicinal herbs may serve as valuable resources for network-based multi-target drug discovery due to its potential treatment effects by synergy. Recently, robustness of multiple systems biology platforms shows powerful to uncover molecular mechanisms and connections between the drugs and their targeting dynamic network. However, optimization methods of drug combination are insufficient, owning to lacking of tighter integration across multiple ‘-omics’ databases. The newly developed algorithm- or network-based computational models can tightly integrate ‘-omics’ databases and optimize combinational regimens of drug development, which encourage using medicinal herbs to develop into new wave of network-based multi-target drugs. However, challenges on further integration across the databases of medicinal herbs with multiple system biology platforms for multi-target drug optimization remain to the uncertain reliability of individual data sets, width and depth and degree of standardization of herbal medicine. Standardization of the methodology and terminology of multiple system biology and herbal database would facilitate the integration. Enhance public accessible databases and the number of research using system biology platform on herbal medicine would be helpful. Further integration across various ‘-omics’ platforms and computational tools would accelerate development of network-based drug discovery and network medicine. PMID:22877768

BIOSPIDA: A Relational Database Translator for NCBI.

PubMed

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.

SAM International Case Studies: DPV Analysis in Mexico

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCall, James D

Presentation demonstrates the use of the System Advisor Model (SAM) in international analyses, specifically Mexico. Two analyses are discussed with relation to SAM modelling efforts: 1) Customer impacts from changes to net metering and billing agreements and 2) Potential benefits of PV for Mexican solar customers, the Mexican Treasury, and the environment. Along with the SAM analyses, integration of the International Utility Rate Database (I-URDB) with SAM and future international SAM work are discussed. Presentation was created for the International Solar Energy Society's (ISES) webinar titled 'International use of the NREL System Advisor Model (SAM) with case studies'.

Integrated driver modelling considering state transition feature for individual adaptation of driver assistance systems

NASA Astrophysics Data System (ADS)

Raksincharoensak, Pongsathorn; Khaisongkram, Wathanyoo; Nagai, Masao; Shimosaka, Masamichi; Mori, Taketoshi; Sato, Tomomasa

2010-12-01

This paper describes the modelling of naturalistic driving behaviour in real-world traffic scenarios, based on driving data collected via an experimental automobile equipped with a continuous sensing drive recorder. This paper focuses on the longitudinal driving situations which are classified into five categories - car following, braking, free following, decelerating and stopping - and are referred to as driving states. Here, the model is assumed to be represented by a state flow diagram. Statistical machine learning of driver-vehicle-environment system model based on driving database is conducted by a discriminative modelling approach called boosting sequential labelling method.

An annotation system for 3D fluid flow visualization

NASA Technical Reports Server (NTRS)

Loughlin, Maria M.; Hughes, John F.

1995-01-01

Annotation is a key activity of data analysis. However, current systems for data analysis focus almost exclusively on visualization. We propose a system which integrates annotations into a visualization system. Annotations are embedded in 3D data space, using the Post-it metaphor. This embedding allows contextual-based information storage and retrieval, and facilitates information sharing in collaborative environments. We provide a traditional database filter and a Magic Lens filter to create specialized views of the data. The system has been customized for fluid flow applications, with features which allow users to store parameters of visualization tools and sketch 3D volumes.

Structure and software tools of AIDA.

PubMed

Duisterhout, J S; Franken, B; Witte, F

1987-01-01

AIDA consists of a set of software tools to allow for fast development and easy-to-maintain Medical Information Systems. AIDA supports all aspects of such a system both during development and operation. It contains tools to build and maintain forms for interactive data entry and on-line input validation, a database management system including a data dictionary and a set of run-time routines for database access, and routines for querying the database and output formatting. Unlike an application generator, the user of AIDA may select parts of the tools to fulfill his needs and program other subsystems not developed with AIDA. The AIDA software uses as host language the ANSI-standard programming language MUMPS, an interpreted language embedded in an integrated database and programming environment. This greatly facilitates the portability of AIDA applications. The database facilities supported by AIDA are based on a relational data model. This data model is built on top of the MUMPS database, the so-called global structure. This relational model overcomes the restrictions of the global structure regarding string length. The global structure is especially powerful for sorting purposes. Using MUMPS as a host language allows the user an easy interface between user-defined data validation checks or other user-defined code and the AIDA tools. AIDA has been designed primarily for prototyping and for the construction of Medical Information Systems in a research environment which requires a flexible approach. The prototyping facility of AIDA operates terminal independent and is even to a great extent multi-lingual. Most of these features are table-driven; this allows on-line changes in the use of terminal type and language, but also causes overhead. AIDA has a set of optimizing tools by which it is possible to build a faster, but (of course) less flexible code from these table definitions. By separating the AIDA software in a source and a run-time version, one is able to write implementation-specific code which can be selected and loaded by a special source loader, being part of the AIDA software. This feature is also accessible for maintaining software on different sites and on different installations.

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

PubMed

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.

Data Entities and Information System Matrix for Integrated Agriculture Information System (IAIS)

NASA Astrophysics Data System (ADS)

Budi Santoso, Halim; Delima, Rosa

2018-03-01

Integrated Agriculture Information System is a system that is developed to process data, information, and knowledge in Agriculture sector. Integrated Agriculture Information System brings valuable information for farmers: (1) Fertilizer price; (2) Agriculture technique and practise; (3) Pest management; (4) Cultivation; (5) Irrigation; (6) Post harvest processing; (7) Innovation in agriculture processing. Integrated Agriculture Information System contains 9 subsystems. To bring an integrated information to the user and stakeholder, it needs an integrated database approach. Thus, researchers describes data entity and its matrix relate to subsystem in Integrated Agriculture Information System (IAIS). As a result, there are 47 data entities as entities in single and integrated database.

Understanding the Effects of Databases as Cognitive Tools in a Problem-Based Multimedia Learning Environment

ERIC Educational Resources Information Center

Li, Rui; Liu, Min

2007-01-01

The purpose of this study is to examine the potential of using computer databases as cognitive tools to share learners' cognitive load and facilitate learning in a multimedia problem-based learning (PBL) environment designed for sixth graders. Two research questions were: (a) can the computer database tool share sixth-graders' cognitive load? and…

The Impact of Environment and Occupation on the Health and Safety of Active Duty Air Force Members - Database Development and De-Identification

DTIC Science & Technology

2015-04-01

et al. Work , obesity , and occupational safety and health . Am J Public Health . 2007; 97(3):428-436. 7. Grunberg L, Moore S, Anderson-Connolly R...AFRL-SA-WP-SR-2015-0005 The Impact of Environment and Occupation on the Health and Safety of Active Duty Air Force Members – Database...TITLE AND SUBTITLE The Impact of Environment and Occupation on the Health and Safety of Active Duty Air Force Members – Database Development and De

A Semantic Sensor Web for Environmental Decision Support Applications

PubMed Central

Gray, Alasdair J. G.; Sadler, Jason; Kit, Oles; Kyzirakos, Kostis; Karpathiotakis, Manos; Calbimonte, Jean-Paul; Page, Kevin; García-Castro, Raúl; Frazer, Alex; Galpin, Ixent; Fernandes, Alvaro A. A.; Paton, Norman W.; Corcho, Oscar; Koubarakis, Manolis; De Roure, David; Martinez, Kirk; Gómez-Pérez, Asunción

2011-01-01

Sensing devices are increasingly being deployed to monitor the physical world around us. One class of application for which sensor data is pertinent is environmental decision support systems, e.g., flood emergency response. For these applications, the sensor readings need to be put in context by integrating them with other sources of data about the surrounding environment. Traditional systems for predicting and detecting floods rely on methods that need significant human resources. In this paper we describe a semantic sensor web architecture for integrating multiple heterogeneous datasets, including live and historic sensor data, databases, and map layers. The architecture provides mechanisms for discovering datasets, defining integrated views over them, continuously receiving data in real-time, and visualising on screen and interacting with the data. Our approach makes extensive use of web service standards for querying and accessing data, and semantic technologies to discover and integrate datasets. We demonstrate the use of our semantic sensor web architecture in the context of a flood response planning web application that uses data from sensor networks monitoring the sea-state around the coast of England. PMID:22164110

Integrated Database And Knowledge Base For Genomic Prospective Cohort Study In Tohoku Medical Megabank Toward Personalized Prevention And Medicine.

PubMed

Ogishima, Soichi; Takai, Takako; Shimokawa, Kazuro; Nagaie, Satoshi; Tanaka, Hiroshi; Nakaya, Jun

2015-01-01

The Tohoku Medical Megabank project is a national project to revitalization of the disaster area in the Tohoku region by the Great East Japan Earthquake, and have conducted large-scale prospective genome-cohort study. Along with prospective genome-cohort study, we have developed integrated database and knowledge base which will be key database for realizing personalized prevention and medicine.

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

PubMed

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.

Soil and Land Resources Information System (SLISYS-Tarim) for Sustainable Management of River Oases along the Tarim River, China

NASA Astrophysics Data System (ADS)

Othmanli, Hussein; Zhao, Chengyi; Stahr, Karl

2017-04-01

The Tarim River Basin is the largest continental basin in China. The region has extremely continental desert climate characterized by little rainfall <50 mm/a and high potential evaporation >3000 mm/a. The climate change is affecting severely the basin causing soil salinization, water shortage, and regression in crop production. Therefore, a Soil and Land Resources Information System (SLISYS-Tarim) for the regional simulation of crop yield production in the basin was developed. The SLISYS-Tarim consists of a database and an agro-ecological simulation model EPIC (Environmental Policy Integrated Climate). The database comprises relational tables including information about soils, terrain conditions, land use, and climate. The soil data implicate information of 50 soil profiles which were dug, analyzed, described and classified in order to characterize the soils in the region. DEM data were integrated with geological maps to build a digital terrain structure. Remote sensing data of Landsat images were applied for soil mapping, and for land use and land cover classification. An additional database for climate data, land management and crop information were linked to the system, too. Construction of the SLISYS-Tarim database was accomplished by integrating and overlaying the recommended thematic maps within environment of the geographic information system (GIS) to meet the data standard of the global and national SOTER digital database. This database forms appropriate input- and output data for the crop modelling with the EPIC model at various scales in the Tarim Basin. The EPIC model was run for simulating cotton production under a constructed scenario characterizing the current management practices, soil properties and climate conditions. For the EPIC model calibration, some parameters were adjusted so that the modeled cotton yield fits to the measured yield on the filed scale. The validation of the modeling results was achieved in a later step based on remote sensing data. The simulated cotton yield varied according to field management, soil type and salinity level, where soil salinity was the main limiting factor. Furthermore, the calibrated and validated EPIC model was run under several scenarios of climate conditions and land management practices to estimate the effect of climate change on cotton production and sustainability of agriculture systems in the basin. The application of SLISYS-Tarim showed that this database can be a suitable framework for storage and retrieval of soil and terrain data at various scales. The simulation with the EPIC model can assess the impact of climate change and management strategies. Therefore, SLISYS-Tarim can be a good tool for regional planning and serve the decision support system on regional and national scale.

Integration of Oracle and Hadoop: Hybrid Databases Affordable at Scale

NASA Astrophysics Data System (ADS)

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.

Pain assessment scales in newborns: integrative review

PubMed Central

de Melo, Gleicia Martins; Lélis, Ana Luíza Paula de Aguiar; de Moura, Alline Falconieri; Cardoso, Maria Vera Lúcia Moreira Leitão; da Silva, Viviane Martins

2014-01-01

OBJECTIVE: To analyze studies on methods used to assess pain in newborns. DATA SOURCES: Integrative review study of articles published from 2001 to 2012, carried out in the following databases: Scopus, PubMed, CINAHL, LILACS and Cochrane. The sample consisted of 13 articles with level of evidence 5. DATA SYNTHESIS: 29 pain assessment scales in newborns, including 13 one-dimensional and 16 multidimensional, that assess acute and prolonged pain in preterm and full-term infants were available in scientific publications. CONCLUSION: Based on the characteristics of scales, one cannot choose a single one as the most appropriate scale, as this choice will depend on gestational age, type of painful stimulus and the environment in which the infant is inserted. It is suggested the use of multidimensional or one-dimensional scales; however, they must be reliable and validated. PMID:25511005

Achieving Integration in Mixed Methods Designs—Principles and Practices

PubMed Central

Fetters, Michael D; Curry, Leslie A; Creswell, John W

2013-01-01

Mixed methods research offers powerful tools for investigating complex processes and systems in health and health care. This article describes integration principles and practices at three levels in mixed methods research and provides illustrative examples. Integration at the study design level occurs through three basic mixed method designs—exploratory sequential, explanatory sequential, and convergent—and through four advanced frameworks—multistage, intervention, case study, and participatory. Integration at the methods level occurs through four approaches. In connecting, one database links to the other through sampling. With building, one database informs the data collection approach of the other. When merging, the two databases are brought together for analysis. With embedding, data collection and analysis link at multiple points. Integration at the interpretation and reporting level occurs through narrative, data transformation, and joint display. The fit of integration describes the extent the qualitative and quantitative findings cohere. Understanding these principles and practices of integration can help health services researchers leverage the strengths of mixed methods. PMID:24279835

Achieving integration in mixed methods designs-principles and practices.

PubMed

Fetters, Michael D; Curry, Leslie A; Creswell, John W

2013-12-01

Mixed methods research offers powerful tools for investigating complex processes and systems in health and health care. This article describes integration principles and practices at three levels in mixed methods research and provides illustrative examples. Integration at the study design level occurs through three basic mixed method designs-exploratory sequential, explanatory sequential, and convergent-and through four advanced frameworks-multistage, intervention, case study, and participatory. Integration at the methods level occurs through four approaches. In connecting, one database links to the other through sampling. With building, one database informs the data collection approach of the other. When merging, the two databases are brought together for analysis. With embedding, data collection and analysis link at multiple points. Integration at the interpretation and reporting level occurs through narrative, data transformation, and joint display. The fit of integration describes the extent the qualitative and quantitative findings cohere. Understanding these principles and practices of integration can help health services researchers leverage the strengths of mixed methods. © Health Research and Educational Trust.

BIOSPIDA: A Relational Database Translator for NCBI

PubMed Central

Hagen, Matthew S.; Lee, Eva K.

2010-01-01

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. PMID:21347013

Design and development of a new facility for teaching and research in clinical anatomy.

PubMed

Greene, John Richard T

2009-01-01

This article discusses factors in the design, commissioning, project management, and intellectual property protection of developments within a new clinical anatomy facility in the United Kingdom. The project was aimed at creating cost-effective facilities that would address widespread concerns over anatomy teaching, and support other activities central to the university mission-namely research and community interaction. The new facilities comprise an engaging learning environment and were designed to support a range of pedagogies appropriate to the needs of healthcare professionals at different stages of their careers. Specific innovations include integrated workstations each comprising of a dissection table, with removable top sections, an overhead operating light, and ceiling-mounted camera. The tables incorporate waterproof touch-screen monitors to display images from the camera, an endoscope or a database of images, videos, and tutorials. The screens work independently so that instructors can run different teaching sessions simultaneously and students can progress at different speeds to suit themselves. Further, database access is provided from within an integrated anatomy and pathology museum and display units dedicated to the correlation of cross-sectional anatomy with medical imaging. A new functional neuroanatomy modeling system, called the BrainTower, has been developed to aid integration of anatomy with physiology and clinical neurology. Many aspects of the new facility are reproduced within a Mobile Teaching Unit, which can be driven to hospitals, colleges, and schools to provide appropriate work-based education and community interaction. (c) 2009 American Association of Anatomists

Solar-Terrestrial Ontology Development

NASA Astrophysics Data System (ADS)

McGuinness, D.; Fox, P.; Middleton, D.; Garcia, J.; Cinquni, L.; West, P.; Darnell, J. A.; Benedict, J.

2005-12-01

The development of an interdisciplinary virtual observatory (the Virtual Solar-Terrestrial Observatory; VSTO) as a scalable environment for searching, integrating, and analyzing databases distributed over the Internet requires a higher level of semantic interoperability than here-to-fore required by most (if not all) distributed data systems or discipline specific virtual observatories. The formalization of semantics using ontologies and their encodings for the internet (e.g. OWL - the Web Ontology Language), as well as the use of accompanying tools, such as reasoning, inference and explanation, open up both a substantial leap in options for interoperability and in the need for formal development principles to guide ontology development and use within modern, multi-tiered network data environments. In this presentation, we outline the formal methodologies we utilize in the VSTO project, the currently developed use-cases, ontologies and their relation to existing ontologies (such as SWEET).

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea.

PubMed

Martin, Stanton L; Blackmon, Barbara P; Rajagopalan, Ravi; Houfek, Thomas D; Sceeles, Robert G; Denn, Sheila O; Mitchell, Thomas K; Brown, Douglas E; Wing, Rod A; Dean, Ralph A

2002-01-01

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.

BNDB - the Biochemical Network Database.

PubMed

Küntzer, Jan; Backes, Christina; Blum, Torsten; Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter

2007-10-02

Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources. We present the Biochemical Network Database (BNDB), a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA) provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB. BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at http://www.bndb.org.

HNS-MS : Improving Member States preparedness to face an HNS pollution of the Marine System

NASA Astrophysics Data System (ADS)

Legrand, Sébastien; Le Floch, Stéphane; Aprin, Laurent; Partenay, Valérie; Donnay, Eric; Parmentier, Koen; Ovidio, Fabrice; Schallier, Ronny; Poncet, Florence; Chataing, Sophie; Poupon, Emmanuelle; Hellouvry, Yann-Hervé

2017-04-01

When dealing with a HNS pollution incident, one of the priority requirements is the identification of the hazard and an assessment of the risk posed to the public and responder safety, the environment and socioeconomic assets upon which a state or coastal community depend. The primary factors which determine the safety, environmental and socioeconomic impact of the released substance(s) relate to their physico-chemical properties and fate in the environment. Until now, preparedness actions at various levels have primarily aimed at classifying the general environmental or public health hazard of an HNS, or at performing a risk analysis of HNS transported in European marine regions. Operational datasheets have been (MIDSIS-TROCS) or are being (MAR-CIS) developed collating detailed, substance-specific information for responders and covering information needs at the first stage of an incident. However, contrary to oil pollution preparedness and response tools, only few decision-support tools used by Member State authorities (Coastguard agencies or other) integrate 3D models that are able to simulate the drift, fate and behaviour of HNS spills in the marine environment. When they do, they usually consider simplified or steady-state environmental conditions. As a significant step forward, a 'one-stop shop' integrated HNS decision-support system has been developed in the framework of the HNS-MS project. Focussing on the Bonn Agreement area, the system integrates 1. A database containing the physico-chemical parameters needed to compute the behaviour in the marine environment of 120 relevant HNS; 2. A digital atlas of the HNS environmental and socioeconomic vulnerability maps ; 3. A three dimensional HNS spill drift and fate model able to simulate HNS behaviour in the marine environment (including floaters, sinkers, evaporators and dissolvers). 4. A user-friendly web-based interface allowing Coastguard stations to launch a HNS drift simulation and visualize post-processed results in support of an incident evaluation and decision-making process. All these results will be further presented.

microRNAs Databases: Developmental Methodologies, Structural and Functional Annotations.

PubMed

Singh, Nagendra Kumar

2017-09-01

microRNA (miRNA) is an endogenous and evolutionary conserved non-coding RNA, involved in post-transcriptional process as gene repressor and mRNA cleavage through RNA-induced silencing complex (RISC) formation. In RISC, miRNA binds in complementary base pair with targeted mRNA along with Argonaut proteins complex, causes gene repression or endonucleolytic cleavage of mRNAs and results in many diseases and syndromes. After the discovery of miRNA lin-4 and let-7, subsequently large numbers of miRNAs were discovered by low-throughput and high-throughput experimental techniques along with computational process in various biological and metabolic processes. The miRNAs are important non-coding RNA for understanding the complex biological phenomena of organism because it controls the gene regulation. This paper reviews miRNA databases with structural and functional annotations developed by various researchers. These databases contain structural and functional information of animal, plant and virus miRNAs including miRNAs-associated diseases, stress resistance in plant, miRNAs take part in various biological processes, effect of miRNAs interaction on drugs and environment, effect of variance on miRNAs, miRNAs gene expression analysis, sequence of miRNAs, structure of miRNAs. This review focuses on the developmental methodology of miRNA databases such as computational tools and methods used for extraction of miRNAs annotation from different resources or through experiment. This study also discusses the efficiency of user interface design of every database along with current entry and annotations of miRNA (pathways, gene ontology, disease ontology, etc.). Here, an integrated schematic diagram of construction process for databases is also drawn along with tabular and graphical comparison of various types of entries in different databases. Aim of this paper is to present the importance of miRNAs-related resources at a single place.

Integration of biological responses from a suite of bioassays for the Venice Lagoon (Italy) through sediment toxicity index - part A: development and comparison of two methodological approaches.

PubMed

Losso, Chiara; Novelli, Alessandra Arizzi; De Salvador, Davide; Ghetti, Pier Francesco; Ghirardini, Annamaria Volpi

2010-12-01

Marine and coastal quality assessment, based on test batteries involving a wide array of endpoints, organisms and test matrices, needs for setting up toxicity indices that integrate multiple toxicological measures for decision-making processes and that classify the continuous toxicity response into discrete categories according to the European Water Framework Directive. Two toxicity indices were developed for the lagoon environment such as the Venice Lagoon. Stepwise procedure included: the construction of a database that identified test-matrix pairs (indicators); the selection of a minimum number of ecotoxicological indicators, called toxicological core metrics (CMs-tox) on the basis of specific criteria; the development of toxicity scores for each CM-tox; the integration of the CMs-tox into two indices, the Toxicity Effect Index (TEI), based on the transformation of Toxic Unit (TU) data that were integrated as logarithmic sum, and the Weighted Average Toxicity Index (WATI), starting from toxicity classes integrated as weighted mean. Results from the indices are compared; advantages and drawbacks of both approaches are discussed. Copyright © 2010. Published by Elsevier Ltd.

Integration of Jeddah Historical BIM and 3D GIS for Documentation and Restoration of Historical Monument

NASA Astrophysics Data System (ADS)

Baik, A.; Yaagoubi, R.; Boehm, J.

2015-08-01

This work outlines a new approach for the integration of 3D Building Information Modelling and the 3D Geographic Information System (GIS) to provide semantically rich models, and to get the benefits from both systems to help document and analyse cultural heritage sites. Our proposed framework is based on the Jeddah Historical Building Information Modelling process (JHBIM). This JHBIM consists of a Hijazi Architectural Objects Library (HAOL) that supports higher level of details (LoD) while decreasing the time of modelling. The Hijazi Architectural Objects Library has been modelled based on the Islamic historical manuscripts and Hijazi architectural pattern books. Moreover, the HAOL is implemented using BIM software called Autodesk Revit. However, it is known that this BIM environment still has some limitations with the non-standard architectural objects. Hence, we propose to integrate the developed 3D JHBIM with 3D GIS for more advanced analysis. To do so, the JHBIM database is exported and semantically enriched with non-architectural information that is necessary for restoration and preservation of historical monuments. After that, this database is integrated with the 3D Model in the 3D GIS solution. At the end of this paper, we'll illustrate our proposed framework by applying it to a Historical Building called Nasif Historical House in Jeddah. First of all, this building is scanned by the use of a Terrestrial Laser Scanner (TLS) and Close Range Photogrammetry. Then, the 3D JHBIM based on the HOAL is designed on Revit Platform. Finally, this model is integrated to a 3D GIS solution through Autodesk InfraWorks. The shown analysis presented in this research highlights the importance of such integration especially for operational decisions and sharing the historical knowledge about Jeddah Historical City. Furthermore, one of the historical buildings in Old Jeddah, Nasif Historical House, was chosen as a test case for the project.

An overview of platforms for cloud based development.

PubMed

Fylaktopoulos, G; Goumas, G; Skolarikis, M; Sotiropoulos, A; Maglogiannis, I

2016-01-01

This paper provides an overview of the state of the art technologies for software development in cloud environments. The surveyed systems cover the whole spectrum of cloud-based development including integrated programming environments, code repositories, software modeling, composition and documentation tools, and application management and orchestration. In this work we evaluate the existing cloud development ecosystem based on a wide number of characteristics like applicability (e.g. programming and database technologies supported), productivity enhancement (e.g. editor capabilities, debugging tools), support for collaboration (e.g. repository functionality, version control) and post-development application hosting and we compare the surveyed systems. The conducted survey proves that software engineering in the cloud era has made its initial steps showing potential to provide concrete implementation and execution environments for cloud-based applications. However, a number of important challenges need to be addressed for this approach to be viable. These challenges are discussed in the article, while a conclusion is drawn that although several steps have been made, a compact and reliable solution does not yet exist.

A network-based training environment: a medical image processing paradigm.

PubMed

Costaridou, L; Panayiotakis, G; Sakellaropoulos, P; Cavouras, D; Dimopoulos, J

1998-01-01

The capability of interactive multimedia and Internet technologies is investigated with respect to the implementation of a distance learning environment. The system is built according to a client-server architecture, based on the Internet infrastructure, composed of server nodes conceptually modelled as WWW sites. Sites are implemented by customization of available components. The environment integrates network-delivered interactive multimedia courses, network-based tutoring, SIG support, information databases of professional interest, as well as course and tutoring management. This capability has been demonstrated by means of an implemented system, validated with digital image processing content, specifically image enhancement. Image enhancement methods are theoretically described and applied to mammograms. Emphasis is given to the interactive presentation of the effects of algorithm parameters on images. The system end-user access depends on available bandwidth, so high-speed access can be achieved via LAN or local ISDN connections. Network based training offers new means of improved access and sharing of learning resources and expertise, as promising supplements in training.

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

PubMed

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.

Spatial Data Integration Using Ontology-Based Approach

NASA Astrophysics Data System (ADS)

Hasani, S.; Sadeghi-Niaraki, A.; Jelokhani-Niaraki, M.

2015-12-01

In today's world, the necessity for spatial data for various organizations is becoming so crucial that many of these organizations have begun to produce spatial data for that purpose. In some circumstances, the need to obtain real time integrated data requires sustainable mechanism to process real-time integration. Case in point, the disater management situations that requires obtaining real time data from various sources of information. One of the problematic challenges in the mentioned situation is the high degree of heterogeneity between different organizations data. To solve this issue, we introduce an ontology-based method to provide sharing and integration capabilities for the existing databases. In addition to resolving semantic heterogeneity, better access to information is also provided by our proposed method. Our approach is consisted of three steps, the first step is identification of the object in a relational database, then the semantic relationships between them are modelled and subsequently, the ontology of each database is created. In a second step, the relative ontology will be inserted into the database and the relationship of each class of ontology will be inserted into the new created column in database tables. Last step is consisted of a platform based on service-oriented architecture, which allows integration of data. This is done by using the concept of ontology mapping. The proposed approach, in addition to being fast and low cost, makes the process of data integration easy and the data remains unchanged and thus takes advantage of the legacy application provided.

MACSIMS : multiple alignment of complete sequences information management system

PubMed Central

Thompson, Julie D; Muller, Arnaud; Waterhouse, Andrew; Procter, Jim; Barton, Geoffrey J; Plewniak, Frédéric; Poch, Olivier

2006-01-01

Background In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. Results MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. Conclusion MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at . PMID:16792820

Topobathymetric elevation model development using a new methodology: Coastal National Elevation Database

USGS Publications Warehouse

Danielson, Jeffrey J.; Poppenga, Sandra K.; Brock, John C.; Evans, Gayla A.; Tyler, Dean; Gesch, Dean B.; Thatcher, Cindy A.; Barras, John

2016-01-01

During the coming decades, coastlines will respond to widely predicted sea-level rise, storm surge, and coastalinundation flooding from disastrous events. Because physical processes in coastal environments are controlled by the geomorphology of over-the-land topography and underwater bathymetry, many applications of geospatial data in coastal environments require detailed knowledge of the near-shore topography and bathymetry. In this paper, an updated methodology used by the U.S. Geological Survey Coastal National Elevation Database (CoNED) Applications Project is presented for developing coastal topobathymetric elevation models (TBDEMs) from multiple topographic data sources with adjacent intertidal topobathymetric and offshore bathymetric sources to generate seamlessly integrated TBDEMs. This repeatable, updatable, and logically consistent methodology assimilates topographic data (land elevation) and bathymetry (water depth) into a seamless coastal elevation model. Within the overarching framework, vertical datum transformations are standardized in a workflow that interweaves spatially consistent interpolation (gridding) techniques with a land/water boundary mask delineation approach. Output gridded raster TBDEMs are stacked into a file storage system of mosaic datasets within an Esri ArcGIS geodatabase for efficient updating while maintaining current and updated spatially referenced metadata. Topobathymetric data provide a required seamless elevation product for several science application studies, such as shoreline delineation, coastal inundation mapping, sediment-transport, sea-level rise, storm surge models, and tsunami impact assessment. These detailed coastal elevation data are critical to depict regions prone to climate change impacts and are essential to planners and managers responsible for mitigating the associated risks and costs to both human communities and ecosystems. The CoNED methodology approach has been used to construct integrated TBDEM models in Mobile Bay, the northern Gulf of Mexico, San Francisco Bay, the Hurricane Sandy region, and southern California.

Methods for structuring scientific knowledge from many areas related to aging research.

PubMed

Zhavoronkov, Alex; Cantor, Charles R

2011-01-01

Aging and age-related disease represents a substantial quantity of current natural, social and behavioral science research efforts. Presently, no centralized system exists for tracking aging research projects across numerous research disciplines. The multidisciplinary nature of this research complicates the understanding of underlying project categories, the establishment of project relations, and the development of a unified project classification scheme. We have developed a highly visual database, the International Aging Research Portfolio (IARP), available at AgingPortfolio.org to address this issue. The database integrates information on research grants, peer-reviewed publications, and issued patent applications from multiple sources. Additionally, the database uses flexible project classification mechanisms and tools for analyzing project associations and trends. This system enables scientists to search the centralized project database, to classify and categorize aging projects, and to analyze the funding aspects across multiple research disciplines. The IARP is designed to provide improved allocation and prioritization of scarce research funding, to reduce project overlap and improve scientific collaboration thereby accelerating scientific and medical progress in a rapidly growing area of research. Grant applications often precede publications and some grants do not result in publications, thus, this system provides utility to investigate an earlier and broader view on research activity in many research disciplines. This project is a first attempt to provide a centralized database system for research grants and to categorize aging research projects into multiple subcategories utilizing both advanced machine algorithms and a hierarchical environment for scientific collaboration.

Evaluation of Online Information Sources on Alien Species in Europe: The Need of Harmonization and Integration

NASA Astrophysics Data System (ADS)

Gatto, Francesca; Katsanevakis, Stelios; Vandekerkhove, Jochen; Zenetos, Argyro; Cardoso, Ana Cristina

2013-06-01

Europe is severely affected by alien invasions, which impact biodiversity, ecosystem services, economy, and human health. A large number of national, regional, and global online databases provide information on the distribution, pathways of introduction, and impacts of alien species. The sufficiency and efficiency of the current online information systems to assist the European policy on alien species was investigated by a comparative analysis of occurrence data across 43 online databases. Large differences among databases were found which are partially explained by variations in their taxonomical, environmental, and geographical scopes but also by the variable efforts for continuous updates and by inconsistencies on the definition of "alien" or "invasive" species. No single database covered all European environments, countries, and taxonomic groups. In many European countries national databases do not exist, which greatly affects the quality of reported information. To be operational and useful to scientists, managers, and policy makers, online information systems need to be regularly updated through continuous monitoring on a country or regional level. We propose the creation of a network of online interoperable web services through which information in distributed resources can be accessed, aggregated and then used for reporting and further analysis at different geographical and political scales, as an efficient approach to increase the accessibility of information. Harmonization, standardization, conformity on international standards for nomenclature, and agreement on common definitions of alien and invasive species are among the necessary prerequisites.

MEPD: a Medaka gene expression pattern database

PubMed Central

Henrich, Thorsten; Ramialison, Mirana; Quiring, Rebecca; Wittbrodt, Beate; Furutani-Seiki, Makoto; Wittbrodt, Joachim; Kondoh, Hisato

2003-01-01

The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensity, category and comments and through a comprehensive, hierarchically organized dictionary of anatomical terms. Sequences of the ESTs are available and searchable through BLAST. ESTs in the database are clustered upon entry and have been blasted against public data-bases. The BLAST results are updated regularly, stored within the database and searchable. The MEPD is a project within the Medaka Genome Initiative (MGI) and entries will be interconnected to integrated genomic map databases. MEPD is accessible through the WWW at http://medaka.dsp.jst.go.jp/MEPD. PMID:12519950

A Summary of the Naval Postgraduate School Research Program

DTIC Science & Technology

1989-08-30

5 Fundamental Theory for Automatically Combining Changes to Software Systems ............................ 6 Database -System Approach to...Software Engineering Environments(SEE’s) .................................. 10 Multilevel Database Security .......................... 11 Temporal... Database Management and Real-Time Database Computers .................................... 12 The Multi-lingual, Multi Model, Multi-Backend Database

Heterogenous database integration in a physician workstation.

PubMed

Annevelink, J; Young, C Y; Tang, P C

1991-01-01

We discuss the integration of a variety of data and information sources in a Physician Workstation (PWS), focusing on the integration of data from DHCP, the Veteran Administration's Distributed Hospital Computer Program. We designed a logically centralized, object-oriented data-schema, used by end users and applications to explore the data accessible through an object-oriented database using a declarative query language. We emphasize the use of procedural abstraction to transparently integrate a variety of information sources into the data schema.

Heterogenous database integration in a physician workstation.

PubMed Central

Annevelink, J.; Young, C. Y.; Tang, P. C.

1991-01-01

We discuss the integration of a variety of data and information sources in a Physician Workstation (PWS), focusing on the integration of data from DHCP, the Veteran Administration's Distributed Hospital Computer Program. We designed a logically centralized, object-oriented data-schema, used by end users and applications to explore the data accessible through an object-oriented database using a declarative query language. We emphasize the use of procedural abstraction to transparently integrate a variety of information sources into the data schema. PMID:1807624

An Imaging Sensor-Aided Vision Navigation Approach that Uses a Geo-Referenced Image Database.

PubMed

Li, Yan; Hu, Qingwu; Wu, Meng; Gao, Yang

2016-01-28

In determining position and attitude, vision navigation via real-time image processing of data collected from imaging sensors is advanced without a high-performance global positioning system (GPS) and an inertial measurement unit (IMU). Vision navigation is widely used in indoor navigation, far space navigation, and multiple sensor-integrated mobile mapping. This paper proposes a novel vision navigation approach aided by imaging sensors and that uses a high-accuracy geo-referenced image database (GRID) for high-precision navigation of multiple sensor platforms in environments with poor GPS. First, the framework of GRID-aided vision navigation is developed with sequence images from land-based mobile mapping systems that integrate multiple sensors. Second, a highly efficient GRID storage management model is established based on the linear index of a road segment for fast image searches and retrieval. Third, a robust image matching algorithm is presented to search and match a real-time image with the GRID. Subsequently, the image matched with the real-time scene is considered to calculate the 3D navigation parameter of multiple sensor platforms. Experimental results show that the proposed approach retrieves images efficiently and has navigation accuracies of 1.2 m in a plane and 1.8 m in height under GPS loss in 5 min and within 1500 m.

An Imaging Sensor-Aided Vision Navigation Approach that Uses a Geo-Referenced Image Database

PubMed Central

Li, Yan; Hu, Qingwu; Wu, Meng; Gao, Yang

2016-01-01

In determining position and attitude, vision navigation via real-time image processing of data collected from imaging sensors is advanced without a high-performance global positioning system (GPS) and an inertial measurement unit (IMU). Vision navigation is widely used in indoor navigation, far space navigation, and multiple sensor-integrated mobile mapping. This paper proposes a novel vision navigation approach aided by imaging sensors and that uses a high-accuracy geo-referenced image database (GRID) for high-precision navigation of multiple sensor platforms in environments with poor GPS. First, the framework of GRID-aided vision navigation is developed with sequence images from land-based mobile mapping systems that integrate multiple sensors. Second, a highly efficient GRID storage management model is established based on the linear index of a road segment for fast image searches and retrieval. Third, a robust image matching algorithm is presented to search and match a real-time image with the GRID. Subsequently, the image matched with the real-time scene is considered to calculate the 3D navigation parameter of multiple sensor platforms. Experimental results show that the proposed approach retrieves images efficiently and has navigation accuracies of 1.2 m in a plane and 1.8 m in height under GPS loss in 5 min and within 1500 m. PMID:26828496

Ultra-Structure database design methodology for managing systems biology data and analyses

PubMed Central

Maier, Christopher W; Long, Jeffrey G; Hemminger, Bradley M; Giddings, Morgan C

2009-01-01

Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping). Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find Ultra-Structure offers substantial benefits for biological information systems, the largest being the integration of diverse information sources into a common framework. This facilitates systems biology research by integrating data from disparate high-throughput techniques. It also enables us to readily incorporate new data types, sources, and domain knowledge with no change to the database structure or associated computer code. Ultra-Structure may be a significant step towards solving the hard problem of data management and integration in the systems biology era. PMID:19691849

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

PubMed Central

Seaver, Samuel M. D.; Gerdes, Svetlana; Frelin, Océane; Lerma-Ortiz, Claudia; Bradbury, Louis M. T.; Zallot, Rémi; Hasnain, Ghulam; Niehaus, Thomas D.; El Yacoubi, Basma; Pasternak, Shiran; Olson, Robert; Pusch, Gordon; Overbeek, Ross; Stevens, Rick; de Crécy-Lagard, Valérie; Ware, Doreen; Hanson, Andrew D.; Henry, Christopher S.

2014-01-01

The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today’s annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed. PMID:24927599

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.

PubMed

Seaver, Samuel M D; Gerdes, Svetlana; Frelin, Océane; Lerma-Ortiz, Claudia; Bradbury, Louis M T; Zallot, Rémi; Hasnain, Ghulam; Niehaus, Thomas D; El Yacoubi, Basma; Pasternak, Shiran; Olson, Robert; Pusch, Gordon; Overbeek, Ross; Stevens, Rick; de Crécy-Lagard, Valérie; Ware, Doreen; Hanson, Andrew D; Henry, Christopher S

2014-07-01

The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed.

A multimedia perioperative record keeper for clinical research.

PubMed

Perrino, A C; Luther, M A; Phillips, D B; Levin, F L

1996-05-01

To develop a multimedia perioperative recordkeeper that provides: 1. synchronous, real-time acquisition of multimedia data, 2. on-line access to the patient's chart data, and 3. advanced data analysis capabilities through integrated, multimedia database and analysis applications. To minimize cost and development time, the system design utilized industry standard hardware components and graphical. software development tools. The system was configured to use a Pentium PC complemented with a variety of hardware interfaces to external data sources. These sources included physiologic monitors with data in digital, analog, video, and audio as well as paper-based formats. The development process was guided by trials in over 80 clinical cases and by the critiques from numerous users. As a result of this process, a suite of custom software applications were created to meet the design goals. The Perioperative Data Acquisition application manages data collection from a variety of physiological monitors. The Charter application provides for rapid creation of an electronic medical record from the patient's paper-based chart and investigator's notes. The Multimedia Medical Database application provides a relational database for the organization and management of multimedia data. The Triscreen application provides an integrated data analysis environment with simultaneous, full-motion data display. With recent technological advances in PC power, data acquisition hardware, and software development tools, the clinical researcher now has the ability to collect and examine a more complete perioperative record. It is hoped that the description of the MPR and its development process will assist and encourage others to advance these tools for perioperative research.

A DBMS-based medical teleconferencing system.

PubMed

Chun, J; Kim, H; Lee, S; Choi, J; Cho, H

2001-01-01

This article presents the design of a medical teleconferencing system that is integrated with a multimedia patient database and incorporates easy-to-use tools and functions to effectively support collaborative work between physicians in remote locations. The design provides a virtual workspace that allows physicians to collectively view various kinds of patient data. By integrating the teleconferencing function into this workspace, physicians are able to conduct conferences using the same interface and have real-time access to the database during conference sessions. The authors have implemented a prototype based on this design. The prototype uses a high-speed network test bed and a manually created substitute for the integrated patient database.

A DBMS-based Medical Teleconferencing System

PubMed Central

Chun, Jonghoon; Kim, Hanjoon; Lee, Sang-goo; Choi, Jinwook; Cho, Hanik

2001-01-01

This article presents the design of a medical teleconferencing system that is integrated with a multimedia patient database and incorporates easy-to-use tools and functions to effectively support collaborative work between physicians in remote locations. The design provides a virtual workspace that allows physicians to collectively view various kinds of patient data. By integrating the teleconferencing function into this workspace, physicians are able to conduct conferences using the same interface and have real-time access to the database during conference sessions. The authors have implemented a prototype based on this design. The prototype uses a high-speed network test bed and a manually created substitute for the integrated patient database. PMID:11522766

MetaMetaDB: a database and analytic system for investigating microbial habitability.

PubMed

Yang, Ching-chia; Iwasaki, Wataru

2014-01-01

MetaMetaDB (http://mmdb.aori.u-tokyo.ac.jp/) is a database and analytic system for investigating microbial habitability, i.e., how a prokaryotic group can inhabit different environments. The interaction between prokaryotes and the environment is a key issue in microbiology because distinct prokaryotic communities maintain distinct ecosystems. Because 16S ribosomal RNA (rRNA) sequences play pivotal roles in identifying prokaryotic species, a system that comprehensively links diverse environments to 16S rRNA sequences of the inhabitant prokaryotes is necessary for the systematic understanding of the microbial habitability. However, existing databases are biased to culturable prokaryotes and exhibit limitations in the comprehensiveness of the data because most prokaryotes are unculturable. Recently, metagenomic and 16S rRNA amplicon sequencing approaches have generated abundant 16S rRNA sequence data that encompass unculturable prokaryotes across diverse environments; however, these data are usually buried in large databases and are difficult to access. In this study, we developed MetaMetaDB (Meta-Metagenomic DataBase), which comprehensively and compactly covers 16S rRNA sequences retrieved from public datasets. Using MetaMetaDB, users can quickly generate hypotheses regarding the types of environments a prokaryotic group may be adapted to. We anticipate that MetaMetaDB will improve our understanding of the diversity and evolution of prokaryotes.

Design of a web portal for interdisciplinary image retrieval from multiple online image resources.

PubMed

Kammerer, F J; Frankewitsch, T; Prokosch, H-U

2009-01-01

Images play an important role in medicine. Finding the desired images within the multitude of online image databases is a time-consuming and frustrating process. Existing websites do not meet all the requirements for an ideal learning environment for medical students. This work intends to establish a new web portal providing a centralized access point to a selected number of online image databases. A back-end system locates images on given websites and extracts relevant metadata. The images are indexed using UMLS and the MetaMap system provided by the US National Library of Medicine. Specially developed functions allow to create individual navigation structures. The front-end system suits the specific needs of medical students. A navigation structure consisting of several medical fields, university curricula and the ICD-10 was created. The images may be accessed via the given navigation structure or using different search functions. Cross-references are provided by the semantic relations of the UMLS. Over 25,000 images were identified and indexed. A pilot evaluation among medical students showed good first results concerning the acceptance of the developed navigation structures and search features. The integration of the images from different sources into the UMLS semantic network offers a quick and an easy-to-use learning environment.

Automated generation and ensemble-learned matching of X-ray absorption spectra

NASA Astrophysics Data System (ADS)

Zheng, Chen; Mathew, Kiran; Chen, Chi; Chen, Yiming; Tang, Hanmei; Dozier, Alan; Kas, Joshua J.; Vila, Fernando D.; Rehr, John J.; Piper, Louis F. J.; Persson, Kristin A.; Ong, Shyue Ping

2018-12-01

X-ray absorption spectroscopy (XAS) is a widely used materials characterization technique to determine oxidation states, coordination environment, and other local atomic structure information. Analysis of XAS relies on comparison of measured spectra to reliable reference spectra. However, existing databases of XAS spectra are highly limited both in terms of the number of reference spectra available as well as the breadth of chemistry coverage. In this work, we report the development of XASdb, a large database of computed reference XAS, and an Ensemble-Learned Spectra IdEntification (ELSIE) algorithm for the matching of spectra. XASdb currently hosts more than 800,000 K-edge X-ray absorption near-edge spectra (XANES) for over 40,000 materials from the open-science Materials Project database. We discuss a high-throughput automation framework for FEFF calculations, built on robust, rigorously benchmarked parameters. FEFF is a computer program uses a real-space Green's function approach to calculate X-ray absorption spectra. We will demonstrate that the ELSIE algorithm, which combines 33 weak "learners" comprising a set of preprocessing steps and a similarity metric, can achieve up to 84.2% accuracy in identifying the correct oxidation state and coordination environment of a test set of 19 K-edge XANES spectra encompassing a diverse range of chemistries and crystal structures. The XASdb with the ELSIE algorithm has been integrated into a web application in the Materials Project, providing an important new public resource for the analysis of XAS to all materials researchers. Finally, the ELSIE algorithm itself has been made available as part of veidt, an open source machine-learning library for materials science.

Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

PubMed Central

Lagkouvardos, Ilias; Weinmaier, Thomas; Lauro, Federico M; Cavicchioli, Ricardo; Rattei, Thomas; Horn, Matthias

2014-01-01

In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22 000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir. PMID:23949660

DSSTox EPA Integrated Risk Information System Structure-Index Locator File: SDF File and Documentation

EPA Science Inventory

EPA's Integrated Risk Information System (IRIS) database was developed and is maintained by EPA's Office of Research and Developement, National Center for Environmental Assessment. IRIS is a database of human health effects that may result from exposure to various substances fou...

Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations.

PubMed

Cario, Clinton L; Witte, John S

2018-03-15

As whole-genome tumor sequence and biological annotation datasets grow in size, number and content, there is an increasing basic science and clinical need for efficient and accurate data management and analysis software. With the emergence of increasingly sophisticated data stores, execution environments and machine learning algorithms, there is also a need for the integration of functionality across frameworks. We present orchid, a python based software package for the management, annotation and machine learning of cancer mutations. Building on technologies of parallel workflow execution, in-memory database storage and machine learning analytics, orchid efficiently handles millions of mutations and hundreds of features in an easy-to-use manner. We describe the implementation of orchid and demonstrate its ability to distinguish tissue of origin in 12 tumor types based on 339 features using a random forest classifier. Orchid and our annotated tumor mutation database are freely available at https://github.com/wittelab/orchid. Software is implemented in python 2.7, and makes use of MySQL or MemSQL databases. Groovy 2.4.5 is optionally required for parallel workflow execution. JWitte@ucsf.edu. Supplementary data are available at Bioinformatics online.

Designing a data portal for synthesis modeling

NASA Astrophysics Data System (ADS)

Holmes, M. A.

2006-12-01

Processing of field and model data in multi-disciplinary integrated science studies is a vital part of synthesis modeling. Collection and storage techniques for field data vary greatly between the participating scientific disciplines due to the nature of the data being collected, whether it be in situ, remotely sensed, or recorded by automated data logging equipment. Spreadsheets, personal databases, text files and binary files are used in the initial storage and processing of the raw data. In order to be useful to scientists, engineers and modelers the data need to be stored in a format that is easily identifiable, accessible and transparent to a variety of computing environments. The Model Operations and Synthesis (MOAS) database and associated web portal were created to provide such capabilities. The industry standard relational database is comprised of spatial and temporal data tables, shape files and supporting metadata accessible over the network, through a menu driven web-based portal or spatially accessible through ArcSDE connections from the user's local GIS desktop software. A separate server provides public access to spatial data and model output in the form of attributed shape files through an ArcIMS web-based graphical user interface.

toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research

PubMed Central

Rhee, David B.; Croken, Matthew McKnight; Shieh, Kevin R.; Sullivan, Julie; Micklem, Gos; Kim, Kami; Golden, Aaron

2015-01-01

Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that must monitor for changes in the host environment and respond accordingly; however, it is still not fully known which genetic or epigenetic factors are involved in regulating virulence traits of T. gondii. There are on-going efforts to elucidate the mechanisms regulating the stage transition process via the application of high-throughput epigenomics, genomics and proteomics techniques. Given the range of experimental conditions and the typical yield from such high-throughput techniques, a new challenge arises: how to effectively collect, organize and disseminate the generated data for subsequent data analysis. Here, we describe toxoMine, which provides a powerful interface to support sophisticated integrative exploration of high-throughput experimental data and metadata, providing researchers with a more tractable means toward understanding how genetic and/or epigenetic factors play a coordinated role in determining pathogenicity of T. gondii. As a data warehouse, toxoMine allows integration of high-throughput data sets with public T. gondii data. toxoMine is also able to execute complex queries involving multiple data sets with straightforward user interaction. Furthermore, toxoMine allows users to define their own parameters during the search process that gives users near-limitless search and query capabilities. The interoperability feature also allows users to query and examine data available in other InterMine systems, which would effectively augment the search scope beyond what is available to toxoMine. toxoMine complements the major community database ToxoDB by providing a data warehouse that enables more extensive integrative studies for T. gondii. Given all these factors, we believe it will become an indispensable resource to the greater infectious disease research community. Database URL: http://toxomine.org PMID:26130662

The EarthServer project: Exploiting Identity Federations, Science Gateways and Social and Mobile Clients for Big Earth Data Analysis

NASA Astrophysics Data System (ADS)

Barbera, Roberto; Bruno, Riccardo; Calanducci, Antonio; Messina, Antonio; Pappalardo, Marco; Passaro, Gianluca

2013-04-01

The EarthServer project (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, aims at establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending leading-edge Array Database technology. The core idea is to use database query languages as client/server interface to achieve barrier-free "mix & match" access to multi-source, any-size, multi-dimensional space-time data -- in short: "Big Earth Data Analytics" - based on the open standards of the Open Geospatial Consortium Web Coverage Processing Service (OGC WCPS) and the W3C XQuery. EarthServer combines both, thereby achieving a tight data/metadata integration. Further, the rasdaman Array Database System (www.rasdaman.com) is extended with further space-time coverage data types. On server side, highly effective optimizations - such as parallel and distributed query processing - ensure scalability to Exabyte volumes. Six Lighthouse Applications are being established in EarthServer, each of which poses distinct challenges on Earth Data Analytics: Cryospheric Science, Airborne Science, Atmospheric Science, Geology, Oceanography, and Planetary Science. Altogether, they cover all Earth Science domains; the Planetary Science use case has been added to challenge concepts and standards in non-standard environments. In addition, EarthLook (maintained by Jacobs University) showcases use of OGC standards in 1D through 5D use cases. In this contribution we will report on the first applications integrated in the EarthServer Science Gateway and on the clients for mobile appliances developed to access them. We will also show how federated and social identity services can allow Big Earth Data Providers to expose their data in a distributed environment keeping a strict and fine-grained control on user authentication and authorisation. The degree of fulfilment of the EarthServer implementation with the recommendations made in the recent TERENA Study on AAA Platforms For Scientific Resources in Europe (https://confluence.terena.org/display/aaastudy/AAA+Study+Home+Page) will also be assessed.

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

PubMed Central

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

2011-01-01

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. PMID:21632604

Hyper-X Engine Design and Ground Test Program

NASA Technical Reports Server (NTRS)

Voland, R. T.; Rock, K. E.; Huebner, L. D.; Witte, D. W.; Fischer, K. E.; McClinton, C. R.

1998-01-01

The Hyper-X Program, NASA's focused hypersonic technology program jointly run by NASA Langley and Dryden, is designed to move hypersonic, air-breathing vehicle technology from the laboratory environment to the flight environment, the last stage preceding prototype development. The Hyper-X research vehicle will provide the first ever opportunity to obtain data on an airframe integrated supersonic combustion ramjet propulsion system in flight, providing the first flight validation of wind tunnel, numerical and analytical methods used for design of these vehicles. A substantial portion of the integrated vehicle/engine flowpath development, engine systems verification and validation and flight test risk reduction efforts are experimentally based, including vehicle aeropropulsive force and moment database generation for flight control law development, and integrated vehicle/engine performance validation. The Mach 7 engine flowpath development tests have been completed, and effort is now shifting to engine controls, systems and performance verification and validation tests, as well as, additional flight test risk reduction tests. The engine wind tunnel tests required for these efforts range from tests of partial width engines in both small and large scramjet test facilities, to tests of the full flight engine on a vehicle simulator and tests of a complete flight vehicle in the Langley 8-Ft. High Temperature Tunnel. These tests will begin in the summer of 1998 and continue through 1999. The first flight test is planned for early 2000.

Free text databases in an Integrated Academic Information System (IAIMS) at Columbia Presbyterian Medical Center.

PubMed Central

Clark, A. S.; Shea, S.

1991-01-01

The use of Folio Views, a PC DOS based product for free text databases, is explored in three applications in an Integrated Academic Information System (IAIMS): (1) a telephone directory, (2) a grants and contracts newsletter, and (3) nursing care plans. PMID:1666967

IN SILICO METHODOLOGIES FOR PREDICTIVE EVALUATION OF TOXICITY BASED ON INTEGRATION OF DATABASES

EPA Science Inventory

In silico methodologies for predictive evaluation of toxicity based on integration of databases

Chihae Yang1 and Ann M. Richard2, 1LeadScope, Inc. 1245 Kinnear Rd. Columbus, OH. 43212 2National Health & Environmental Effects Research Lab, U.S. EPA, Research Triangle Park, ...

A Relational Database System for Student Use.

ERIC Educational Resources Information Center

Fertuck, Len

1982-01-01

Describes an APL implementation of a relational database system suitable for use in a teaching environment in which database development and database administration are studied, and discusses the functions of the user and the database administrator. An appendix illustrating system operation and an eight-item reference list are attached. (Author/JL)

The Qatar National Historic Environment Record: a Platform for the Development of a Fully-Integrated Cultural Heritage Management Application

NASA Astrophysics Data System (ADS)

Cuttler, R. T. H.; Tonner, T. W. W.; Al-Naimi, F. A.; Dingwall, L. M.; Al-Hemaidi, N.

2013-07-01

The development of the Qatar National Historic Environment Record (QNHER) by the Qatar Museums Authority and the University of Birmingham in 2008 was based on a customised, bilingual Access database and ArcGIS. While both platforms are stable and well supported, neither was designed for the documentation and retrieval of cultural heritage data. As a result it was decided to develop a custom application using Open Source code. The core module of this application is now completed and is orientated towards the storage and retrieval of geospatial heritage data for the curation of heritage assets. Based on MIDAS Heritage data standards and regionally relevant thesauri, it is a truly bilingual system. Significant attention has been paid to the user interface, which is userfriendly and intuitive. Based on a suite of web services and accessed through a web browser, the system makes full use of internet resources such as Google Maps and Bing Maps. The application avoids long term vendor ''tie-ins'' and as a fully integrated data management system, is now an important tool for both cultural resource managers and heritage researchers in Qatar.

Combining GPS, GIS, and accelerometry: methodological issues in the assessment of location and intensity of travel behaviors.

PubMed

Oliver, Melody; Badland, Hannah; Mavoa, Suzanne; Duncan, Mitch J; Duncan, Scott

2010-01-01

Global positioning systems (GPS), geographic information systems (GIS), and accelerometers are powerful tools to explain activity within a built environment, yet little integration of these tools has taken place. This study aimed to assess the feasibility of combining GPS, GIS, and accelerometry to understand transport-related physical activity (TPA) in adults. Forty adults wore an accelerometer and portable GPS unit over 7 consecutive days and completed a demographics questionnaire and 7-day travel log. Accelerometer and GPS data were extracted for commutes to/from workplace and integrated into a GIS database. GIS maps were generated to visually explore physical activity intensity, GPS speeds and routes traveled. GPS, accelerometer, and survey data were collected for 37 participants. Loss of GPS data was substantial due to a range of methodological issues, such as low battery life, signal drop out, and participant noncompliance. Nonetheless, greater travel distances and significantly higher speeds were observed for motorized trips when compared with TPA. Pragmatic issues of using GPS monitoring to understand TPA behaviors and methodological recommendations for future research were identified. Although methodologically challenging, the combination of GPS monitoring, accelerometry and GIS technologies holds promise for understanding TPA within the built environment.

Integrative medicine for managing the symptoms of lupus nephritis: A protocol for systematic review and meta-analysis.

PubMed

Choi, Tae-Young; Jun, Ji Hee; Lee, Myeong Soo

2018-03-01

Integrative medicine is claimed to improve symptoms of lupus nephritis. No systematic reviews have been performed for the application of integrative medicine for lupus nephritis on patients with systemic lupus erythematosus (SLE). Thus, this review will aim to evaluate the current evidence on the efficacy of integrative medicine for the management of lupus nephritis in patients with SLE. The following electronic databases will be searched for studies published from their dates of inception February 2018: Medline, EMBASE and the Cochrane Central Register of Controlled Trials (CENTRAL), as well as 6 Korean medical databases (Korea Med, the Oriental Medicine Advanced Search Integrated System [OASIS], DBpia, the Korean Medical Database [KM base], the Research Information Service System [RISS], and the Korean Studies Information Services System [KISS]), and 1 Chinese medical database (the China National Knowledge Infrastructure [CNKI]). Study selection, data extraction, and assessment will be performed independently by 2 researchers. The risk of bias (ROB) will be assessed using the Cochrane ROB tool. This systematic review will be published in a peer-reviewed journal and disseminated both electronically and in print. The review will be updated to inform and guide healthcare practice and policy. PROSPERO 2018 CRD42018085205.

Kentucky geotechnical database.

DOT National Transportation Integrated Search

2005-03-01

Development of a comprehensive dynamic, geotechnical database is described. Computer software selected to program the client/server application in windows environment, components and structure of the geotechnical database, and primary factors cons...

How to Find Lessons from the Public Health Literature: Example of a Scoping Study Protocol on the Neighborhood Environment

PubMed Central

Levasseur, Mélanie; Généreux, Mélissa; Desroches, Josiane; Carrier, Annie; Lacasse, Francis; Chabot, Éric; Abecia, Ana; Gosselin, Louise; Vanasse, Alain

2016-01-01

Background: As key determinants of many favorable health and quality of life outcomes, it is important to identify factors associated with mobility and social participation. Although several investigations have been carried out on mobility, social participation and neighborhood environment, there is no clear integration of these results. This paper presents a scoping study protocol that aims to provide a comprehensive understanding of how the physical and social neighborhood environment is associated with or influences mobility and social participation in older adults. Methods: The rigorous methodological framework for scoping studies is used to synthesize and disseminate current knowledge on the associations or influence of the neighborhood environment on mobility and social participation in aging. Nine databases from public health and other fields are searched with 51 predetermined keywords. Using content analysis, all data are exhaustively analyzed, organized, and synthesized independently by two research assistants. Discussion: A comprehensive synthesis of empirical studies provides decision-makers, clinicians and researchers with current knowledge and best practices regarding neighborhood environments with a view to enhancing mobility and social participation. Such a synthesis represents an original contribution and can ultimately support decisions and development of innovative interventions and clear guidelines for the creation of age-supportive environments. Improvements in public health and clinical interventions might be the new innovation needed to foster health and quality of life for aging population. Finally, the aspects of the associations or influence of the neighborhood environment on mobility and social participation not covered by previous research are identified. Conclusions: Among factors that impact mobility and social participation, the neighborhood environment is important since interventions targeting it may have a greater impact on an individual's mobility and social participation than those targeting individual factors. Although investigations from various domains have been carried out on this topic, no clear integration of these results is available yet. PMID:27413514

[Technical improvement of cohort constitution in administrative health databases: Providing a tool for integration and standardization of data applicable in the French National Health Insurance Database (SNIIRAM)].

PubMed

Ferdynus, C; Huiart, L

2016-09-01

Administrative health databases such as the French National Heath Insurance Database - SNIIRAM - are a major tool to answer numerous public health research questions. However the use of such data requires complex and time-consuming data management. Our objective was to develop and make available a tool to optimize cohort constitution within administrative health databases. We developed a process to extract, transform and load (ETL) data from various heterogeneous sources in a standardized data warehouse. This data warehouse is architected as a star schema corresponding to an i2b2 star schema model. We then evaluated the performance of this ETL using data from a pharmacoepidemiology research project conducted in the SNIIRAM database. The ETL we developed comprises a set of functionalities for creating SAS scripts. Data can be integrated into a standardized data warehouse. As part of the performance assessment of this ETL, we achieved integration of a dataset from the SNIIRAM comprising more than 900 million lines in less than three hours using a desktop computer. This enables patient selection from the standardized data warehouse within seconds of the request. The ETL described in this paper provides a tool which is effective and compatible with all administrative health databases, without requiring complex database servers. This tool should simplify cohort constitution in health databases; the standardization of warehouse data facilitates collaborative work between research teams. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

An Integrated Approach for Urban Earthquake Vulnerability Analyses

NASA Astrophysics Data System (ADS)

Düzgün, H. S.; Yücemen, M. S.; Kalaycioglu, H. S.

2009-04-01

The earthquake risk for an urban area has increased over the years due to the increasing complexities in urban environments. The main reasons are the location of major cities in hazard prone areas, growth in urbanization and population and rising wealth measures. In recent years physical examples of these factors are observed through the growing costs of major disasters in urban areas which have stimulated a demand for in-depth evaluation of possible strategies to manage the large scale damaging effects of earthquakes. Understanding and formulation of urban earthquake risk requires consideration of a wide range of risk aspects, which can be handled by developing an integrated approach. In such an integrated approach, an interdisciplinary view should be incorporated into the risk assessment. Risk assessment for an urban area requires prediction of vulnerabilities related to elements at risk in the urban area and integration of individual vulnerability assessments. However, due to complex nature of an urban environment, estimating vulnerabilities and integrating them necessities development of integrated approaches in which vulnerabilities of social, economical, structural (building stock and infrastructure), cultural and historical heritage are estimated for a given urban area over a given time period. In this study an integrated urban earthquake vulnerability assessment framework, which considers vulnerability of urban environment in a holistic manner and performs the vulnerability assessment for the smallest administrative unit, namely at neighborhood scale, is proposed. The main motivation behind this approach is the inability to implement existing vulnerability assessment methodologies for countries like Turkey, where the required data are usually missing or inadequate and decision makers seek for prioritization of their limited resources in risk reduction in the administrative districts from which they are responsible. The methodology integrates socio-economical, structural, coastal, ground condition, organizational vulnerabilities, as well as accessibility to critical services within the framework. The proposed framework has the following eight components: Seismic hazard analysis, soil response analysis, tsunami inundation analysis, structural vulnerability analysis, socio-economic vulnerability analysis, accessibility to critical services, GIS-based integrated vulnerability assessment, and visualization of vulnerabilities in 3D virtual city model The integrated model for various vulnerabilities obtained for the urban area is developed in GIS environment by using individual vulnerability assessments for considered elements at risk and serve for establishing the backbone of the spatial decision support system. The stages followed in the model are: Determination of a common mapping unit for each aspect of urban earthquake vulnerability, formation of a geo-database for the vulnerabilities, evaluation of urban vulnerability based on multi attribute utility theory with various weighting algorithms, mapping of the evaluated integrated earthquake risk in geographic information systems (GIS) in the neighborhood scale. The framework is also applicable to larger geographical mapping scales, for example, the building scale. When illustrating the results in building scale, 3-D visualizations with remote sensing data is used so that decision-makers can easily interpret the outputs. The proposed vulnerability assessment framework is flexible and can easily be applied to urban environments at various geographical scales with different mapping units. The obtained total vulnerability maps for the urban area provide a baseline for the development of risk reduction strategies for the decision makers. Moreover, as several aspects of elements at risk for an urban area is considered through vulnerability analyses, effect on changes in vulnerability conditions on the total can easily be determined. The developed approach also enables decision makers to monitor temporal and spatial changes in the urban environment due to implementation of risk reduction strategies.

SSME environment database development

NASA Technical Reports Server (NTRS)

Reardon, John

1987-01-01

The internal environment of the Space Shuttle Main Engine (SSME) is being determined from hot firings of the prototype engines and from model tests using either air or water as the test fluid. The objectives are to develop a database system to facilitate management and analysis of test measurements and results, to enter available data into the the database, and to analyze available data to establish conventions and procedures to provide consistency in data normalization and configuration geometry references.

Operationalization of Prediction, Hindcast, and Evaluation Systems using the Freie Univ Evaluation System Framework (Freva) incl. a Showcase in Decadal Climate Prediction

NASA Astrophysics Data System (ADS)

Kadow, Christopher; Illing, Sebastian; Schartner, Thomas; Ulbrich, Uwe; Cubasch, Ulrich

2017-04-01

Operationalization processes are important for Weather and Climate Services. Complex data and work flows need to be combined fast to fulfill the needs of service centers. Standards in data and software formats help in automatic solutions. In this study we show a software solution in between hindcasts, forecasts, and validation to be operationalized. Freva (see below) structures data and evaluation procedures and can easily be monitored. Especially in the development process of operationalized services, Freva supports scientists and project partners. The showcase of the decadal climate prediction project MiKlip (fona-miklip.de) shows such a complex development process. Different predictions, scientists input, tasks, and time evolving adjustments need to be combined to host precise climate informations in a web environment without losing track of its evolution. The Freie Univ Evaluation System Framework (Freva - freva.met.fu-berlin.de) is a software infrastructure for standardized data and tool solutions in Earth system science. Freva runs on high performance computers to handle customizable evaluation systems of research projects, institutes or universities. It combines different software technologies into one common hybrid infrastructure, including all features present in the shell and web environment. The database interface satisfies the international standards provided by the Earth System Grid Federation (ESGF). Freva indexes different data projects into one common search environment by storing the meta data information of the self-describing model, reanalysis and observational data sets in a database. This implemented meta data system with its advanced but easy-to-handle search tool supports users, developers and their plugins to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitation of the provision and usage of tools and climate data automatically increases the number of scientists working with the data sets and identifying discrepancies. The integrated webshell (shellinabox) adds a degree of freedom in the choice of the working environment and can be used as a gateto the research projects HPC. Plugins are able to integrate their e.g. post-processed results into the database ofthe user. This allows e.g. post-processing plugins to feed statistical analysis plugins, which fosters an active exchange between plugin developers of a research project. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a database. Configurations and results of the tools can be shared among scientists via shell or web system. Therefore, plugged-in tools benefit from transparency and reproducibility. Furthermore, if configurations match while starting an evaluation plugin, the system suggests to use results already produced by other users - saving CPU/h, I/O, disk space and time. The efficient interaction between different technologies improves the Earth system modeling science framed by Freva.

Environment/Health/Safety (EHS): Databases

Science.gov Websites

Hazard Documents Database Biosafety Authorization System CATS (Corrective Action Tracking System) (for findings 12/2005 to present) Chemical Management System Electrical Safety Ergonomics Database (for new Learned / Best Practices REMS - Radiation Exposure Monitoring System SJHA Database - Subcontractor Job

Surveillance of obesity-related policies in multiple environments: the Missouri Obesity, Nutrition, and Activity Policy Database, 2007-2009.

PubMed

Haire-Joshu, Debra; Elliott, Michael; Schermbeck, Rebecca; Taricone, Elsa; Green, Scoie; Brownson, Ross C

2010-07-01

The objective of this study was to develop the Missouri Obesity, Nutrition, and Activity Policy Database, a geographically representative baseline of Missouri's existing obesity-related local policies on healthy eating and physical activity. The database is organized to reflect 7 local environments (government, community, health care, worksite, school, after school, and child care) and to describe the prevalence of obesity-related policies in these environments. We employed a stratified nested cluster design using key informant interviews and review of public records to sample 2,356 sites across the 7 target environments for the presence or absence of obesity-related policies. The school environment had the most policies (88%), followed by after school (47%) and health care (32%). Community, government, and child care environments reported smaller proportions of obesity-related policies but higher rates of funding for these policies. Worksite environments had low numbers of obesity-related policies and low funding levels (17% and 6%, respectively). Sixteen of the sampled counties had high obesity-related policy occurrence; 65 had moderate and 8 had low occurrences. Except in Missouri schools, the presence of obesity-related policies is limited. More obesity-related policies are needed so that people have access to environments that support the model behaviors necessary to halt the obesity epidemic. The Missouri Obesity, Nutrition, and Activity Policy Database provides a benchmark for evaluating progress toward the development of obesity-related policies across multiple environments in Missouri.

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

PubMed

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.

40 CFR 1400.13 - Read-only database.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Read-only database. 1400.13 Section 1400.13 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY AND DEPARTMENT OF JUSTICE ACCIDENTAL RELEASE PREVENTION REQUIREMENTS; RISK MANAGEMENT PROGRAMS UNDER THE CLEAN AIR ACT SECTION 112(r)(7...

Crowdsourcing-Assisted Radio Environment Database for V2V Communication.

PubMed

Katagiri, Keita; Sato, Koya; Fujii, Takeo

2018-04-12

In order to realize reliable Vehicle-to-Vehicle (V2V) communication systems for autonomous driving, the recognition of radio propagation becomes an important technology. However, in the current wireless distributed network systems, it is difficult to accurately estimate the radio propagation characteristics because of the locality of the radio propagation caused by surrounding buildings and geographical features. In this paper, we propose a measurement-based radio environment database for improving the accuracy of the radio environment estimation in the V2V communication systems. The database first gathers measurement datasets of the received signal strength indicator (RSSI) related to the transmission/reception locations from V2V systems. By using the datasets, the average received power maps linked with transmitter and receiver locations are generated. We have performed measurement campaigns of V2V communications in the real environment to observe RSSI for the database construction. Our results show that the proposed method has higher accuracy of the radio propagation estimation than the conventional path loss model-based estimation.

Crowdsourcing-Assisted Radio Environment Database for V2V Communication †

PubMed Central

Katagiri, Keita; Fujii, Takeo

2018-01-01

In order to realize reliable Vehicle-to-Vehicle (V2V) communication systems for autonomous driving, the recognition of radio propagation becomes an important technology. However, in the current wireless distributed network systems, it is difficult to accurately estimate the radio propagation characteristics because of the locality of the radio propagation caused by surrounding buildings and geographical features. In this paper, we propose a measurement-based radio environment database for improving the accuracy of the radio environment estimation in the V2V communication systems. The database first gathers measurement datasets of the received signal strength indicator (RSSI) related to the transmission/reception locations from V2V systems. By using the datasets, the average received power maps linked with transmitter and receiver locations are generated. We have performed measurement campaigns of V2V communications in the real environment to observe RSSI for the database construction. Our results show that the proposed method has higher accuracy of the radio propagation estimation than the conventional path loss model-based estimation. PMID:29649174

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

PubMed Central

Liu, Zhi-Ping; Wu, Canglin; Miao, Hongyu; Wu, Hulin

2015-01-01

Transcriptional and post-transcriptional regulation of gene expression is of fundamental importance to numerous biological processes. Nowadays, an increasing amount of gene regulatory relationships have been documented in various databases and literature. However, to more efficiently exploit such knowledge for biomedical research and applications, it is necessary to construct a genome-wide regulatory network database to integrate the information on gene regulatory relationships that are widely scattered in many different places. Therefore, in this work, we build a knowledge-based database, named ‘RegNetwork’, of gene regulatory networks for human and mouse by collecting and integrating the documented regulatory interactions among transcription factors (TFs), microRNAs (miRNAs) and target genes from 25 selected databases. Moreover, we also inferred and incorporated potential regulatory relationships based on transcription factor binding site (TFBS) motifs into RegNetwork. As a result, RegNetwork contains a comprehensive set of experimentally observed or predicted transcriptional and post-transcriptional regulatory relationships, and the database framework is flexibly designed for potential extensions to include gene regulatory networks for other organisms in the future. Based on RegNetwork, we characterized the statistical and topological properties of genome-wide regulatory networks for human and mouse, we also extracted and interpreted simple yet important network motifs that involve the interplays between TF-miRNA and their targets. In summary, RegNetwork provides an integrated resource on the prior information for gene regulatory relationships, and it enables us to further investigate context-specific transcriptional and post-transcriptional regulatory interactions based on domain-specific experimental data. Database URL: http://www.regnetworkweb.org PMID:26424082

Application driven interface generation for EASIE. M.S. Thesis

NASA Technical Reports Server (NTRS)

Kao, Ya-Chen

1992-01-01

The Environment for Application Software Integration and Execution (EASIE) provides a user interface and a set of utility programs which support the rapid integration and execution of analysis programs about a central relational database. EASIE provides users with two basic modes of execution. One of them is a menu-driven execution mode, called Application-Driven Execution (ADE), which provides sufficient guidance to review data, select a menu action item, and execute an application program. The other mode of execution, called Complete Control Execution (CCE), provides an extended executive interface which allows in-depth control of the design process. Currently, the EASIE system is based on alphanumeric techniques only. It is the purpose of this project to extend the flexibility of the EASIE system in the ADE mode by implementing it in a window system. Secondly, a set of utilities will be developed to assist the experienced engineer in the generation of an ADE application.

IRIS Toxicological Review of Ammonia Noncancer Inhalation ...

EPA Pesticide Factsheets

EPA has finalized the Integrated Risk Information System (IRIS) Assessment of Ammonia (Noncancer Inhalation). This assessment addresses the potential noncancer human health effects from long-term inhalation exposure to ammonia. Now final, this assessment will update the current toxicological information on ammonia posted in 1991. EPA’s program and regional offices may use this assessment to inform decisions to protect human health. EPA completed the Integrated Risk Information System (IRIS) health assessment for ammonia. IRIS is an EPA database containing Agency scientific positions on potential adverse human health effects that may result from chronic (or lifetime) exposure to chemicals in the environment. IRIS contains chemical-specific summaries of qualitative and quantitative health information in support of two steps of the risk assessment paradigm, i.e., hazard identification and dose-response evaluation. IRIS assessments are used in combination with specific situational exposure assessment information to evaluate potential public health risk associated with environmental contaminants.

MASCAL: RFID Tracking of Patients, Staff and Equipment to Enhance Hospital Response to Mass Casualty Events

PubMed Central

Fry, Emory A.; Lenert, Leslie A.

2005-01-01

Most medical facilities practice managing the large numbers of seriously injured patients expected during catastrophic events. As the demands on the healthcare team increase, however, the challenges faced by managers escalate, workflow bottlenecks develop and system capacity decreases. This paper describes MASCAL, an integrated software–hardware system designed to enhance management of resources at a hospital during a mass casualty situation. MASCAL uses active 802.11b asset tags to track patients, equipment and staff during the response to a disaster. The system integrates tag position information with data from personnel databases, medical information systems, registration applications and the US Navy’s TACMEDCS triage application in a custom visual disaster management environment. MASCAL includes interfaces for a hospital command center, local area managers (emergency room, operating suites, radiology, etc.) and registration personnel. MASCAL is an operational system undergoing functional evaluation at the Naval Medical Center, San Diego, CA. PMID:16779042

Consequences of "going digital" for pathology professionals - entering the cloud.

PubMed

Laurinavicius, Arvydas; Raslavicus, Paul

2012-01-01

New opportunities and the adoption of digital technologies will transform the way pathology professionals and services work. Many areas of our daily life as well as medical professions have experienced this change already which has resulted in a paradigm shift in many activities. Pathology is an image-based discipline, therefore, arrival of digital imaging into this domain promises major shift in our work and required mentality. Recognizing the physical and digital duality of the pathology workflow, we can prepare for the imminent increase of the digital component, synergize and enjoy its benefits. Development of a new generation of laboratory information systems along with seamless integration of digital imaging, decision-support, and knowledge databases will enable pathologists to work in a distributed environment. The paradigm of "cloud pathology" is proposed as an ultimate vision of digital pathology workstations plugged into the integrated multidisciplinary patient care systems.

A Web-GIS Procedure Based on Satellite Multi-Spectral and Airborne LIDAR Data to Map the Road blockage Due to seismic Damages of Built-Up Urban Areas

NASA Astrophysics Data System (ADS)

Costanzo, Antonio; Montuori, Antonio; Silva, Juan Pablo; Silvestri, Malvina; Musacchio, Massimo; Buongiorno, Maria Fabrizia; Stramondo, Salvatore

2016-08-01

In this work, a web-GIS procedure to map the risk of road blockage in urban environments through the combined use of space-borne and airborne remote sensing sensors is presented. The methodology concerns (1) the provision of a geo-database through the integration of space-borne multispectral images and airborne LiDAR data products; (2) the modeling of building vulnerability, based on the corresponding 3D geometry and construction time information; (3) the GIS-based mapping of road closure due to seismic- related building collapses based on the building characteristic height and the width of the road. Experimental results, gathered for the Cosenza urban area, allow demonstrating the benefits of both the proposed approach and the GIS-based integration of multi-platforms remote sensing sensors and techniques for seismic road assessment purposes.

The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience

PubMed Central

Akil, Huda; Ascoli, Giorgio A.; Bowden, Douglas M.; Bug, William; Donohue, Duncan E.; Goldberg, David H.; Grafstein, Bernice; Grethe, Jeffrey S.; Gupta, Amarnath; Halavi, Maryam; Kennedy, David N.; Marenco, Luis; Martone, Maryann E.; Miller, Perry L.; Müller, Hans-Michael; Robert, Adrian; Shepherd, Gordon M.; Sternberg, Paul W.; Van Essen, David C.; Williams, Robert W.

2009-01-01

With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience resources: the Neuroscience Information Framework. The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of neuroinformatics by the Human Brain Project and others, and directly derives from the Society for Neuroscience’s Neuroscience Database Gateway. Partnered with the Society, its Neuroinformatics Committee, and volunteer consultant-collaborators, our multi-site consortium has developed: (1) a comprehensive, dynamic, inventory of Web-accessible neuroscience resources, (2) an extended and integrated terminology describing resources and contents, and (3) a framework accepting and aiding concept-based queries. Evolving instantiations of the Framework may be viewed at http://nif.nih.gov, http://neurogateway.org, and other sites as they come on line. PMID:18946742

The neuroscience information framework: a data and knowledge environment for neuroscience.

PubMed

Gardner, Daniel; Akil, Huda; Ascoli, Giorgio A; Bowden, Douglas M; Bug, William; Donohue, Duncan E; Goldberg, David H; Grafstein, Bernice; Grethe, Jeffrey S; Gupta, Amarnath; Halavi, Maryam; Kennedy, David N; Marenco, Luis; Martone, Maryann E; Miller, Perry L; Müller, Hans-Michael; Robert, Adrian; Shepherd, Gordon M; Sternberg, Paul W; Van Essen, David C; Williams, Robert W

2008-09-01

With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience resources: the Neuroscience Information Framework. The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of neuroinformatics by the Human Brain Project and others, and directly derives from the Society for Neuroscience's Neuroscience Database Gateway. Partnered with the Society, its Neuroinformatics Committee, and volunteer consultant-collaborators, our multi-site consortium has developed: (1) a comprehensive, dynamic, inventory of Web-accessible neuroscience resources, (2) an extended and integrated terminology describing resources and contents, and (3) a framework accepting and aiding concept-based queries. Evolving instantiations of the Framework may be viewed at http://nif.nih.gov , http://neurogateway.org , and other sites as they come on line.

iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation.

PubMed

Komaki, Shohei; Shiwa, Yuh; Furukawa, Ryohei; Hachiya, Tsuyoshi; Ohmomo, Hideki; Otomo, Ryo; Satoh, Mamoru; Hitomi, Jiro; Sobue, Kenji; Sasaki, Makoto; Shimizu, Atsushi

2018-01-01

We launched an integrative multi-omics database, iMETHYL (http://imethyl.iwate-megabank.org). iMETHYL provides whole-DNA methylation (~24 million autosomal CpG sites), whole-genome (~9 million single-nucleotide variants), and whole-transcriptome (>14 000 genes) data for CD4 + T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. These data were obtained from whole-genome bisulfite sequencing, whole-genome sequencing, and whole-transcriptome sequencing, making iMETHYL a comprehensive database.

Tomato functional genomics database (TFGD): a comprehensive collection and analysis package for tomato functional genomics

USDA-ARS?s Scientific Manuscript database

Tomato Functional Genomics Database (TFGD; http://ted.bti.cornell.edu) provides a comprehensive systems biology resource to store, mine, analyze, visualize and integrate large-scale tomato functional genomics datasets. The database is expanded from the previously described Tomato Expression Database...

Relationship mapping

NASA Astrophysics Data System (ADS)

Benachenhou, D.

2009-04-01

Information-technology departments in large enterprises spend 40% of budget on information integration-combining information from different data sources into a coherent form. IDC, a market-intelligence firm, estimates that the market for data integration and access software (which includes the key enabling technology for information integration) was about 2.5 billion in 2007, and is expected to grow to 3.8 billion in 2012. This is only the cost estimate for structured or traditional database information integration. Just imagine the market for transforming text into structured information and subsequent fusion with traditional databases.

Scalable global grid catalogue for Run3 and beyond

NASA Astrophysics Data System (ADS)

Martinez Pedreira, M.; Grigoras, C.; ALICE Collaboration

2017-10-01

The AliEn (ALICE Environment) file catalogue is a global unique namespace providing mapping between a UNIX-like logical name structure and the corresponding physical files distributed over 80 storage elements worldwide. Powerful search tools and hierarchical metadata information are integral parts of the system and are used by the Grid jobs as well as local users to store and access all files on the Grid storage elements. The catalogue has been in production since 2005 and over the past 11 years has grown to more than 2 billion logical file names. The backend is a set of distributed relational databases, ensuring smooth growth and fast access. Due to the anticipated fast future growth, we are looking for ways to enhance the performance and scalability by simplifying the catalogue schema while keeping the functionality intact. We investigated different backend solutions, such as distributed key value stores, as replacement for the relational database. This contribution covers the architectural changes in the system, together with the technology evaluation, benchmark results and conclusions.

[THE USE OF OPEN REAL ESTATE DATABASES FOR THE ANALYSIS OF INFLUENCE OF CONCOMITANT FACTORS ON THE STATE OF THE URBAN POPULATION'S HEALTH].

PubMed

Zheleznyak, E V; Khripach, L V

2015-01-01

There was suggested a new method of the assessment of certain social-lifestyle factors in hygienic health examination of the urban population, based on the work with the open real estate databases on residential areas of the given city. On the example of the Moscow FlatInfo portal for a sample of 140 residents of the city of Moscow there was studied the distribution of such available for analysis factors as a typical design of the building, where studied citizen resides, the year of its construction and the market price of 1m2 of housing space in this house. The latter value is a quantitative integrated assessment of the social and lifestyle quality of housing, depending on the type and technical condition of the building, neighborhood environment, infrastructure of the region and many other factors, and may be a useful supplemental index in hygienic research.

Geology of the Palo Alto 30 x 60 minute quadrangle, California: A digital database

USGS Publications Warehouse

Brabb, Earl E.; Graymer, R.W.; Jones, David Lawrence

1998-01-01

This map database represents the integration of previously published and unpublished maps by several workers (see Sources of Data index map on Sheet 2 and the corresponding table below) and new geologic mapping and field checking by the authors with the previously published geologic map of San Mateo County (Brabb and Pampeyan, 1983) and Santa Cruz County (Brabb, 1989, Brabb and others, 1997), and various sources in a small part of Santa Clara County. These new data are released in digital form to provide an opportunity for regional planners, local, state, and federal agencies, teachers, consultants, and others interested in geologic data to have the new data long before a traditional paper map is published. The new data include a new depiction of Quaternary units in the San Francisco Bay plain emphasizing depositional environment, important new observations between the San Andreas and Pilarcitos faults, and a new interpretation of structural and stratigraphic relationships of rock packages (Assemblages).

Earth System Model Development and Analysis using FRE-Curator and Live Access Servers: On-demand analysis of climate model output with data provenance.

NASA Astrophysics Data System (ADS)

Radhakrishnan, A.; Balaji, V.; Schweitzer, R.; Nikonov, S.; O'Brien, K.; Vahlenkamp, H.; Burger, E. F.

2016-12-01

There are distinct phases in the development cycle of an Earth system model. During the model development phase, scientists make changes to code and parameters and require rapid access to results for evaluation. During the production phase, scientists may make an ensemble of runs with different settings, and produce large quantities of output, that must be further analyzed and quality controlled for scientific papers and submission to international projects such as the Climate Model Intercomparison Project (CMIP). During this phase, provenance is a key concern:being able to track back from outputs to inputs. We will discuss one of the paths taken at GFDL in delivering tools across this lifecycle, offering on-demand analysis of data by integrating the use of GFDL's in-house FRE-Curator, Unidata's THREDDS and NOAA PMEL's Live Access Servers (LAS).Experience over this lifecycle suggests that a major difficulty in developing analysis capabilities is only partially the scientific content, but often devoted to answering the questions "where is the data?" and "how do I get to it?". "FRE-Curator" is the name of a database-centric paradigm used at NOAA GFDL to ingest information about the model runs into an RDBMS (Curator database). The components of FRE-Curator are integrated into Flexible Runtime Environment workflow and can be invoked during climate model simulation. The front end to FRE-Curator, known as the Model Development Database Interface (MDBI) provides an in-house web-based access to GFDL experiments: metadata, analysis output and more. In order to provide on-demand visualization, MDBI uses Live Access Servers which is a highly configurable web server designed to provide flexible access to geo-referenced scientific data, that makes use of OPeNDAP. Model output saved in GFDL's tape archive, the size of the database and experiments, continuous model development initiatives with more dynamic configurations add complexity and challenges in providing an on-demand visualization experience to our GFDL users.

Archaeal Viruses: Diversity, Replication, and Structure.

PubMed

Dellas, Nikki; Snyder, Jamie C; Bolduc, Benjamin; Young, Mark J

2014-11-01

The Archaea-and their viruses-remain the most enigmatic of life's three domains. Once thought to inhabit only extreme environments, archaea are now known to inhabit diverse environments. Even though the first archaeal virus was described over 40 years ago, only 117 archaeal viruses have been discovered to date. Despite this small number, these viruses have painted a portrait of enormous morphological and genetic diversity. For example, research centered around the various steps of the archaeal virus life cycle has led to the discovery of unique mechanisms employed by archaeal viruses during replication, maturation, and virion release. In many instances, archaeal virus proteins display very low levels of sequence homology to other proteins listed in the public database, and therefore, structural characterization of these proteins has played an integral role in functional assignment. These structural studies have not only provided insights into structure-function relationships but have also identified links between viruses across all three domains of life.

Security Framework for Pervasive Healthcare Architectures Utilizing MPEG-21 IPMP Components.

PubMed

Fragopoulos, Anastasios; Gialelis, John; Serpanos, Dimitrios

2009-01-01

Nowadays in modern and ubiquitous computing environments, it is imperative more than ever the necessity for deployment of pervasive healthcare architectures into which the patient is the central point surrounded by different types of embedded and small computing devices, which measure sensitive physical indications, interacting with hospitals databases, allowing thus urgent medical response in occurrences of critical situations. Such environments must be developed satisfying the basic security requirements for real-time secure data communication, and protection of sensitive medical data and measurements, data integrity and confidentiality, and protection of the monitored patient's privacy. In this work, we argue that the MPEG-21 Intellectual Property Management and Protection (IPMP) components can be used in order to achieve protection of transmitted medical information and enhance patient's privacy, since there is selective and controlled access to medical data that sent toward the hospital's servers.

Spatial Indexing for Data Searching in Mobile Sensing Environments.

PubMed

Zhou, Yuchao; De, Suparna; Wang, Wei; Moessner, Klaus; Palaniswami, Marimuthu S

2017-06-18

Data searching and retrieval is one of the fundamental functionalities in many Web of Things applications, which need to collect, process and analyze huge amounts of sensor stream data. The problem in fact has been well studied for data generated by sensors that are installed at fixed locations; however, challenges emerge along with the popularity of opportunistic sensing applications in which mobile sensors keep reporting observation and measurement data at variable intervals and changing geographical locations. To address these challenges, we develop the Geohash-Grid Tree, a spatial indexing technique specially designed for searching data integrated from heterogeneous sources in a mobile sensing environment. Results of the experiments on a real-world dataset collected from the SmartSantander smart city testbed show that the index structure allows efficient search based on spatial distance, range and time windows in a large time series database.

Spatial Indexing for Data Searching in Mobile Sensing Environments

PubMed Central

Zhou, Yuchao; De, Suparna; Wang, Wei; Moessner, Klaus; Palaniswami, Marimuthu S.

2017-01-01

Data searching and retrieval is one of the fundamental functionalities in many Web of Things applications, which need to collect, process and analyze huge amounts of sensor stream data. The problem in fact has been well studied for data generated by sensors that are installed at fixed locations; however, challenges emerge along with the popularity of opportunistic sensing applications in which mobile sensors keep reporting observation and measurement data at variable intervals and changing geographical locations. To address these challenges, we develop the Geohash-Grid Tree, a spatial indexing technique specially designed for searching data integrated from heterogeneous sources in a mobile sensing environment. Results of the experiments on a real-world dataset collected from the SmartSantander smart city testbed show that the index structure allows efficient search based on spatial distance, range and time windows in a large time series database. PMID:28629156

Exploring consumer exposure pathways and patterns of use for chemicals in the environment through the Chemical/Product Categories Database

EPA Pesticide Factsheets

Exploring consumer exposure pathways and patterns of use for chemicals in the environment through the Chemical/Product Categories Database (CPCat) (Presented by: Kathie Dionisio, Sc.D., NERL, US EPA, Research Triangle Park, NC (1/23/2014).

Lessons learned while building the Deepwater Horizon Database: Toward improved data sharing in coastal science

NASA Astrophysics Data System (ADS)

Thessen, Anne E.; McGinnis, Sean; North, Elizabeth W.

2016-02-01

Process studies and coupled-model validation efforts in geosciences often require integration of multiple data types across time and space. For example, improved prediction of hydrocarbon fate and transport is an important societal need which fundamentally relies upon synthesis of oceanography and hydrocarbon chemistry. Yet, there are no publically accessible databases which integrate these diverse data types in a georeferenced format, nor are there guidelines for developing such a database. The objective of this research was to analyze the process of building one such database to provide baseline information on data sources and data sharing and to document the challenges and solutions that arose during this major undertaking. The resulting Deepwater Horizon Database was approximately 2.4 GB in size and contained over 8 million georeferenced data points collected from industry, government databases, volunteer networks, and individual researchers. The major technical challenges that were overcome were reconciliation of terms, units, and quality flags which were necessary to effectively integrate the disparate data sets. Assembling this database required the development of relationships with individual researchers and data managers which often involved extensive e-mail contacts. The average number of emails exchanged per data set was 7.8. Of the 95 relevant data sets that were discovered, 38 (40%) were obtained, either in whole or in part. Over one third (36%) of the requests for data went unanswered. The majority of responses were received after the first request (64%) and within the first week of the first request (67%). Although fewer than half of the potentially relevant datasets were incorporated into the database, the level of sharing (40%) was high compared to some other disciplines where sharing can be as low as 10%. Our suggestions for building integrated databases include budgeting significant time for e-mail exchanges, being cognizant of the cost versus benefits of pursuing reticent data providers, and building trust through clear, respectful communication and with flexible and appropriate attributions.

Integrated Functional and Executional Modelling of Software Using Web-Based Databases

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Marietta, Roberta

1998-01-01

NASA's software subsystems undergo extensive modification and updates over the operational lifetimes. It is imperative that modified software should satisfy safety goals. This report discusses the difficulties encountered in doing so and discusses a solution based on integrated modelling of software, use of automatic information extraction tools, web technology and databases.

The Relationship between Treatment Integrity and Acceptability of Reading Interventions for Children with Attention-Deficit/Hyperactivity Disorder

ERIC Educational Resources Information Center

Mautone, Jennifer A.; DuPaul, George J.; Jitendra, Asha K.; Tresco, Katy E.; Junod, Rosemary Vile; Volpe, Robert J.

2009-01-01

This study examined the relationship between treatment integrity and acceptability for reading interventions across two consultation models, intensive data-based academic intervention (IDAI) and traditional data-based academic intervention (TDAI). Participants included 83 first- through fourth-grade students who met research criteria for…

The Problem with the Delta Cost Project Database

ERIC Educational Resources Information Center

Jaquette, Ozan; Parra, Edna

2016-01-01

The Integrated Postsecondary Education System (IPEDS) collects data on Title IV institutions. The Delta Cost Project (DCP) integrated data from multiple IPEDS survey components into a public-use longitudinal dataset. The DCP Database was the basis for dozens of journal articles and a series of influential policy reports. Unfortunately, a flaw in…

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.

DOT National Transportation Integrated Search

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 ...

Service Management Database for DSN Equipment

NASA Technical Reports Server (NTRS)

Zendejas, Silvino; Bui, Tung; Bui, Bach; Malhotra, Shantanu; Chen, Fannie; Wolgast, Paul; Allen, Christopher; Luong, Ivy; Chang, George; Sadaqathulla, Syed

2009-01-01

This data- and event-driven persistent storage system leverages the use of commercial software provided by Oracle for portability, ease of maintenance, scalability, and ease of integration with embedded, client-server, and multi-tiered applications. In this role, the Service Management Database (SMDB) is a key component of the overall end-to-end process involved in the scheduling, preparation, and configuration of the Deep Space Network (DSN) equipment needed to perform the various telecommunication services the DSN provides to its customers worldwide. SMDB makes efficient use of triggers, stored procedures, queuing functions, e-mail capabilities, data management, and Java integration features provided by the Oracle relational database management system. SMDB uses a third normal form schema design that allows for simple data maintenance procedures and thin layers of integration with client applications. The software provides an integrated event logging system with ability to publish events to a JMS messaging system for synchronous and asynchronous delivery to subscribed applications. It provides a structured classification of events and application-level messages stored in database tables that are accessible by monitoring applications for real-time monitoring or for troubleshooting and analysis over historical archives.

MetaMetaDB: A Database and Analytic System for Investigating Microbial Habitability

PubMed Central

Yang, Ching-chia; Iwasaki, Wataru

2014-01-01

MetaMetaDB (http://mmdb.aori.u-tokyo.ac.jp/) is a database and analytic system for investigating microbial habitability, i.e., how a prokaryotic group can inhabit different environments. The interaction between prokaryotes and the environment is a key issue in microbiology because distinct prokaryotic communities maintain distinct ecosystems. Because 16S ribosomal RNA (rRNA) sequences play pivotal roles in identifying prokaryotic species, a system that comprehensively links diverse environments to 16S rRNA sequences of the inhabitant prokaryotes is necessary for the systematic understanding of the microbial habitability. However, existing databases are biased to culturable prokaryotes and exhibit limitations in the comprehensiveness of the data because most prokaryotes are unculturable. Recently, metagenomic and 16S rRNA amplicon sequencing approaches have generated abundant 16S rRNA sequence data that encompass unculturable prokaryotes across diverse environments; however, these data are usually buried in large databases and are difficult to access. In this study, we developed MetaMetaDB (Meta-Metagenomic DataBase), which comprehensively and compactly covers 16S rRNA sequences retrieved from public datasets. Using MetaMetaDB, users can quickly generate hypotheses regarding the types of environments a prokaryotic group may be adapted to. We anticipate that MetaMetaDB will improve our understanding of the diversity and evolution of prokaryotes. PMID:24475242

GIS applications for military operations in coastal zones

USGS Publications Warehouse

Fleming, S.; Jordan, T.; Madden, M.; Usery, E.L.; Welch, R.

2009-01-01

In order to successfully support current and future US military operations in coastal zones, geospatial information must be rapidly integrated and analyzed to meet ongoing force structure evolution and new mission directives. Coastal zones in a military-operational environment are complex regions that include sea, land and air features that demand high-volume databases of extreme detail within relatively narrow geographic corridors. Static products in the form of analog maps at varying scales traditionally have been used by military commanders and their operational planners. The rapidly changing battlefield of 21st Century warfare, however, demands dynamic mapping solutions. Commercial geographic information system (GIS) software for military-specific applications is now being developed and employed with digital databases to provide customized digital maps of variable scale, content and symbolization tailored to unique demands of military units. Research conducted by the Center for Remote Sensing and Mapping Science at the University of Georgia demonstrated the utility of GIS-based analysis and digital map creation when developing large-scale (1:10,000) products from littoral warfare databases. The methodology employed-selection of data sources (including high resolution commercial images and Lidar), establishment of analysis/modeling parameters, conduct of vehicle mobility analysis, development of models and generation of products (such as a continuous sea-land DEM and geo-visualization of changing shorelines with tidal levels)-is discussed. Based on observations and identified needs from the National Geospatial-Intelligence Agency, formerly the National Imagery and Mapping Agency, and the Department of Defense, prototype GIS models for military operations in sea, land and air environments were created from multiple data sets of a study area at US Marine Corps Base Camp Lejeune, North Carolina. Results of these models, along with methodologies for developing large-scale littoral warfare databases, aid the National Geospatial-Intelligence Agency in meeting littoral warfare analysis, modeling and map generation requirements for US military organizations. ?? 2008 International Society for Photogrammetry and Remote Sensing, Inc. (ISPRS).

GIS applications for military operations in coastal zones

NASA Astrophysics Data System (ADS)

Fleming, S.; Jordan, T.; Madden, M.; Usery, E. L.; Welch, R.

In order to successfully support current and future US military operations in coastal zones, geospatial information must be rapidly integrated and analyzed to meet ongoing force structure evolution and new mission directives. Coastal zones in a military-operational environment are complex regions that include sea, land and air features that demand high-volume databases of extreme detail within relatively narrow geographic corridors. Static products in the form of analog maps at varying scales traditionally have been used by military commanders and their operational planners. The rapidly changing battlefield of 21st Century warfare, however, demands dynamic mapping solutions. Commercial geographic information system (GIS) software for military-specific applications is now being developed and employed with digital databases to provide customized digital maps of variable scale, content and symbolization tailored to unique demands of military units. Research conducted by the Center for Remote Sensing and Mapping Science at the University of Georgia demonstrated the utility of GIS-based analysis and digital map creation when developing large-scale (1:10,000) products from littoral warfare databases. The methodology employed-selection of data sources (including high resolution commercial images and Lidar), establishment of analysis/modeling parameters, conduct of vehicle mobility analysis, development of models and generation of products (such as a continuous sea-land DEM and geo-visualization of changing shorelines with tidal levels)-is discussed. Based on observations and identified needs from the National Geospatial-Intelligence Agency, formerly the National Imagery and Mapping Agency, and the Department of Defense, prototype GIS models for military operations in sea, land and air environments were created from multiple data sets of a study area at US Marine Corps Base Camp Lejeune, North Carolina. Results of these models, along with methodologies for developing large-scale littoral warfare databases, aid the National Geospatial-Intelligence Agency in meeting littoral warfare analysis, modeling and map generation requirements for US military organizations.

The salinity tolerant poplar database (STPD): a comprehensive database for studying tree salt-tolerant adaption and poplar genomics.

PubMed

Ma, Yazhen; Xu, Ting; Wan, Dongshi; Ma, Tao; Shi, Sheng; Liu, Jianquan; Hu, Quanjun

2015-03-17

Soil salinity is a significant factor that impairs plant growth and agricultural productivity, and numerous efforts are underway to enhance salt tolerance of economically important plants. Populus species are widely cultivated for diverse uses. Especially, they grow in different habitats, from salty soil to mesophytic environment, and are therefore used as a model genus for elucidating physiological and molecular mechanisms of stress tolerance in woody plants. The Salinity Tolerant Poplar Database (STPD) is an integrative database for salt-tolerant poplar genome biology. Currently the STPD contains Populus euphratica genome and its related genetic resources. P. euphratica, with a preference of the salty habitats, has become a valuable genetic resource for the exploitation of tolerance characteristics in trees. This database contains curated data including genomic sequence, genes and gene functional information, non-coding RNA sequences, transposable elements, simple sequence repeats and single nucleotide polymorphisms information of P. euphratica, gene expression data between P. euphratica and Populus tomentosa, and whole-genome alignments between Populus trichocarpa, P. euphratica and Salix suchowensis. The STPD provides useful searching and data mining tools, including GBrowse genome browser, BLAST servers and genome alignments viewer, which can be used to browse genome regions, identify similar sequences and visualize genome alignments. Datasets within the STPD can also be downloaded to perform local searches. A new Salinity Tolerant Poplar Database has been developed to assist studies of salt tolerance in trees and poplar genomics. The database will be continuously updated to incorporate new genome-wide data of related poplar species. This database will serve as an infrastructure for researches on the molecular function of genes, comparative genomics, and evolution in closely related species as well as promote advances in molecular breeding within Populus. The STPD can be accessed at http://me.lzu.edu.cn/stpd/ .

A geo-spatial data management system for potentially active volcanoes—GEOWARN project

NASA Astrophysics Data System (ADS)

Gogu, Radu C.; Dietrich, Volker J.; Jenny, Bernhard; Schwandner, Florian M.; Hurni, Lorenz

2006-02-01

Integrated studies of active volcanic systems for the purpose of long-term monitoring and forecast and short-term eruption prediction require large numbers of data-sets from various disciplines. A modern database concept has been developed for managing and analyzing multi-disciplinary volcanological data-sets. The GEOWARN project (choosing the "Kos-Yali-Nisyros-Tilos volcanic field, Greece" and the "Campi Flegrei, Italy" as test sites) is oriented toward potentially active volcanoes situated in regions of high geodynamic unrest. This article describes the volcanological database of the spatial and temporal data acquired within the GEOWARN project. As a first step, a spatial database embedded in a Geographic Information System (GIS) environment was created. Digital data of different spatial resolution, and time-series data collected at different intervals or periods, were unified in a common, four-dimensional representation of space and time. The database scheme comprises various information layers containing geographic data (e.g. seafloor and land digital elevation model, satellite imagery, anthropogenic structures, land-use), geophysical data (e.g. from active and passive seismicity, gravity, tomography, SAR interferometry, thermal imagery, differential GPS), geological data (e.g. lithology, structural geology, oceanography), and geochemical data (e.g. from hydrothermal fluid chemistry and diffuse degassing features). As a second step based on the presented database, spatial data analysis has been performed using custom-programmed interfaces that execute query scripts resulting in a graphical visualization of data. These query tools were designed and compiled following scenarios of known "behavior" patterns of dormant volcanoes and first candidate signs of potential unrest. The spatial database and query approach is intended to facilitate scientific research on volcanic processes and phenomena, and volcanic surveillance.

Atlas - a data warehouse for integrative bioinformatics.

PubMed

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire M S; Ling, John; Ouellette, B F Francis

2005-02-21

We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/

Atlas – a data warehouse for integrative bioinformatics

PubMed Central

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire MS; Ling, John; Ouellette, BF Francis

2005-01-01

Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: PMID:15723693

Barriers and facilitators to healthy eating for nurses in the workplace: an integrative review.

PubMed

Nicholls, Rachel; Perry, Lin; Duffield, Christine; Gallagher, Robyn; Pierce, Heather

2017-05-01

The aim was to conduct an integrative systematic review to identify barriers and facilitators to healthy eating for working nurses. There is growing recognition of the influence of the workplace environment on the eating habits of the workforce, which in turn may contribute to increased overweight and obesity. Overweight and obesity exact enormous costs in terms of reduced well-being, worker productivity and increased risk of non-communicable diseases. The workplace is an ideal place to intervene and support healthy behaviours. This review aimed to identify barriers and facilitators to nurses' healthy eating in the workplace. Integrative mixed method review. Five electronic databases were searched: CINAHL, MEDLINE, PROQUEST Health and Medicine, ScienceDirect and PsycINFO. Reference lists were searched. Included papers were published in English between 2000-2016. Of 26 included papers, 21 were qualitative and five quantitative. An integrative literature review was undertaken. Quality appraisal of included studies used standardized checklists. A social-ecological framework was used to examine workplace facilitators and constraints to healthy eating, derived from the literature. Emergent themes were identified by thematic analysis. Review participants were Registered, Enrolled and/or Nurse Assistants primarily working in hospitals in middle or high income countries. The majority of studies reported barriers to healthy eating related to adverse work schedules, individual barriers, aspects of the physical workplace environment and social eating practices at work. Few facilitators were reported. Overall, studies found the workplace exerts a considerable negative influence on nurses' dietary intake. Reorientation of the workplace to promote healthy eating among nurses is required. © 2016 John Wiley & Sons Ltd.

MIPS PlantsDB: a database framework for comparative plant genome research.

PubMed

Nussbaumer, Thomas; Martis, Mihaela M; Roessner, Stephan K; Pfeifer, Matthias; Bader, Kai C; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

2013-01-01

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.

MIPS PlantsDB: a database framework for comparative plant genome research

PubMed Central

Nussbaumer, Thomas; Martis, Mihaela M.; Roessner, Stephan K.; Pfeifer, Matthias; Bader, Kai C.; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

2013-01-01

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB–plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834–D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB. PMID:23203886

Generation of large scale urban environments to support advanced sensor and seeker simulation

NASA Astrophysics Data System (ADS)

Giuliani, Joseph; Hershey, Daniel; McKeown, David, Jr.; Willis, Carla; Van, Tan

2009-05-01

One of the key aspects for the design of a next generation weapon system is the need to operate in cluttered and complex urban environments. Simulation systems rely on accurate representation of these environments and require automated software tools to construct the underlying 3D geometry and associated spectral and material properties that are then formatted for various objective seeker simulation systems. Under an Air Force Small Business Innovative Research (SBIR) contract, we have developed an automated process to generate 3D urban environments with user defined properties. These environments can be composed from a wide variety of source materials, including vector source data, pre-existing 3D models, and digital elevation models, and rapidly organized into a geo-specific visual simulation database. This intermediate representation can be easily inspected in the visible spectrum for content and organization and interactively queried for accuracy. Once the database contains the required contents, it can then be exported into specific synthetic scene generation runtime formats, preserving the relationship between geometry and material properties. To date an exporter for the Irma simulation system developed and maintained by AFRL/Eglin has been created and a second exporter to Real Time Composite Hardbody and Missile Plume (CHAMP) simulation system for real-time use is currently being developed. This process supports significantly more complex target environments than previous approaches to database generation. In this paper we describe the capabilities for content creation for advanced seeker processing algorithms simulation and sensor stimulation, including the overall database compilation process and sample databases produced and exported for the Irma runtime system. We also discuss the addition of object dynamics and viewer dynamics within the visual simulation into the Irma runtime environment.

Interventions developed with the Intervention Mapping protocol in the field of cancer: A systematic review.

PubMed

Lamort-Bouché, Marion; Sarnin, Philippe; Kok, Gerjo; Rouat, Sabrina; Péron, Julien; Letrilliart, Laurent; Fassier, Jean-Baptiste

2018-04-01

The Intervention Mapping (IM) protocol provides a structured framework to develop, implement, and evaluate complex interventions. The main objective of this review was to identify and describe the content of the interventions developed in the field of cancer with the IM protocol. Secondary objectives were to assess their fidelity to the IM protocol and to review their theoretical frameworks. Medline, Web of Science, PsycINFO, PASCAL, FRANCIS, and BDSP databases were searched. All titles and abstracts were reviewed. A standardized extraction form was developed. All included studies were reviewed by 2 reviewers blinded to each other. Sixteen studies were identified, and these reported 15 interventions. The objectives were to increase cancer screening participation (n = 7), early consultation (n = 1), and aftercare/quality of life among cancer survivors (n = 7). Six reported a complete participatory planning group, and 7 described a complete logic model of the problem. Ten studies described a complete logic model of change. The main theoretical frameworks used were the theory of planned behaviour (n = 8), the transtheoretical model (n = 6), the health belief model (n = 6), and the social cognitive theory (n = 6). The environment was rarely integrated in the interventions (n = 4). Five interventions were reported as effective. Culturally relevant interventions were developed with the IM protocol that were effective to increase cancer screening and reduce social disparities, particularly when they were developed through a participative approach and integrated the environment. Stakeholders' involvement and the role of the environment were heterogeneously integrated in the interventions. Copyright © 2017 John Wiley & Sons, Ltd.

Integrating geo web services for a user driven exploratory analysis

NASA Astrophysics Data System (ADS)

Moncrieff, Simon; Turdukulov, Ulanbek; Gulland, Elizabeth-Kate

2016-04-01

In data exploration, several online data sources may need to be dynamically aggregated or summarised over spatial region, time interval, or set of attributes. With respect to thematic data, web services are mainly used to present results leading to a supplier driven service model limiting the exploration of the data. In this paper we propose a user need driven service model based on geo web processing services. The aim of the framework is to provide a method for the scalable and interactive access to various geographic data sources on the web. The architecture combines a data query, processing technique and visualisation methodology to rapidly integrate and visually summarise properties of a dataset. We illustrate the environment on a health related use case that derives Age Standardised Rate - a dynamic index that needs integration of the existing interoperable web services of demographic data in conjunction with standalone non-spatial secure database servers used in health research. Although the example is specific to the health field, the architecture and the proposed approach are relevant and applicable to other fields that require integration and visualisation of geo datasets from various web services and thus, we believe is generic in its approach.

Real-Time Integrity Monitoring of Stored Geo-Spatial Data Using Forward-Looking Remote Sensing Technology

NASA Technical Reports Server (NTRS)

Young, Steven D.; Harrah, Steven D.; deHaag, Maarten Uijt

2002-01-01

Terrain Awareness and Warning Systems (TAWS) and Synthetic Vision Systems (SVS) provide pilots with displays of stored geo-spatial data (e.g. terrain, obstacles, and/or features). As comprehensive validation is impractical, these databases typically have no quantifiable level of integrity. This lack of a quantifiable integrity level is one of the constraints that has limited certification and operational approval of TAWS/SVS to "advisory-only" systems for civil aviation. Previous work demonstrated the feasibility of using a real-time monitor to bound database integrity by using downward-looking remote sensing technology (i.e. radar altimeters). This paper describes an extension of the integrity monitor concept to include a forward-looking sensor to cover additional classes of terrain database faults and to reduce the exposure time associated with integrity threats. An operational concept is presented that combines established feature extraction techniques with a statistical assessment of similarity measures between the sensed and stored features using principles from classical detection theory. Finally, an implementation is presented that uses existing commercial-off-the-shelf weather radar sensor technology.

The integration of quantitative information with an intelligent decision support system for residential energy retrofits

NASA Astrophysics Data System (ADS)

Mo, Yunjeong

The purpose of this research is to support the development of an intelligent Decision Support System (DSS) by integrating quantitative information with expert knowledge in order to facilitate effective retrofit decision-making. To achieve this goal, the Energy Retrofit Decision Process Framework is analyzed. Expert system shell software, a retrofit measure cost database, and energy simulation software are needed for developing the DSS; Exsys Corvid, the NREM database and BEopt were chosen for implementing an integration model. This integration model demonstrates the holistic function of a residential energy retrofit system for existing homes, by providing a prioritized list of retrofit measures with cost information, energy simulation and expert advice. The users, such as homeowners and energy auditors, can acquire all of the necessary retrofit information from this unified system without having to explore several separate systems. The integration model plays the role of a prototype for the finalized intelligent decision support system. It implements all of the necessary functions for the finalized DSS, including integration of the database, energy simulation and expert knowledge.

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

PubMed

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaponov, Yu.A.; Igarashi, N.; Hiraki, M.

2004-05-12

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,more » 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.« less

CEO Sites Mission Management System (SMMS)

NASA Technical Reports Server (NTRS)

Trenchard, Mike

2014-01-01

Late in fiscal year 2011, the Crew Earth Observations (CEO) team was tasked to upgrade its science site database management tool, which at the time was integrated with the Automated Mission Planning System (AMPS) originally developed for Earth Observations mission planning in the 1980s. Although AMPS had been adapted and was reliably used by CEO for International Space Station (ISS) payload operations support, the database structure was dated, and the compiler required for modifications would not be supported in the Windows 7 64-bit operating system scheduled for implementation the following year. The Sites Mission Management System (SMMS) is now the tool used by CEO to manage a heritage Structured Query Language (SQL) database of more than 2,000 records for Earth science sites. SMMS is a carefully designed and crafted in-house software package with complete and detailed help files available for the user and meticulous internal documentation for future modifications. It was delivered in February 2012 for test and evaluation. Following acceptance, it was implemented for CEO mission operations support in April 2012. The database spans the period from the earliest systematic requests for astronaut photography during the shuttle era to current ISS mission support of the CEO science payload. Besides logging basic image information (site names, locations, broad application categories, and mission requests), the upgraded database management tool now tracks dates of creation, modification, and activation; imagery acquired in response to requests; the status and location of ancillary site information; and affiliations with studies, their sponsors, and collaborators. SMMS was designed to facilitate overall mission planning in terms of site selection and activation and provide the necessary site parameters for the Satellite Tool Kit (STK) Integrated Message Production List Editor (SIMPLE), which is used by CEO operations to perform daily ISS mission planning. The CEO team uses the SMMS for three general functions - database queries of content and status, individual site creation and updates, and mission planning. The CEO administrator of the science site database is able to create or modify the content of sites and activate or deactivate them based on the requirements of the sponsors. The administrator supports and implements ISS mission planning by assembling, reporting, and activating mission-specific site selections for management; deactivating sites as requirements are met; and creating new sites, such as International Charter sites for disasters, as circumstances warrant. In addition to the above CEO internal uses, when site planning for a specific ISS mission is complete and approved, the SMMS can produce and export those essential site database elements for the mission into XML format for use by onboard Earth-location systems, such as Worldmap. The design, development, and implementation of the SMMS resulted in a superior database management system for CEO science sites by focusing on the functions and applications of the database alone instead of integrating the database with the multipurpose configuration of the AMPS. Unlike the AMPS, it can function and be modified within the existing Windows 7 environment. The functions and applications of the SMMS were expanded to accommodate more database elements, report products, and a streamlined interface for data entry and review. A particularly elegant enhancement in data entry was the integration of the Google Earth application for the visual display and definition of site coordinates for site areas defined by multiple coordinates. Transfer between the SMMS and Google Earth is accomplished with a Keyhole Markup Language (KML) expression of geographic data (see figures 3 and 4). Site coordinates may be entered into the SMMS panel directly for display in Google Earth, or the coordinates may be defined on the Google Earth display as a mouse-controlled polygonal definition and transferred back into the SMMS as KML input. This significantly reduces the possibility of errors in coordinate entries and provides visualization of the scale of the site being defined. CEO now has a powerful tool for managing and defining sites on the Earth's surface for both targets of astronaut photography or other onboard remote sensing systems. It can also record and track results by sponsor, collaborator, or type of study.

Concordance of Commercial Data Sources for Neighborhood-Effects Studies

PubMed Central

Schootman, Mario

2010-01-01

Growing evidence supports a relationship between neighborhood-level characteristics and important health outcomes. One source of neighborhood data includes commercial databases integrated with geographic information systems to measure availability of certain types of businesses or destinations that may have either favorable or adverse effects on health outcomes; however, the quality of these data sources is generally unknown. This study assessed the concordance of two commercial databases for ascertaining the presence, locations, and characteristics of businesses. Businesses in the St. Louis, Missouri area were selected based on their four-digit Standard Industrial Classification (SIC) codes and classified into 14 business categories. Business listings in the two commercial databases were matched by standardized business name within specified distances. Concordance and coverage measures were calculated using capture–recapture methods for all businesses and by business type, with further stratification by census-tract-level population density, percent below poverty, and racial composition. For matched listings, distance between listings and agreement in four-digit SIC code, sales volume, and employee size were calculated. Overall, the percent agreement was 32% between the databases. Concordance and coverage estimates were lowest for health-care facilities and leisure/entertainment businesses; highest for popular walking destinations, eating places, and alcohol/tobacco establishments; and varied somewhat by population density. The mean distance (SD) between matched listings was 108.2 (179.0) m with varying levels of agreement in four-digit SIC (percent agreement = 84.6%), employee size (weighted kappa = 0.63), and sales volume (weighted kappa = 0.04). Researchers should cautiously interpret findings when using these commercial databases to yield measures of the neighborhood environment. PMID:20480397

Holocene = Anthropocene? The HYDE database for integrated global change research over the past 12,000 years

NASA Astrophysics Data System (ADS)

Klein Goldewijk, K.

2008-12-01

More and more studies of global (climate) change are focusing on the past. Hundreds and thousands of years of land use, driven by population growth have left their trace/mark on the Earth's surface. We are only at the beginning to understand the complex relationship of human induced disturbances of the global environment, and the consequences for future climate. It is therefore essential that we get a clear picture/understanding of past relationships between population growth, land use and climate. In order to facilitate climate modelers to examine these relationships, the HYDE database has been updated and extended. The update of HYDE described here (Klein Goldewijk et al. 2006; Klein Goldewijk et al. 2007) includes several improvements compared to its predecessor: (i) the HYDE 2 version used a Boolean approach with a 30 minute degree resolution, while HYDE 3 uses fractional land use on a 5 minute resolution; (ii) more and better sub-national (population) data (Klein Goldewijk, 2005) to improve the historical (urban and rural) population maps as a basis for allocation of land cover; (iii) implementation of different allocation algorithms with time-dependent weighting maps for cropland and grassland; (iv) the period covered has now been extended from the emergence of agriculture (10,000 B.C) to present time (2,000 A.D.), with different time intervals. Examples of (future) use of the database is to help test the 'Ruddiman hypothesis', who proposed a theory that mankind already altered the global atmosphere much earlier than the start of the Industrial Revolution in the early 18th century (Ruddiman, 2003), which put forward the research question whether we detect a pre- Industrial Revolution anthropogenic signal, and how strong is that signal? References Klein Goldewijk, K. A.F. Bouwman and G. van Drecht, 2007. Mapping current global cropland and grassland distributions on a 5 by 5 minute resolution, Journal of Land Use Science, Vol 2(3): 167-190. Klein Goldewijk, K. and G. van Drecht, 2006. HYDE 3: Current and historical population and land cover. MNP (2006) (Edited by A.F. Bouwman, T. Kram and K. Klein Goldewijk), Integrated modelling of global environmental change. An overview of IMAGE 2.4. Netherlands Environmental Assessment Agency (MNP), Bilthoven, The Netherlands Klein Goldewijk, K. 2005. Three centuries of global population growth: A spatial referenced population density database for 1700 - 2000, Population and Environment, 26 (5): 343-367. Ruddiman, WF, 2003. The anthropogenic greenhouse era bagan thousands of years ago, Climatic Change, 61(3), 261-293.

Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance

PubMed Central

Squires, R. Burke; Noronha, Jyothi; Hunt, Victoria; García‐Sastre, Adolfo; Macken, Catherine; Baumgarth, Nicole; Suarez, David; Pickett, Brett E.; Zhang, Yun; Larsen, Christopher N.; Ramsey, Alvin; Zhou, Liwei; Zaremba, Sam; Kumar, Sanjeev; Deitrich, Jon; Klem, Edward; Scheuermann, Richard H.

2012-01-01

Please cite this paper as: Squires et al. (2012) Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza and Other Respiratory Viruses 6(6), 404–416. Background  The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. Design  The Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly‐accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user‐friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in‐protected ‘workbench’ spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. Results  To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross‐protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. Conclusions  The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics. PMID:22260278

Integrative medicine for managing the symptoms of lupus nephritis

PubMed Central

Choi, Tae-Young; Jun, Ji Hee; Lee, Myeong Soo

2018-01-01

Abstract Background: Integrative medicine is claimed to improve symptoms of lupus nephritis. No systematic reviews have been performed for the application of integrative medicine for lupus nephritis on patients with systemic lupus erythematosus (SLE). Thus, this review will aim to evaluate the current evidence on the efficacy of integrative medicine for the management of lupus nephritis in patients with SLE. Methods and analyses: The following electronic databases will be searched for studies published from their dates of inception February 2018: Medline, EMBASE and the Cochrane Central Register of Controlled Trials (CENTRAL), as well as 6 Korean medical databases (Korea Med, the Oriental Medicine Advanced Search Integrated System [OASIS], DBpia, the Korean Medical Database [KM base], the Research Information Service System [RISS], and the Korean Studies Information Services System [KISS]), and 1 Chinese medical database (the China National Knowledge Infrastructure [CNKI]). Study selection, data extraction, and assessment will be performed independently by 2 researchers. The risk of bias (ROB) will be assessed using the Cochrane ROB tool. Dissemination: This systematic review will be published in a peer-reviewed journal and disseminated both electronically and in print. The review will be updated to inform and guide healthcare practice and policy. Trial registration number: PROSPERO 2018 CRD42018085205 PMID:29595669

Toward unification of taxonomy databases in a distributed computer environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kitakami, Hajime; Tateno, Yoshio; Gojobori, Takashi

1994-12-31

All the taxonomy databases constructed with the DNA databases of the international DNA data banks are powerful electronic dictionaries which aid in biological research by computer. The taxonomy databases are, however not consistently unified with a relational format. If we can achieve consistent unification of the taxonomy databases, it will be useful in comparing many research results, and investigating future research directions from existent research results. In particular, it will be useful in comparing relationships between phylogenetic trees inferred from molecular data and those constructed from morphological data. The goal of the present study is to unify the existent taxonomymore » databases and eliminate inconsistencies (errors) that are present in them. Inconsistencies occur particularly in the restructuring of the existent taxonomy databases, since classification rules for constructing the taxonomy have rapidly changed with biological advancements. A repair system is needed to remove inconsistencies in each data bank and mismatches among data banks. This paper describes a new methodology for removing both inconsistencies and mismatches from the databases on a distributed computer environment. The methodology is implemented in a relational database management system, SYBASE.« less

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

PubMed Central

Nascimento, Leandro Costa; Salazar, Marcela Mendes; Lepikson-Neto, Jorge; Camargo, Eduardo Leal Oliveira; Parreiras, Lucas Salera; Carazzolle, Marcelo Falsarella

2017-01-01

Abstract Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. Database URL: http://www.lge.ibi.unicamp.br/eucalyptusdb PMID:29220468

The Mouse Heart Attack Research Tool (mHART) 1.0 Database.

PubMed

DeLeon-Pennell, Kristine Y; Iyer, Rugmani Padmanabhan; Ma, Yonggang; Yabluchanskiy, Andriy; Zamilpa, Rogelio; Chiao, Ying Ann; Cannon, Presley; Cates, Courtney; Flynn, Elizabeth R; Halade, Ganesh V; de Castro Bras, Lisandra E; Lindsey, Merry L

2018-05-18

The generation of Big Data has enabled systems-level dissections into the mechanisms of cardiovascular pathology. Integration of genetic, proteomic, and pathophysiological variables across platforms and laboratories fosters discoveries through multidisciplinary investigations and minimizes unnecessary redundancy in research efforts. The Mouse Heart Attack Research Tool (mHART) consolidates a large dataset of over 10 years of experiments from a single laboratory for cardiovascular investigators to generate novel hypotheses and identify new predictive markers of progressive left ventricular remodeling following myocardial infarction (MI) in mice. We designed the mHART REDCap database using our own data to integrate cardiovascular community participation. We generated physiological, biochemical, cellular, and proteomic outputs from plasma and left ventricles obtained from post-MI and no MI (naïve) control groups. We included both male and female mice ranging in age from 3 to 36 months old. After variable collection, data underwent quality assessment for data curation (e.g. eliminate technical errors, check for completeness, remove duplicates, and define terms). Currently, mHART 1.0 contains >888,000 data points and includes results from >2,100 unique mice. Database performance was tested and an example provided to illustrate database utility. This report explains how the first version of the mHART database was established and provides researchers with a standard framework to aid in the integration of their data into our database or in the development of a similar database.

Columba: an integrated database of proteins, structures, and annotations.

PubMed

Trissl, Silke; Rother, Kristian; Müller, Heiko; Steinke, Thomas; Koch, Ina; Preissner, Robert; Frömmel, Cornelius; Leser, Ulf

2005-03-31

Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. COLUMBA currently integrates twelve different databases, including PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME. The database can be searched using either keyword search or data source-specific web forms. Users can thus quickly select and download PDB entries that, for instance, participate in a particular pathway, are classified as containing a certain CATH architecture, are annotated as having a certain molecular function in the Gene Ontology, and whose structures have a resolution under a defined threshold. The results of queries are provided in both machine-readable extensible markup language and human-readable format. The structures themselves can be viewed interactively on the web. The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. It allows to combine queries on a number of structure-related databases not covered by other projects at present. Thus, information on both many and few protein structures can be used efficiently. The web interface for COLUMBA is available at http://www.columba-db.de.

Overview of ICRP Committee 5: protection of the environment.

PubMed

Larsson, C-M

2016-06-01

Protection of the environment is integral to the system of radiological protection, as outlined in the 2007 Recommendations of the International Commission on Radiological Protection (ICRP, Publication 103). The Commission's activities in this area are mainly pursued by Committee 5 and its associated Task Groups. Publication 91 broadly outlines the approach to radiological protection of the environment, and its alignment with approaches to environmental protection from hazardous substances in general. Publications 108 and 114 provide the cornerstones of the environmental protection system and relevant databases. Publication 124 considers its application in planned, existing, and emergency exposure situations. The system centres on 12 Reference Animals and Plants (RAPs) with broad relevance for environmental protection based on their ubiquity and significance as well as other criteria, as described in Publication 108 The databases comprise general biology of the RAPs, transfer parameters, dose conversion coefficients, and effects data. Derived Consideration Reference Levels (DCRLs) were established for each RAP; a DCRL represents a band of dose rates that might result in some deleterious effects in individuals of that type of RAP. Newly established Task Group 99 will compile the RAP-specific reference information into monographs, with the view of updating information and improving the applicability of the system in different exposure situations. For certain scenarios, more precise and ecosystem-specific protection benchmarks may be justified, which would have to be informed by consideration of representative organisms (i.e. representative of a particular ecosystem and relevant to the specific scenario; Publication 124). Committee 5 will explore this further, making use of a limited number of case studies. © The International Society for Prosthetics and Orthotics.

78 FR 2363 - Notification of Deletion of a System of Records; Automated Trust Funds Database

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-11

... Database AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION: Notice of deletion of a system... establishing the Automated Trust Funds (ATF) database system of records. The Federal Information Security... Integrity Act of 1982, Public Law 97-255, provided authority for the system. The ATF database has been...

A User's Applications of Imaging Techniques: The University of Maryland Historic Textile Database.

ERIC Educational Resources Information Center

Anderson, Clarita S.

1991-01-01

Describes the incorporation of textile images into the University of Maryland Historic Textile Database by a computer user rather than a computer expert. Selection of a database management system is discussed, and PICTUREPOWER, a system that integrates photographic quality images with text and numeric information in databases, is described. (three…

Integrating Databases with Maps: The Delivery of Cultural Data through TimeMap.

ERIC Educational Resources Information Center

Johnson, Ian

TimeMap is a unique integration of database management, metadata and interactive maps, designed to contextualise and deliver cultural data through maps. TimeMap extends conventional maps with the time dimension, creating and animating maps "on-the-fly"; delivers them as a kiosk application or embedded in Web pages; links flexibly to…

Information integration for a sky survey by data warehousing

NASA Astrophysics Data System (ADS)

Luo, A.; Zhang, Y.; Zhao, Y.

The virtualization service of data system for a sky survey LAMOST is very important for astronomers The service needs to integrate information from data collections catalogs and references and support simple federation of a set of distributed files and associated metadata Data warehousing has been in existence for several years and demonstrated superiority over traditional relational database management systems by providing novel indexing schemes that supported efficient on-line analytical processing OLAP of large databases Now relational database systems such as Oracle etc support the warehouse capability which including extensions to the SQL language to support OLAP operations and a number of metadata management tools have been created The information integration of LAMOST by applying data warehousing is to effectively provide data and knowledge on-line

Charting a Path to Location Intelligence for STD Control.

PubMed

Gerber, Todd M; Du, Ping; Armstrong-Brown, Janelle; McNutt, Louise-Anne; Coles, F Bruce

2009-01-01

This article describes the New York State Department of Health's GeoDatabase project, which developed new methods and techniques for designing and building a geocoding and mapping data repository for sexually transmitted disease (STD) control. The GeoDatabase development was supported through the Centers for Disease Control and Prevention's Outcome Assessment through Systems of Integrated Surveillance workgroup. The design and operation of the GeoDatabase relied upon commercial-off-the-shelf tools that other public health programs may also use for disease-control systems. This article provides a blueprint of the structure and software used to build the GeoDatabase and integrate location data from multiple data sources into the everyday activities of STD control programs.

RNAcentral: an international database of ncRNA sequences

DOE PAGES

Williams, Kelly Porter

2014-10-28

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

E-MSD: an integrated data resource for bioinformatics.

PubMed

Golovin, A; Oldfield, T J; Tate, J G; Velankar, S; Barton, G J; Boutselakis, H; Dimitropoulos, D; Fillon, J; Hussain, A; Ionides, J M C; John, M; Keller, P A; Krissinel, E; McNeil, P; Naim, A; Newman, R; Pajon, A; Pineda, J; Rachedi, A; Copeland, J; Sitnov, A; Sobhany, S; Suarez-Uruena, A; Swaminathan, G J; Tagari, M; Tromm, S; Vranken, W; Henrick, K

2004-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).

E-MSD: an integrated data resource for bioinformatics

PubMed Central

Golovin, A.; Oldfield, T. J.; Tate, J. G.; Velankar, S.; Barton, G. J.; Boutselakis, H.; Dimitropoulos, D.; Fillon, J.; Hussain, A.; Ionides, J. M. C.; John, M.; Keller, P. A.; Krissinel, E.; McNeil, P.; Naim, A.; Newman, R.; Pajon, A.; Pineda, J.; Rachedi, A.; Copeland, J.; Sitnov, A.; Sobhany, S.; Suarez-Uruena, A.; Swaminathan, G. J.; Tagari, M.; Tromm, S.; Vranken, W.; Henrick, K.

2004-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD ‘atlas pages’ show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www.ebi.ac.uk/msd-srv/docs/roadshow_tutorial/). PMID:14681397

Hbim to VR. Semantic Awareness and Data Enrichment Interoperability for Parametric Libraries of Historical Architecture

NASA Astrophysics Data System (ADS)

Quattrini, R.; Battini, C.; Mammoli, R.

2018-05-01

Recently we assist to an increasing availability of HBIM models rich in geometric and informative terms. Instead, there is still a lack of researches implementing dedicated libraries, based on parametric intelligence and semantically aware, related to the architectural heritage. Additional challenges became from their portability in non-desktop environment (such as VR). The research article demonstrates the validity of a workflow applied to the architectural heritage, which starting from the semantic modeling reaches the visualization in a virtual reality environment, passing through the necessary phases of export, data migration and management. The three-dimensional modeling of the classical Doric order takes place in the BIM work environment and is configured as a necessary starting point for the implementation of data, parametric intelligences and definition of ontologies that exclusively qualify the model. The study also enables an effective method for data migration from the BIM model to databases integrated into VR technologies for AH. Furthermore, the process intends to propose a methodology, applicable in a return path, suited to the achievement of an appropriate data enrichment of each model and to the possibility of interaction in VR environment with the model.

Web-Based Environment for Maintaining Legacy Software

NASA Technical Reports Server (NTRS)

Tigges, Michael; Thompson, Nelson; Orr, Mark; Fox, Richard

2007-01-01

Advanced Tool Integration Environment (ATIE) is the name of both a software system and a Web-based environment created by the system for maintaining an archive of legacy software and expertise involved in developing the legacy software. ATIE can also be used in modifying legacy software and developing new software. The information that can be encapsulated in ATIE includes experts documentation, input and output data of tests cases, source code, and compilation scripts. All of this information is available within a common environment and retained in a database for ease of access and recovery by use of powerful search engines. ATIE also accommodates the embedment of supporting software that users require for their work, and even enables access to supporting commercial-off-the-shelf (COTS) software within the flow of the experts work. The flow of work can be captured by saving the sequence of computer programs that the expert uses. A user gains access to ATIE via a Web browser. A modern Web-based graphical user interface promotes efficiency in the retrieval, execution, and modification of legacy code. Thus, ATIE saves time and money in the support of new and pre-existing programs.

Integrated Space Asset Management Database and Modeling

NASA Technical Reports Server (NTRS)

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 visualizations. In addition, tight control of information sharing policy will increase confidence in the system, which would encourage industry partners to provide commercial data. Combined with the integration of new and legacy M&S tools, a SIMON-based architecture will provide a robust environment that can be extended and expanded indefinitely.

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

ERIC Educational Resources Information Center

Rush, James E.

1980-01-01

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

40 CFR 1400.13 - Read-only database.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 34 2012-07-01 2012-07-01 false Read-only database. 1400.13 Section... INFORMATION Other Provisions § 1400.13 Read-only database. The Administrator is authorized to establish... public off-site consequence analysis information by means of a central database under the control of the...

40 CFR 1400.13 - Read-only database.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 33 2014-07-01 2014-07-01 false Read-only database. 1400.13 Section... INFORMATION Other Provisions § 1400.13 Read-only database. The Administrator is authorized to establish... public off-site consequence analysis information by means of a central database under the control of the...

40 CFR 1400.13 - Read-only database.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 33 2011-07-01 2011-07-01 false Read-only database. 1400.13 Section... INFORMATION Other Provisions § 1400.13 Read-only database. The Administrator is authorized to establish... public off-site consequence analysis information by means of a central database under the control of the...

40 CFR 1400.13 - Read-only database.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 34 2013-07-01 2013-07-01 false Read-only database. 1400.13 Section... INFORMATION Other Provisions § 1400.13 Read-only database. The Administrator is authorized to establish... public off-site consequence analysis information by means of a central database under the control of the...

Mapping the interprofessional education landscape for students on rural clinical placements: an integrative literature review.

PubMed

Walker, Lorraine; Cross, Merylin; Barnett, Tony

2018-05-01

Interprofessional collaboration and effective teamwork are core to optimising rural health outcomes; however, little is known about the opportunities available for interprofessional education (IPE) in rural clinical learning environments. This integrative literature review addresses this deficit by identifying, analysing and synthesising the research available about the nature of and potential for IPE provided to undergraduate students undertaking rural placements, the settings and disciplines involved and the outcomes achieved. An integrative review method was adopted to capture the breadth of evidence available about IPE in the rural context. This integrative review is based on a search of nine electronic databases: CINAHL, Cochrane Library, EMBASE, MEDLINE, ProQuest, PubMed, SCOPUS, Web of Science and Google Scholar. Search terms were adapted to suit those used by different disciplines and each database and included key words related to IPE, rurality, undergraduate students and clinical placement. The inclusion criteria included primary research and reports of IPE in rural settings, peer reviewed, and published in English between 2000 and mid-2016. This review integrates the results of 27 primary research studies undertaken in seven countries: Australia, Canada, USA, New Zealand, the Philippines, South Africa and Tanzania. Despite geographical, cultural and health system differences, all of the studies reviewed were concerned with developing collaborative, interprofessional practice-ready graduates and adopted a similar mix of research methods. Overall, the 27 studies involved more than 3800 students (range 3-1360) from 36 disciplinary areas, including some not commonly associated with interprofessional education, such as theology. Interprofessional education was provided in a combination of university and rural placement settings including hospitals, community health services and other rural venues. The education activities most frequently utilised were seminars, tutorial discussion groups (n=21, 84%), case presentations (n=11, 44%) and community projects (n=11, 44%) augmented by preliminary orientation and ongoing interaction with clinicians during placement. The studies reviewed demonstrate that rural clinical learning environments provide rich and varied IPE opportunities for students that increase their interprofessional understanding, professional respect for other roles, and awareness of the collaborative and interprofessional nature of rural practice. This review addresses the lack of attention given to understanding IPE in the rural context, provides Australian and international evidence that initiatives are being offered to diverse student groups undertaking placements in rural settings and proposes a research agenda to develop a relevant framework to support rural IPE. Rural clinical learning environments afford a rich resource whereby health professionals can conceptualise IPE creatively and holistically to construct transformative learning experiences for students. This review develops a case for supporting the development, trialling, evaluation and translation of IPE initiatives that harness the opportunities afforded by rural placements. Further research is required to examine the ways to optimise IPE opportunities in the rural clinical context, including the potential for simulation-based activities, the challenges to achieving sustainable programs, and to evaluate the impact of interprofessional education on collaboration and health outcomes.

National Vulnerability Database (NVD)

National Institute of Standards and Technology Data Gateway

National Vulnerability Database (NVD) (Web, free access)   NVD is a comprehensive cyber security vulnerability database that integrates all publicly available U.S. Government vulnerability resources and provides references to industry resources. It is based on and synchronized with the CVE vulnerability naming standard.

Computer Databases as an Educational Tool in the Basic Sciences.

ERIC Educational Resources Information Center

Friedman, Charles P.; And Others

1990-01-01

The University of North Carolina School of Medicine developed a computer database, INQUIRER, containing scientific information in bacteriology, and then integrated the database into routine educational activities for first-year medical students in their microbiology course. (Author/MLW)

The development of a new database of gas emissions: MAGA, a collaborative web environment for collecting data

NASA Astrophysics Data System (ADS)

Cardellini, C.; Chiodini, G.; Frigeri, A.; Bagnato, E.; Aiuppa, A.; McCormick, B.

2013-12-01

The data on volcanic and non-volcanic gas emissions available online are, as today, incomplete and most importantly, fragmentary. Hence, there is need for common frameworks to aggregate available data, in order to characterize and quantify the phenomena at various spatial and temporal scales. Building on the Googas experience we are now extending its capability, particularly on the user side, by developing a new web environment for collecting and publishing data. We have started to create a new and detailed web database (MAGA: MApping GAs emissions) for the deep carbon degassing in the Mediterranean area. This project is part of the Deep Earth Carbon Degassing (DECADE) research initiative, lunched in 2012 by the Deep Carbon Observatory (DCO) to improve the global budget of endogenous carbon from volcanoes. MAGA database is planned to complement and integrate the work in progress within DECADE in developing CARD (Carbon Degassing) database. MAGA database will allow researchers to insert data interactively and dynamically into a spatially referred relational database management system, as well as to extract data. MAGA kicked-off with the database set up and a complete literature survey on publications on volcanic gas fluxes, by including data on active craters degassing, diffuse soil degassing and fumaroles both from dormant closed-conduit volcanoes (e.g., Vulcano, Phlegrean Fields, Santorini, Nysiros, Teide, etc.) and open-vent volcanoes (e.g., Etna, Stromboli, etc.) in the Mediterranean area and Azores. For each geo-located gas emission site, the database holds images and description of the site and of the emission type (e.g., diffuse emission, plume, fumarole, etc.), gas chemical-isotopic composition (when available), gas temperature and gases fluxes magnitude. Gas sampling, analysis and flux measurement methods are also reported together with references and contacts to researchers expert of the site. Data can be accessed on the network from a web interface or as a data-driven web service, where software clients can request data directly from the database. This way Geographical Information Systems (GIS) and Virtual Globes (e.g., Google Earth) can easily access the database, and data can be exchanged with other database. In details the database now includes: i) more than 1000 flux data about volcanic plume degassing from Etna (4 summit craters and bulk degassing) and Stromboli volcanoes, with time averaged CO2 fluxes of ~ 18000 and 766 t/d, respectively; ii) data from ~ 30 sites of diffuse soil degassing from Napoletan volcanoes, Azores, Canary, Etna, Stromboli, and Vulcano Island, with a wide range of CO2 fluxes (from les than 1 to 1500 t/d) and iii) several data on fumarolic emissions (~ 7 sites) with CO2 fluxes up to 1340 t/day (i.e., Stromboli). When available, time series of compositional data have been archived in the database (e.g., for Campi Flegrei fumaroles). We believe MAGA data-base is an important starting point to develop a large scale, expandable data-base aimed to excite, inspire, and encourage participation among researchers. In addition, the possibility to archive location and qualitative information for gas emission/sites not yet investigated, could stimulate the scientific community for future researches and will provide an indication on the current uncertainty on deep carbon fluxes global estimates.

Establishment of an international database for genetic variants in esophageal cancer.

PubMed

Vihinen, Mauno

2016-10-01

The establishment of a database has been suggested in order to collect, organize, and distribute genetic information about esophageal cancer. The World Organization for Specialized Studies on Diseases of the Esophagus and the Human Variome Project will be in charge of a central database of information about esophageal cancer-related variations from publications, databases, and laboratories; in addition to genetic details, clinical parameters will also be included. The aim will be to get all the central players in research, clinical, and commercial laboratories to contribute. The database will follow established recommendations and guidelines. The database will require a team of dedicated curators with different backgrounds. Numerous layers of systematics will be applied to facilitate computational analyses. The data items will be extensively integrated with other information sources. The database will be distributed as open access to ensure exchange of the data with other databases. Variations will be reported in relation to reference sequences on three levels--DNA, RNA, and protein-whenever applicable. In the first phase, the database will concentrate on genetic variations including both somatic and germline variations for susceptibility genes. Additional types of information can be integrated at a later stage. © 2016 New York Academy of Sciences.

Dutch virtual integration of healthcare information.

PubMed

de Graaf, J C; Vlug, A E; van Boven, G J

2007-01-01

As information technology creates opportunities for cooperation which crosses the boundaries between healthcare institutions, it will become an integral part of the Dutch healthcare system. Along with many involved organizations in healthcare the National IT Institute for Healthcare in the Netherlands (NICTIZ) is working on the realization of a national IT infrastructure for healthcare and a national electronic patient record (EPR). An underlying national architecture is designed to enable the Dutch EPR virtually, not in a national database, nor on a patient's smartcard. The required secure infrastructure provides generic functions for healthcare applications: patient identification, authentication and authorization of healthcare professionals. The first national applications in the EPR program using a national index of where patient data is stored, are the electronic medication record and the electronic record for after hours GP services. The rollout of the electronic medication record and electronic record for after hours GP services has been started in 2007. To guarantee progress of electronic data exchange in healthcare in the Netherlands we have primarily opted for two healthcare applications: the electronic medication record and the electronic record for after hours GP services. The use of a national switch-point containing the registry of where to find what information, guarantees that the professional receives the most recent information and omits large databases to contain downloaded data. Proper authorization, authentication as well as tracing by the national switchpoint also ensures a secure environment for the communication of delicate information.

[LONI & Co: about the epistemic specificity of digital spaces of knowledge in cognitive neuroscience].

PubMed

Huber, Lara

2011-06-01

In the neurosciences digital databases more and more are becoming important tools of data rendering and distributing. This development is due to the growing impact of imaging based trial design in cognitive neuroscience, including morphological as much as functional imaging technologies. As the case of the 'Laboratory of Neuro Imaging' (LONI) is showing, databases are attributed a specific epistemological power: Since the 1990s databasing is seen to foster the integration of neuroscientific data, although local regimes of data production, -manipulation and--interpretation are also challenging this development. Databasing in the neurosciences goes along with the introduction of new structures of integrating local data, hence establishing digital spaces of knowledge (epistemic spaces): At this stage, inherent norms of digital databases are affecting regimes of imaging-based trial design, for example clinical research into Alzheimer's disease.

Lost in search: (Mal-)adaptation to probabilistic decision environments in children and adults.

PubMed

Betsch, Tilmann; Lehmann, Anne; Lindow, Stefanie; Lang, Anna; Schoemann, Martin

2016-02-01

Adaptive decision making in probabilistic environments requires individuals to use probabilities as weights in predecisional information searches and/or when making subsequent choices. Within a child-friendly computerized environment (Mousekids), we tracked 205 children's (105 children 5-6 years of age and 100 children 9-10 years of age) and 103 adults' (age range: 21-22 years) search behaviors and decisions under different probability dispersions (.17; .33, .83 vs. .50, .67, .83) and constraint conditions (instructions to limit search: yes vs. no). All age groups limited their depth of search when instructed to do so and when probability dispersion was high (range: .17-.83). Unlike adults, children failed to use probabilities as weights for their searches, which were largely not systematic. When examining choices, however, elementary school children (unlike preschoolers) systematically used probabilities as weights in their decisions. This suggests that an intuitive understanding of probabilities and the capacity to use them as weights during integration is not a sufficient condition for applying simple selective search strategies that place one's focus on weight distributions. PsycINFO Database Record (c) 2016 APA, all rights reserved.

Development of a user-centered radiology teaching file system

NASA Astrophysics Data System (ADS)

dos Santos, Marcelo; Fujino, Asa

2011-03-01

Learning radiology requires systematic and comprehensive study of a large knowledge base of medical images. In this work is presented the development of a digital radiology teaching file system. The proposed system has been created in order to offer a set of customized services regarding to users' contexts and their informational needs. This has been done by means of an electronic infrastructure that provides easy and integrated access to all relevant patient data at the time of image interpretation, so that radiologists and researchers can examine all available data to reach well-informed conclusions, while protecting patient data privacy and security. The system is presented such as an environment which implements a distributed clinical database, including medical images, authoring tools, repository for multimedia documents, and also a peer-reviewed model which assures dataset quality. The current implementation has shown that creating clinical data repositories on networked computer environments points to be a good solution in terms of providing means to review information management practices in electronic environments and to create customized and contextbased tools for users connected to the system throughout electronic interfaces.

IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data.

PubMed

Legehar, Ashenafi; Xhaard, Henri; Ghemtio, Leo

2016-01-01

The disposition of a pharmaceutical compound within an organism, i.e. its Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) properties and adverse effects, critically affects late stage failure of drug candidates and has led to the withdrawal of approved drugs. Computational methods are effective approaches to reduce the number of safety issues by analyzing possible links between chemical structures and ADMET or adverse effects, but this is limited by the size, quality, and heterogeneity of the data available from individual sources. Thus, large, clean and integrated databases of approved drug data, associated with fast and efficient predictive tools are desirable early in the drug discovery process. We have built a relational database (IDAAPM) to integrate available approved drug data such as drug approval information, ADMET and adverse effects, chemical structures and molecular descriptors, targets, bioactivity and related references. The database has been coupled with a searchable web interface and modern data analytics platform (KNIME) to allow data access, data transformation, initial analysis and further predictive modeling. Data were extracted from FDA resources and supplemented from other publicly available databases. Currently, the database contains information regarding about 19,226 FDA approval applications for 31,815 products (small molecules and biologics) with their approval history, 2505 active ingredients, together with as many ADMET properties, 1629 molecular structures, 2.5 million adverse effects and 36,963 experimental drug-target bioactivity data. IDAAPM is a unique resource that, in a single relational database, provides detailed information on FDA approved drugs including their ADMET properties and adverse effects, the corresponding targets with bioactivity data, coupled with a data analytics platform. It can be used to perform basic to complex drug-target ADMET or adverse effects analysis and predictive modeling. IDAAPM is freely accessible at http://idaapm.helsinki.fi and can be exploited through a KNIME workflow connected to the database.Graphical abstractFDA approved drug data integration for predictive modeling.

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

An integrated chronostratigraphic data system for the twenty-first century

USGS Publications Warehouse

Sikora, P.J.; Ogg, James G.; Gary, A.; Cervato, C.; Gradstein, Felix; Huber, B.T.; Marshall, C.; Stein, J.A.; Wardlaw, B.

2006-01-01

Research in stratigraphy is increasingly multidisciplinary and conducted by diverse research teams whose members can be widely separated. This developing distributed-research process, facilitated by the availability of the Internet, promises tremendous future benefits to researchers. However, its full potential is hindered by the absence of a development strategy for the necessary infrastructure. At a National Science Foundation workshop convened in November 2001, thirty quantitative stratigraphers and database specialists from both academia and industry met to discuss how best to integrate their respective chronostratigraphic databases. The main goal was to develop a strategy that would allow efficient distribution and integration of existing data relevant to the study of geologic time. Discussions concentrated on three major themes: database standards and compatibility, strategies and tools for information retrieval and analysis of all types of global and regional stratigraphic data, and future directions for database integration and centralization of currently distributed depositories. The result was a recommendation to establish an integrated chronostratigraphic database, to be called Chronos, which would facilitate greater efficiency in stratigraphic studies (http://www.chronos.org/) . The Chronos system will both provide greater ease of data gathering and allow for multidisciplinary synergies, functions of fundamental importance in a variety of research, including time scale construction, paleoenvironmental analysis, paleoclimatology and paleoceanography. Beyond scientific research, Chronos will also provide educational and societal benefits by providing an accessible source of information of general interest (e.g., mass extinctions) and concern (e.g., climatic change). The National Science Foundation has currently funded a three-year program for implementing Chronos.. ?? 2006 Geological Society of America. All rights reserved.

Dynamic analysis environment for nuclear forensic analyses

NASA Astrophysics Data System (ADS)

Stork, C. L.; Ummel, C. C.; Stuart, D. S.; Bodily, S.; Goldblum, B. L.

2017-01-01

A Dynamic Analysis Environment (DAE) software package is introduced to facilitate group inclusion/exclusion method testing, evaluation and comparison for pre-detonation nuclear forensics applications. Employing DAE, the multivariate signatures of a questioned material can be compared to the signatures for different, known groups, enabling the linking of the questioned material to its potential process, location, or fabrication facility. Advantages of using DAE for group inclusion/exclusion include built-in query tools for retrieving data of interest from a database, the recording and documentation of all analysis steps, a clear visualization of the analysis steps intelligible to a non-expert, and the ability to integrate analysis tools developed in different programming languages. Two group inclusion/exclusion methods are implemented in DAE: principal component analysis, a parametric feature extraction method, and k nearest neighbors, a nonparametric pattern recognition method. Spent Fuel Isotopic Composition (SFCOMPO), an open source international database of isotopic compositions for spent nuclear fuels (SNF) from 14 reactors, is used to construct PCA and KNN models for known reactor groups, and 20 simulated SNF samples are utilized in evaluating the performance of these group inclusion/exclusion models. For all 20 simulated samples, PCA in conjunction with the Q statistic correctly excludes a large percentage of reactor groups and correctly includes the true reactor of origination. Employing KNN, 14 of the 20 simulated samples are classified to their true reactor of origination.

Identifying opportune landing sites in degraded visual environments with terrain and cultural databases

NASA Astrophysics Data System (ADS)

Moody, Marc; Fisher, Robert; Little, J. Kristin

2014-06-01

Boeing has developed a degraded visual environment navigational aid that is flying on the Boeing AH-6 light attack helicopter. The navigational aid is a two dimensional software digital map underlay generated by the Boeing™ Geospatial Embedded Mapping Software (GEMS) and fully integrated with the operational flight program. The page format on the aircraft's multi function displays (MFD) is termed the Approach page. The existing work utilizes Digital Terrain Elevation Data (DTED) and OpenGL ES 2.0 graphics capabilities to compute the pertinent graphics underlay entirely on the graphics processor unit (GPU) within the AH-6 mission computer. The next release will incorporate cultural databases containing Digital Vertical Obstructions (DVO) to warn the crew of towers, buildings, and power lines when choosing an opportune landing site. Future IRAD will include Light Detection and Ranging (LIDAR) point cloud generating sensors to provide 2D and 3D synthetic vision on the final approach to the landing zone. Collision detection with respect to terrain, cultural, and point cloud datasets may be used to further augment the crew warning system. The techniques for creating the digital map underlay leverage the GPU almost entirely, making this solution viable on most embedded mission computing systems with an OpenGL ES 2.0 capable GPU. This paper focuses on the AH-6 crew interface process for determining a landing zone and flying the aircraft to it.

The Edinburgh Electronic Veterinary Curriculum: an online program-wide learning and support environment for veterinary education.

PubMed

Ellaway, Rachel; Pettigrew, Graham; Rhind, Susan; Dewhurst, David

2005-01-01

The Edinburgh Electronic Veterinary Curriculum (EEVeC) is a purpose-built virtual learning support environment for the veterinary medicine program at the University of Edinburgh. It is Web based and adapted from a system developed for the human medical curriculum. It is built around a set of databases and learning objects and incorporates features such as course materials, personalized timetables, staff and student contact pages, a notice board, and discussion forums. The EEVeC also contains global or generic resources such as information on quality enhancement and research options. Many of these features contribute to the aim of building a learning community, but a challenge has been to introduce specific features that enhance student learning. One of these is a searchable lecture database in which learning activities such as quizzes and computer-aided learning exercises (CALs) can be embedded to supplement a synopsis of the lecture and address the key needs of integration and reinforcement of learning. Statistics of use indicate extensive student activity during evenings and weekends, with a pattern of increased usage over the years as more features become available and staff and students progressively engage with the system. An essential feature of EEVeC is its flexibility and the way in which it is evolving to meet the changing needs of the teaching program.

Satellite Imagery Assisted Road-Based Visual Navigation System

NASA Astrophysics Data System (ADS)

Volkova, A.; Gibbens, P. W.

2016-06-01

There is a growing demand for unmanned aerial systems as autonomous surveillance, exploration and remote sensing solutions. Among the key concerns for robust operation of these systems is the need to reliably navigate the environment without reliance on global navigation satellite system (GNSS). This is of particular concern in Defence circles, but is also a major safety issue for commercial operations. In these circumstances, the aircraft needs to navigate relying only on information from on-board passive sensors such as digital cameras. An autonomous feature-based visual system presented in this work offers a novel integral approach to the modelling and registration of visual features that responds to the specific needs of the navigation system. It detects visual features from Google Earth* build a feature database. The same algorithm then detects features in an on-board cameras video stream. On one level this serves to localise the vehicle relative to the environment using Simultaneous Localisation and Mapping (SLAM). On a second level it correlates them with the database to localise the vehicle with respect to the inertial frame. The performance of the presented visual navigation system was compared using the satellite imagery from different years. Based on comparison results, an analysis of the effects of seasonal, structural and qualitative changes of the imagery source on the performance of the navigation algorithm is presented. * The algorithm is independent of the source of satellite imagery and another provider can be used

Quality assessment of clinical practice guidelines for integrative medicine in China: A systematic review.

PubMed

Yao, Sha; Wei, Dang; Chen, Yao-Long; Wang, Qi; Wang, Xiao-Qin; Zeng, Zhao; Li, Hui

2017-05-01

To assess the quality of integrative medicine clinical practice guidelines (CPGs) published before 2014. A systematic search of the scientific literature published before 2014 was conducted to select integrative medicine CPGs. Four major Chinese integrated databases and one guideline database were searched: the Chinese Biomedical Literature Database (CBM), the China National Knowledge Infrastructure (CNKI), China Science and Technology Journal Database (VIP), Wanfang Data, and the China Guideline Clearinghouse (CGC). Four reviewers independently assessed the quality of the included guidelines using the Appraisal of Guidelines for Research and Evaluation (AGREE) II Instrument. Overall consensus among the reviewers was assessed using the intra-class correlation coefficient (ICC). A total of 41 guidelines published from 2003 to 2014 were included. The overall consensus among the reviewers was good [ICC: 0.928; 95% confifi dence interval (CI): 0.920 to 0.935]. The scores on the 6 AGREE domains were: 17% for scope and purpose (range: 6% to 32%), 11% for stakeholder involvement (range: 0 to 24%), 10% for rigor of development (range: 3% to 22%), 39% for clarity and presentation (range: 25% to 64%), 11% for applicability (range: 4% to 24%), and 1% for editorial independence (range: 0 to 15%). The quality of integrative medicine CPGs was low, the development of integrative medicine CPGs should be guided by systematic methodology. More emphasis should be placed on multi-disciplinary guideline development groups, quality of evidence, management of funding and conflfl icts of interest, and guideline updates in the process of developing integrative medicine CPGs in China.

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

PubMed Central

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

2015-01-01

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

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

PubMed

Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo; Dobson, Paul D; Dunstan, Mark; Jervis, Adrian J; Vinaixa, Maria; Williams, Alan R; Ananiadou, Sophia; Faulon, Jean-Loup; Mendes, Pedro; Kell, Douglas B; Scrutton, Nigel S; Breitling, Rainer

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and-crucially-the relationships between them. Such a resource should be extensible, such that newly discovered relationships-for example, those between novel, synthetic enzymes and non-natural products-can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists.

biochem4j: Integrated and extensible biochemical knowledge through graph databases

PubMed Central

Batista-Navarro, Riza; Dunstan, Mark; Jervis, Adrian J.; Vinaixa, Maria; Ananiadou, Sophia; Faulon, Jean-Loup; Kell, Douglas B.

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and–crucially–the relationships between them. Such a resource should be extensible, such that newly discovered relationships–for example, those between novel, synthetic enzymes and non-natural products–can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists. PMID:28708831

Real-time terrain storage generation from multiple sensors towards mobile robot operation interface.

PubMed

Song, Wei; Cho, Seoungjae; Xi, Yulong; Cho, Kyungeun; Um, Kyhyun

2014-01-01

A mobile robot mounted with multiple sensors is used to rapidly collect 3D point clouds and video images so as to allow accurate terrain modeling. In this study, we develop a real-time terrain storage generation and representation system including a nonground point database (PDB), ground mesh database (MDB), and texture database (TDB). A voxel-based flag map is proposed for incrementally registering large-scale point clouds in a terrain model in real time. We quantize the 3D point clouds into 3D grids of the flag map as a comparative table in order to remove the redundant points. We integrate the large-scale 3D point clouds into a nonground PDB and a node-based terrain mesh using the CPU. Subsequently, we program a graphics processing unit (GPU) to generate the TDB by mapping the triangles in the terrain mesh onto the captured video images. Finally, we produce a nonground voxel map and a ground textured mesh as a terrain reconstruction result. Our proposed methods were tested in an outdoor environment. Our results show that the proposed system was able to rapidly generate terrain storage and provide high resolution terrain representation for mobile mapping services and a graphical user interface between remote operators and mobile robots.

Sharing and executing linked data queries in a collaborative environment.

PubMed

García Godoy, María Jesús; López-Camacho, Esteban; Navas-Delgado, Ismael; Aldana-Montes, José F

2013-07-01

Life Sciences have emerged as a key domain in the Linked Data community because of the diversity of data semantics and formats available through a great variety of databases and web technologies. Thus, it has been used as the perfect domain for applications in the web of data. Unfortunately, bioinformaticians are not exploiting the full potential of this already available technology, and experts in Life Sciences have real problems to discover, understand and devise how to take advantage of these interlinked (integrated) data. In this article, we present Bioqueries, a wiki-based portal that is aimed at community building around biological Linked Data. This tool has been designed to aid bioinformaticians in developing SPARQL queries to access biological databases exposed as Linked Data, and also to help biologists gain a deeper insight into the potential use of this technology. This public space offers several services and a collaborative infrastructure to stimulate the consumption of biological Linked Data and, therefore, contribute to implementing the benefits of the web of data in this domain. Bioqueries currently contains 215 query entries grouped by database and theme, 230 registered users and 44 end points that contain biological Resource Description Framework information. The Bioqueries portal is freely accessible at http://bioqueries.uma.es. Supplementary data are available at Bioinformatics online.

IRIS Toxicological Review of Tert-Butyl Alcohol (Tert-Butanol) ...

EPA Pesticide Factsheets

On April 29, 2016, the Toxicological Review of tert-Butyl Alcohol (tert-Butanol) (Public Comment Draft) was released for public comment. The draft Toxicological Review and charge were reviewed internally by EPA and by other federal agencies and the Executive Office of the President during Step 3 (Interagency Science Consultation) before public release. As part of the IRIS process, all written interagency comments on IRIS assessments will be made publicly available. Accordingly, interagency comments with EPA's response and the interagency science consultation drafts of the IRIS Toxicological Review of tert-Butanol and charge to external peer reviewers are posted on this site. EPA is undertaking a new health assessment for t-butyl alcohol (tert-butanol) for the Integrated Risk Information System (IRIS). The outcome of this project will be a Toxicological Review and IRIS and IRIS Summary of TBA that will be entered on the IRIS database. IRIS is an EPA database containing Agency scientific positions on potential adverse human health effects that may result from chronic (or lifetime) exposure to chemicals in the environment. IRIS contains chemical-specific summaries of qualitative and quantitative health information to evaluate potential public health risks associated with environmental contaminants. The IRIS database is relied on for the development of risk assessments, site-specific environmental decisions, and rule making.

IRIS Toxicological Review of Biphenyl (Interagency Science ...

EPA Pesticide Factsheets

On September 30, 2011, the draft Toxicological Review of Biphenyl and the charge to external peer reviewers were released for external peer review and public comment. The Toxicological Review and charge were reviewed internally by EPA and by other federal agencies and White House Offices before public release. In the new IRIS process (May 2009), introduced by the EPA Administrator, all written comments on IRIS assessments submitted by other federal agencies and White House Offices will be made publicly available. Accordingly, interagency comments and the interagency science consultation draft of the IRIS Toxicological Review of Biphenyl and the charge to external peer reviewers are posted on this site. EPA is undertaking a new health assessment for biphenyl for the Integrated Risk Information System (IRIS). The outcome of this project will be a Toxicological Review and IRIS and IRIS Summary of biohenyl that will be entered on the IRIS database. IRIS is an EPA database containing Agency scientific positions on potential adverse human health effects that may result from chronic (or lifetime) exposure to chemicals in the environment. IRIS contains chemical-specific summaries of qualitative and quantitative health information to evaluate potential public health risks associated with exposure assessment information to evaluate potential public health risks associated with environmental contaminants. The IRIS database is relied on for the development of risk ass

An "EAR" on environmental surveillance and monitoring: A ...

EPA Pesticide Factsheets

Current environmental monitoring approaches focus primarily on chemical occurrence. However, based on chemical concentration alone, it can be difficult to identify which compounds may be of toxicological concern for prioritization for further monitoring or management. This can be problematic because toxicological characterization is lacking for many emerging contaminants. New sources of high throughput screening data like the ToxCast™ database, which contains data for over 9,000 compounds screened through up to 1,100 assays, are now available. Integrated analysis of chemical occurrence data with HTS data offers new opportunities to prioritize chemicals, sites, or biological effects for further investigation based on concentrations detected in the environment linked to relative potencies in pathway-based bioassays. As a case study, chemical occurrence data from a 2012 study in the Great Lakes Basin along with the ToxCast™ effects database were used to calculate exposure-activity ratios (EARs) as a prioritization tool. Technical considerations of data processing and use of the ToxCast™ database are presented and discussed. EAR prioritization identified multiple sites, biological pathways, and chemicals that warrant further investigation. Biological pathways were then linked to adverse outcome pathways to identify potential adverse outcomes and biomarkers for use in subsequent monitoring efforts. Anthropogenic contaminants are frequently reported in environm

Real-Time Terrain Storage Generation from Multiple Sensors towards Mobile Robot Operation Interface

PubMed Central

Cho, Seoungjae; Xi, Yulong; Cho, Kyungeun

2014-01-01

A mobile robot mounted with multiple sensors is used to rapidly collect 3D point clouds and video images so as to allow accurate terrain modeling. In this study, we develop a real-time terrain storage generation and representation system including a nonground point database (PDB), ground mesh database (MDB), and texture database (TDB). A voxel-based flag map is proposed for incrementally registering large-scale point clouds in a terrain model in real time. We quantize the 3D point clouds into 3D grids of the flag map as a comparative table in order to remove the redundant points. We integrate the large-scale 3D point clouds into a nonground PDB and a node-based terrain mesh using the CPU. Subsequently, we program a graphics processing unit (GPU) to generate the TDB by mapping the triangles in the terrain mesh onto the captured video images. Finally, we produce a nonground voxel map and a ground textured mesh as a terrain reconstruction result. Our proposed methods were tested in an outdoor environment. Our results show that the proposed system was able to rapidly generate terrain storage and provide high resolution terrain representation for mobile mapping services and a graphical user interface between remote operators and mobile robots. PMID:25101321

High-temperature experimental and thermodynamic modelling research on the pyrometallurgical processing of copper

NASA Astrophysics Data System (ADS)

Hidayat, Taufiq; Shishin, Denis; Decterov, Sergei A.; Hayes, Peter C.; Jak, Evgueni

2017-01-01

Uncertainty in the metal price and competition between producers mean that the daily operation of a smelter needs to target high recovery of valuable elements at low operating cost. Options for the improvement of the plant operation can be examined and decision making can be informed based on accurate information from laboratory experimentation coupled with predictions using advanced thermodynamic models. Integrated high-temperature experimental and thermodynamic modelling research on phase equilibria and thermodynamics of copper-containing systems have been undertaken at the Pyrometallurgy Innovation Centre (PYROSEARCH). The experimental phase equilibria studies involve high-temperature equilibration, rapid quenching and direct measurement of phase compositions using electron probe X-ray microanalysis (EPMA). The thermodynamic modelling deals with the development of accurate thermodynamic database built through critical evaluation of experimental data, selection of solution models, and optimization of models parameters. The database covers the Al-Ca-Cu-Fe-Mg-O-S-Si chemical system. The gas, slag, matte, liquid and solid metal phases, spinel solid solution as well as numerous solid oxide and sulphide phases are included. The database works within the FactSage software environment. Examples of phase equilibria data and thermodynamic models of selected systems, as well as possible implementation of the research outcomes to selected copper making processes are presented.

The prevalence of co-morbid depression among employees with type 2 diabetes in a Japanese corporation: a descriptive study using an integrated health database.

PubMed

Arima, Hideaki; Miwa, Makiko; Kawahara, Kazuo

2007-03-01

To determine the prevalence of comorbid depression among people with type 2 diabetes using the integrated health database. A total of 6543 people aged 18-65 years were selected from the employees of a Japanese corporation. Using the corporation's integrated health database, which consisted of medical claims data and a self-reported questionnaire from the fiscal year 2000, this study was undertaken to identify the prevalence, the odds ratio and some related factors. The prevalence of co-morbid depression among people with type 2 diabetes was 2.6%. The crude odds ratio of co-morbid depression among those with type 2 diabetes was 2.20 (95% CI 0.88-5.50). After adjustment for covariates (gender, age, alcohol drinking, smoking, exercise, and dietary restriction), the odds ratio of co-morbid depression among those with type 2 diabetes was 2.33 (0.86-6.33). Using the integrated health database, it was suggested that patients with type 2 diabetes were more likely to suffer from depression and there was a relationship between depression and dietary restriction of portion control.

Anatomy of a decision III: Evaluation of national disposal at sea program action level efficacy considering 2 chemical action levels.

PubMed

Apitz, Sabine E; Vivian, Chris; Agius, Suzanne

2017-11-01

The potential performance (i.e., ability to separate nontoxic from toxic sediments) of a range of international Disposal at Sea (DaS) chemical Action Levels (ALs) was compared using a sediment chemical and toxicological database. The use of chemistry alone (without the use of further lines of evidence) did not perform well at reducing costs and protecting the environment. Although some approaches for interpreting AL1 results are very effective at filtering out the majority of acutely toxic sediments, without subsequent toxicological assessment, a large proportion of nontoxic sediments would be unnecessarily subjected to treatment and containment, and a number of sublethally toxic sediments would be missed. Even the best tiered systems that collect and evaluate information sequentially resulted in the failure to catch at least some sublethally or acutely toxic sediments. None of the AL2s examined were particularly effective in distinguishing between non-, sublethally, or acutely toxic sediments. Thus, this review did not support the use of chemical AL2s to predict the degree to which sediments will be toxic. Integr Environ Assess Manag 2017;13:1086-1099.© 2017 The Authors. Integrated Environmental Assessment and Management Published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC). © 2017 The Authors. Integrated Environmental Assessment and Management Published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Integrated modeling: a look back

NASA Astrophysics Data System (ADS)

Briggs, Clark

2015-09-01

This paper discusses applications and implementation approaches used for integrated modeling of structural systems with optics over the past 30 years. While much of the development work focused on control system design, significant contributions were made in system modeling and computer-aided design (CAD) environments. Early work appended handmade line-of-sight models to traditional finite element models, such as the optical spacecraft concept from the ACOSS program. The IDEAS2 computational environment built in support of Space Station collected a wider variety of existing tools around a parametric database. Later, IMOS supported interferometer and large telescope mission studies at JPL with MATLAB modeling of structural dynamics, thermal analysis, and geometric optics. IMOS's predecessor was a simple FORTRAN command line interpreter for LQG controller design with additional functions that built state-space finite element models. Specialized language systems such as CAESY were formulated and prototyped to provide more complex object-oriented functions suited to control-structure interaction. A more recent example of optical modeling directly in mechanical CAD is used to illustrate possible future directions. While the value of directly posing the optical metric in system dynamics terms is well understood today, the potential payoff is illustrated briefly via project-based examples. It is quite likely that integrated structure thermal optical performance (STOP) modeling could be accomplished in a commercial off-the-shelf (COTS) tool set. The work flow could be adopted, for example, by a team developing a small high-performance optical or radio frequency (RF) instrument.

The designing and implementation of PE teaching information resource database based on broadband network

NASA Astrophysics Data System (ADS)

Wang, Jian

2017-01-01

In order to change traditional PE teaching mode and realize the interconnection, interworking and sharing of PE teaching resources, a distance PE teaching platform based on broadband network is designed and PE teaching information resource database is set up. The designing of PE teaching information resource database takes Windows NT 4/2000Server as operating system platform, Microsoft SQL Server 7.0 as RDBMS, and takes NAS technology for data storage and flow technology for video service. The analysis of system designing and implementation shows that the dynamic PE teaching information resource sharing platform based on Web Service can realize loose coupling collaboration, realize dynamic integration and active integration and has good integration, openness and encapsulation. The distance PE teaching platform based on Web Service and the design scheme of PE teaching information resource database can effectively solve and realize the interconnection, interworking and sharing of PE teaching resources and adapt to the informatization development demands of PE teaching.

Team Composition Issues for Future Space Exploration: A Review and Directions for Future Research.

PubMed

Bell, Suzanne T; Brown, Shanique G; Abben, Daniel R; Outland, Neal B

2015-06-01

Future space exploration, such as a mission to Mars, will require space crews to live and work in extreme environments unlike those of previous space missions. Extreme conditions such as prolonged confinement, isolation, and expected communication time delays will require that crews have a higher level of interpersonal compatibility and be able to work autonomously, adapting to unforeseen challenges in order to ensure mission success. Team composition, or the configuration of member attributes, is an important consideration for maximizing crewmember well-being and team performance. We conducted an extensive search to find articles about team composition in long-distance space exploration (LDSE)-analogue environments, including a search of databases, specific relevant journals, and by contacting authors who publish in the area. We review the team composition research conducted in analogue environments in terms of two paths through which team composition is likely to be related to LDSE mission success, namely by 1) affecting social integration, and 2) the team processes and emergent states related to team task completion. Suggestions for future research are summarized as: 1) the need to identify ways to foster unit-level social integration within diverse crews; 2) the missed opportunity to use team composition variables as a way to improve team processes, emergent states, and task completion; and 3) the importance of disentangling the effect of specific team composition variables to determine the traits (e.g., personality, values) that are associated with particular risks (e.g., subgrouping) to performance.

The research and development of water resources management information system based on ArcGIS

NASA Astrophysics Data System (ADS)

Cui, Weiqun; Gao, Xiaoli; Li, Yuzhi; Cui, Zhencai

According to that there are large amount of data, complexity of data type and format in the water resources management, we built the water resources calculation model and established the water resources management information system based on the advanced ArcGIS and Visual Studio.NET development platform. The system can integrate the spatial data and attribute data organically, and manage them uniformly. It can analyze spatial data, inquire by map and data bidirectionally, provide various charts and report forms automatically, link multimedia information, manage database etc. . So it can provide spatial and static synthetical information services for study, management and decision of water resources, regional geology and eco-environment etc..

Managing and Querying Image Annotation and Markup in XML.

PubMed

Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel

2010-01-01

Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid.

Managing and Querying Image Annotation and Markup in XML

PubMed Central

Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel

2010-01-01

Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid. PMID:21218167

Integrating data to acquire new knowledge: Three modes of integration in plant science.

PubMed

Leonelli, Sabina

2013-12-01

This paper discusses what it means and what it takes to integrate data in order to acquire new knowledge about biological entities and processes. Maureen O'Malley and Orkun Soyer have pointed to the scientific work involved in data integration as important and distinct from the work required by other forms of integration, such as methodological and explanatory integration, which have been more successful in captivating the attention of philosophers of science. Here I explore what data integration involves in more detail and with a focus on the role of data-sharing tools, like online databases, in facilitating this process; and I point to the philosophical implications of focusing on data as a unit of analysis. I then analyse three cases of data integration in the field of plant science, each of which highlights a different mode of integration: (1) inter-level integration, which involves data documenting different features of the same species, aims to acquire an interdisciplinary understanding of organisms as complex wholes and is exemplified by research on Arabidopsis thaliana; (2) cross-species integration, which involves data acquired on different species, aims to understand plant biology in all its different manifestations and is exemplified by research on Miscanthus giganteus; and (3) translational integration, which involves data acquired from sources within as well as outside academia, aims at the provision of interventions to improve human health (e.g. by sustaining the environment in which humans thrive) and is exemplified by research on Phytophtora ramorum. Recognising the differences between these efforts sheds light on the dynamics and diverse outcomes of data dissemination and integrative research; and the relations between the social and institutional roles of science, the development of data-sharing infrastructures and the production of scientific knowledge. Copyright © 2013 Elsevier Ltd. All rights reserved.

INTAROS: Development of an integrated Arctic observation system under Horizon 2020

NASA Astrophysics Data System (ADS)

Beszczynska-Möller, Agnieszka; Sandven, Stein; Sagen, Hanne

2017-04-01

INTAROS is a research and innovation action funded under the H2020-BG-09 call for the five-year period 2016-2021. INTAROS will develop an integrated Arctic Observation System (iAOS) by extending, improving and unifying existing systems in the different regions of the Arctic. INTAROS will have a strong multidisciplinary focus, with tools for integration of data from atmosphere, ocean, cryosphere and terrestrial sciences, provided by institutions in Europe, North America and Asia. Satellite earth observation (EO) data plays an increasingly important role in such observing systems, because the amount of EO data for observing the global climate and environment grows year by year. EO data will therefore be integrated into iAOS based on existing products and databases. In situ observing systems are much more limited due to logistical constraints and cost limitations. The sparseness of in situ data is therefore the largest gap in the overall observing system. INTAROS will assess strengths and weaknesses of existing Arctic observing systems and contribute with innovative solutions to fill some of the critical gaps in the selected networks. INTAROS will develop a platform, iAOS, to search for and access data from distributed databases. The evolution into a sustainable Arctic observing system requires coordination, mobilization and cooperation between the existing European and international infrastructures (in-situ and remote, including space-based), the modeling communities and relevant stakeholder groups. INTAROS will include development of community-based observing systems, where local knowledge is merged with scientific data. Multidisciplinary data integrated under INTAROS will contribute to better understanding of interactions and coupling in the complex Arctic ice-ocean-land-atmosphere system. An integrated Arctic Observation System will enable better-informed decisions and better-documented processes within key sectors (e.g. local communities, shipping, tourism, fishing), in order to strengthen the societal and economic role of the Arctic region and support the EU strategy for the Arctic and related maritime and environmental policies. Following the SAON goal, INTAROS will support and strengthen the EU engagement in developing the sustained and coordinated pan-Arctic observing and data sharing systems.

Mapping integration of midwives across the United States: Impact on access, equity, and outcomes

PubMed Central

Stoll, Kathrin; MacDorman, Marian; Declercq, Eugene; Cramer, Renee; Cheyney, Melissa; Fisher, Timothy; Butt, Emma; Yang, Y. Tony; Powell Kennedy, Holly

2018-01-01

Poor coordination of care across providers and birth settings has been associated with adverse maternal-newborn outcomes. Research suggests that integration of midwives into regional health systems is a key determinant of optimal maternal-newborn outcomes, yet, to date, the characteristics of an integrated system have not been described, nor linked to health disparities. Methods Our multidisciplinary team examined published regulatory data to inform a 50-state database describing the environment for midwifery practice and interprofessional collaboration. Items (110) detailed differences across jurisdictions in scope of practice, autonomy, governance, and prescriptive authority; as well as restrictions that can affect patient safety, quality, and access to maternity providers across birth settings. A nationwide survey of state regulatory experts (n = 92) verified the ‘on the ground’ relevance, importance, and realities of local interpretation of these state laws. Using a modified Delphi process, we selected 50/110 key items to include in a weighted, composite Midwifery Integration Scoring (MISS) system. Higher scores indicate greater integration of midwives across all settings. We ranked states by MISS scores; and, using reliable indicators in the CDC-Vital Statistics Database, we calculated correlation coefficients between MISS scores and maternal-newborn outcomes by state, as well as state density of midwives and place of birth. We conducted hierarchical linear regression analysis to control for confounding effects of race. Results MISS scores ranged from lowest at 17 (North Carolina) to highest at 61 (Washington), out of 100 points. Higher MISS scores were associated with significantly higher rates of spontaneous vaginal delivery, vaginal birth after cesarean, and breastfeeding, and significantly lower rates of cesarean, preterm birth, low birth weight infants, and neonatal death. MISS scores also correlated with density of midwives and access to care across birth settings. Significant differences in newborn outcomes accounted for by MISS scores persisted after controlling for proportion of African American births in each state. Conclusion The MISS scoring system assesses the level of integration of midwives and evaluates regional access to high quality maternity care. In the United States, higher MISS Scores were associated with significantly higher rates of physiologic birth, less obstetric interventions, and fewer adverse neonatal outcomes. PMID:29466389

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.

PubMed

Xu, Huilei; Baroukh, Caroline; Dannenfelser, Ruth; Chen, Edward Y; Tan, Christopher M; Kou, Yan; Kim, Yujin E; Lemischka, Ihor R; Ma'ayan, Avi

2013-01-01

High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community. Database URL: http://www.maayanlab.net/ESCAPE

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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, themore » 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.« less

The ChEMBL database as linked open data

PubMed Central

2013-01-01

Background Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs). RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data analysis. Results This paper describes recent developments in an ongoing project converting data from the ChEMBL database into RDF triples. Relative to earlier versions, this updated version of ChEMBL-RDF uses recently introduced ontologies, including CHEMINF and CiTO; exposes more information from the database; and is now available as dereferencable, linked data. To demonstrate these new features, we present novel use cases showing further integration with other web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standard ontologies for querying. Conclusions We have illustrated the advantages of using open standards and ontologies to link the ChEMBL database to other databases. Using those links and the knowledge encoded in standards and ontologies, the ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications, such as the presented decision support. PMID:23657106

A DBMS architecture for global change research

NASA Astrophysics Data System (ADS)

Hachem, Nabil I.; Gennert, Michael A.; Ward, Matthew O.

1993-08-01

The goal of this research is the design and development of an integrated system for the management of very large scientific databases, cartographic/geographic information processing, and exploratory scientific data analysis for global change research. The system will represent both spatial and temporal knowledge about natural and man-made entities on the eath's surface, following an object-oriented paradigm. A user will be able to derive, modify, and apply, procedures to perform operations on the data, including comparison, derivation, prediction, validation, and visualization. This work represents an effort to extend the database technology with an intrinsic class of operators, which is extensible and responds to the growing needs of scientific research. Of significance is the integration of many diverse forms of data into the database, including cartography, geography, hydrography, hypsography, images, and urban planning data. Equally important is the maintenance of metadata, that is, data about the data, such as coordinate transformation parameters, map scales, and audit trails of previous processing operations. This project will impact the fields of geographical information systems and global change research as well as the database community. It will provide an integrated database management testbed for scientific research, and a testbed for the development of analysis tools to understand and predict global change.

A web-based system architecture for ontology-based data integration in the domain of IT benchmarking

NASA Astrophysics Data System (ADS)

Pfaff, Matthias; Krcmar, Helmut

2018-03-01

In the domain of IT benchmarking (ITBM), a variety of data and information are collected. Although these data serve as the basis for business analyses, no unified semantic representation of such data yet exists. Consequently, data analysis across different distributed data sets and different benchmarks is almost impossible. This paper presents a system architecture and prototypical implementation for an integrated data management of distributed databases based on a domain-specific ontology. To preserve the semantic meaning of the data, the ITBM ontology is linked to data sources and functions as the central concept for database access. Thus, additional databases can be integrated by linking them to this domain-specific ontology and are directly available for further business analyses. Moreover, the web-based system supports the process of mapping ontology concepts to external databases by introducing a semi-automatic mapping recommender and by visualizing possible mapping candidates. The system also provides a natural language interface to easily query linked databases. The expected result of this ontology-based approach of knowledge representation and data access is an increase in knowledge and data sharing in this domain, which will enhance existing business analysis methods.

The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases.

PubMed

Mostaguir, Khaled; Hoogland, Christine; Binz, Pierre-Alain; Appel, Ron D

2003-08-01

The Make 2D-DB tool has been previously developed to help build federated two-dimensional gel electrophoresis (2-DE) databases on one's own web site. The purpose of our work is to extend the strength of the first package and to build a more efficient environment. Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2-DE techniques and the increasing amount of distributed experimental data.

A New Approach To Secure Federated Information Bases Using Agent Technology.

ERIC Educational Resources Information Center

Weippi, Edgar; Klug, Ludwig; Essmayr, Wolfgang

2003-01-01

Discusses database agents which can be used to establish federated information bases by integrating heterogeneous databases. Highlights include characteristics of federated information bases, including incompatible database management systems, schemata, and frequently changing context; software agent technology; Java agents; system architecture;…

Research environments that promote integrity.

PubMed

Jeffers, Brenda Recchia; Whittemore, Robin

2005-01-01

The body of empirical knowledge about research integrity and the factors that promote research integrity in nursing research environments remains small. To propose an internal control model as an innovative framework for the design and structure of nursing research environments that promote integrity. An internal control model is adapted to illustrate its use for conceptualizing and designing research environments that promote integrity. The internal control model integrates both the organizational elements necessary to promote research integrity and the processes needed to assess research environments. The model provides five interrelated process components within which any number of research integrity variables and processes may be used and studied: internal control environment, risk assessment, internal control activities, monitoring, and information and communication. The components of the proposed research integrity internal control model proposed comprise an integrated conceptualization of the processes that provide reasonable assurance that research integrity will be promoted within the nursing research environment. Schools of nursing can use the model to design, implement, and evaluate systems that promote research integrity. The model process components need further exploration to substantiate the use of the model in nursing research environments.

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

PubMed Central

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

Intersection of participation and environmental factors: a complex interactive process.

PubMed

Noreau, Luc; Boschen, Kathryn

2010-09-01

The objective was to review contemporary and historical rehabilitation-focused literature on conceptualizations of the environment, broadly defined, and environmental measures. Data sources included historical nonempirical American-based literature from 1935 to the present and descriptive and empirical rehabilitation articles worldwide, retrieved from computerized databases predominantly from past 10 years depicting a participation-environment association. Literature selection required relevance to 3 combined topics: physical disability rehabilitation, participation/community integration, and impact of environmental barriers and facilitators. The ultimate focus was on spinal cord injury for recent literature and measures reviewed. Data extraction was based on author-assessed relevance to both participation and environmental considerations. Nonempirical literature from last three quarters of a century suggests an environmental impact on participation, focusing on "person-environment fit." Recent empirical evidence supports environmental contributions to participation, but the magnitude of the contribution is low. Despite the obvious theoretic impact of the environment, scientific demonstration of environmental contribution to participation restriction or facilitation has yet to be achieved. Participation-environment interaction could be illustrated better by (1) taking into account critical elements in environmental measures (eg, comprehensiveness of approach to environment, scales describing spectrum of environmental influence, subjective vs objective perspectives), (2) addressing the concept of participation in a dimension-specific approach, and (3) avoiding environmental features in construction of participation measures. Copyright 2010 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Arrhythmia Evaluation in Wearable ECG Devices

PubMed Central

Sadrawi, Muammar; Lin, Chien-Hung; Hsieh, Yita; Kuo, Chia-Chun; Chien, Jen Chien; Haraikawa, Koichi; Abbod, Maysam F.; Shieh, Jiann-Shing

2017-01-01

This study evaluates four databases from PhysioNet: The American Heart Association database (AHADB), Creighton University Ventricular Tachyarrhythmia database (CUDB), MIT-BIH Arrhythmia database (MITDB), and MIT-BIH Noise Stress Test database (NSTDB). The ANSI/AAMI EC57:2012 is used for the evaluation of the algorithms for the supraventricular ectopic beat (SVEB), ventricular ectopic beat (VEB), atrial fibrillation (AF), and ventricular fibrillation (VF) via the evaluation of the sensitivity, positive predictivity and false positive rate. Sample entropy, fast Fourier transform (FFT), and multilayer perceptron neural network with backpropagation training algorithm are selected for the integrated detection algorithms. For this study, the result for SVEB has some improvements compared to a previous study that also utilized ANSI/AAMI EC57. In further, VEB sensitivity and positive predictivity gross evaluations have greater than 80%, except for the positive predictivity of the NSTDB database. For AF gross evaluation of MITDB database, the results show very good classification, excluding the episode sensitivity. In advanced, for VF gross evaluation, the episode sensitivity and positive predictivity for the AHADB, MITDB, and CUDB, have greater than 80%, except for MITDB episode positive predictivity, which is 75%. The achieved results show that the proposed integrated SVEB, VEB, AF, and VF detection algorithm has an accurate classification according to ANSI/AAMI EC57:2012. In conclusion, the proposed integrated detection algorithm can achieve good accuracy in comparison with other previous studies. Furthermore, more advanced algorithms and hardware devices should be performed in future for arrhythmia detection and evaluation. PMID:29068369

An Integrated Molecular Database on Indian Insects.

PubMed

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/.

Incivility, retention and new graduate nurses: an integrated review of the literature.

PubMed

D'Ambra, Amanda M; Andrews, Diane R

2014-09-01

To evaluate the influence of incivility on the new graduate nurse transition experience. Incivility in the work environment is a major source of dissatisfaction and new graduate nurses are especially vulnerable. Incivility contributes to the high levels of turnover associated within the first 2 years of new graduate nurse employment. An integrated review of the literature was conducted using MEDLINE-EBSCOhost, PsycInfo and CINAHL databases. Relevant articles were reviewed for appropriateness related to inclusion/exclusion criteria and for quality using established criteria. Sixteen studies were included in the final analysis. Themes that emerged included workplace incivility, nurse residency programmes, mentoring through preceptors and empowerment/work environment. Findings indicated that incivility in the workplace was a significant predictor of low job satisfaction in new graduate nurses transitioning into practice. While graduate nurse transition programmes are associated with improved satisfaction and retention, they appear to address incivility by acculturating new graduate nurses to the experience of incivility. There is little evidence that the culture of incivility has been addressed. Nurse managers have the responsibility to be aware of the prevalence of incivility, assess for its occurrence, and implement strategies which eliminate workplace incivility and tolerance for uncivil behaviours. © 2013 John Wiley & Sons Ltd.

A temporal forecast of radiation environments for future space exploration missions.

PubMed

Kim, Myung-Hee Y; Cucinotta, Francis A; Wilson, John W

2007-06-01

The understanding of future space radiation environments is an important goal for space mission operations, design, and risk assessment. We have developed a solar cycle statistical model in which sunspot number is coupled to space-related quantities, such as the galactic cosmic radiation (GCR) deceleration potential (phi) and the mean occurrence frequency of solar particle events (SPEs). Future GCR fluxes were derived from a predictive model, in which the temporal dependence represented by phi was derived from GCR flux and ground-based Climax neutron monitor rate measurements over the last four decades. These results showed that the point dose equivalent inside a typical spacecraft in interplanetary space was influenced by solar modulation by up to a factor of three. It also has been shown that a strong relationship exists between large SPE occurrences and phi. For future space exploration missions, cumulative probabilities of SPEs at various integral fluence levels during short-period missions were defined using a database of proton fluences of past SPEs. Analytic energy spectra of SPEs at different ranks of the integral fluences for energies greater than 30 MeV were constructed over broad energy ranges extending out to GeV for the analysis of representative exposure levels at those fluences. Results will guide the design of protection systems for astronauts during future space exploration missions.

A web-based institutional DICOM distribution system with the integration of the Clinical Trial Processor (CTP).

PubMed

Aryanto, K Y E; Broekema, A; Langenhuysen, R G A; Oudkerk, M; van Ooijen, P M A

2015-05-01

To develop and test a fast and easy rule-based web-environment with optional de-identification of imaging data to facilitate data distribution within a hospital environment. A web interface was built using Hypertext Preprocessor (PHP), an open source scripting language for web development, and Java with SQL Server to handle the database. The system allows for the selection of patient data and for de-identifying these when necessary. Using the services provided by the RSNA Clinical Trial Processor (CTP), the selected images were pushed to the appropriate services using a protocol based on the module created for the associated task. Five pipelines, each performing a different task, were set up in the server. In a 75 month period, more than 2,000,000 images are transferred and de-identified in a proper manner while 20,000,000 images are moved from one node to another without de-identification. While maintaining a high level of security and stability, the proposed system is easy to setup, it integrate well with our clinical and research practice and it provides a fast and accurate vendor-neutral process of transferring, de-identifying, and storing DICOM images. Its ability to run different de-identification processes in parallel pipelines is a major advantage in both clinical and research setting.

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

PubMed

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

2012-01-01

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 methods are presented for an adapted CTP test set-up. In the first method, images are pushed from the Picture Archiving and Communication System (PACS) using the DICOM protocol through a local network. In the second method, images are transferred through the internet using the HTTPS protocol. In total 25,000 images from 50 patients were moved from the PACS, anonymised and stored within roughly 2 h using the first method. In the second method, an average of 10 images per minute were transferred and processed over a residential connection. In both methods, no duplicated images were stored when previous images were retransferred. The anonymised images are stored in appropriate directories. The CTP can transfer and process DICOM images correctly in a very easy set-up providing a fast, secure and stable environment. The adapted CTP allows easy integration into an environment in which patient data are already included in an existing information system.

DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation.

PubMed

Wolf, Beat; Kuonen, Pierre; Dandekar, Thomas; Atlan, David

2015-01-01

Over recent years next generation sequencing (NGS) technologies evolved from costly tools used by very few, to a much more accessible and economically viable technology. Through this recently gained popularity, its use-cases expanded from research environments into clinical settings. But the technical know-how and infrastructure required to analyze the data remain an obstacle for a wider adoption of this technology, especially in smaller laboratories. We present GensearchNGS, a commercial DNAseq software suite distributed by Phenosystems SA. The focus of GensearchNGS is the optimal usage of already existing infrastructure, while keeping its use simple. This is achieved through the integration of existing tools in a comprehensive software environment, as well as custom algorithms developed with the restrictions of limited infrastructures in mind. This includes the possibility to connect multiple computers to speed up computing intensive parts of the analysis such as sequence alignments. We present a typical DNAseq workflow for NGS data analysis and the approach GensearchNGS takes to implement it. The presented workflow goes from raw data quality control to the final variant report. This includes features such as gene panels and the integration of online databases, like Ensembl for annotations or Cafe Variome for variant sharing.

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

PubMed Central

Nayfach, Stephen; Rodriguez-Mueller, Beltran; Garud, Nandita

2016-01-01

We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 bacterial reference genomes that we clustered into species groups. These cover the majority of abundant species in the human microbiome but only a small proportion of microbes in other environments, including soil and seawater. We applied MIDAS to stool metagenomes from 98 Swedish mothers and their infants over one year and used rare SNPs to track strains between hosts. Using this approach, we found that although species compositions of mothers and infants converged over time, strain-level similarity diverged. Specifically, early colonizing bacteria were often transmitted from an infant’s mother, while late colonizing bacteria were often transmitted from other sources in the environment and were enriched for spore-formation genes. We also applied MIDAS to 198 globally distributed marine metagenomes and used gene content to show that many prevalent bacterial species have population structure that correlates with geographic location. Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynamics that are obscured when data are analyzed at a coarser taxonomic resolution. PMID:27803195

A reflective framework to foster emotionally intelligent leadership in nursing.

PubMed

Heckemann, Birgit; Schols, Jos M G A; Halfens, Ruud J G

2015-09-01

To propose a reflective framework based on the perspective of emotional intelligence (EI) in nurse leadership literature. Emotional intelligence is a self-development construct aimed at enhancing the management of feelings and interpersonal relationships, which has become increasingly popular in nurse leadership. Reflection is an established means to foster learning. Integrating those aspects of emotional intelligence pertinent to nurse leadership into a reflective framework might support the development of nurse leadership in a practical context. A sample of 22 articles, retrieved via electronic databases (Ovid/Medline, BNI, psycArticles, Zetoc and CINAHL) and published between January 1996 and April 2009, was analysed in a qualitative descriptive content analysis. Three dimensions that characterise emotional intelligence leadership in the context of nursing - the nurse leader as a 'socio-cultural architect', as a 'responsive carer' and as a 'strategic visionary' - emerged from the analysis. To enable practical application, these dimensions were contextualised into a reflective framework. Emotional intelligence skills are regarded as essential for establishing empowering work environments in nursing. A reflective framework might aid the translation of emotional intelligence into a real-world context. The proposed framework may supplement learning about emotional intelligence skills and aid the integration of emotional intelligence in a clinical environment. © 2014 John Wiley & Sons Ltd.

An ICT infrastructure to integrate clinical and molecular data in oncology research

PubMed Central

2012-01-01

Background The ONCO-i2b2 platform is a bioinformatics tool designed to integrate clinical and research data and support translational research in oncology. It is implemented by the University of Pavia and the IRCCS Fondazione Maugeri hospital (FSM), and grounded on the software developed by the Informatics for Integrating Biology and the Bedside (i2b2) research center. I2b2 has delivered an open source suite based on a data warehouse, which is efficiently interrogated to find sets of interesting patients through a query tool interface. Methods Onco-i2b2 integrates data coming from multiple sources and allows the users to jointly query them. I2b2 data are then stored in a data warehouse, where facts are hierarchically structured as ontologies. Onco-i2b2 gathers data from the FSM pathology unit (PU) database and from the hospital biobank and merges them with the clinical information from the hospital information system. Our main effort was to provide a robust integrated research environment, giving a particular emphasis to the integration process and facing different challenges, consecutively listed: biospecimen samples privacy and anonymization; synchronization of the biobank database with the i2b2 data warehouse through a series of Extract, Transform, Load (ETL) operations; development and integration of a Natural Language Processing (NLP) module, to retrieve coded information, such as SNOMED terms and malignant tumors (TNM) classifications, and clinical tests results from unstructured medical records. Furthermore, we have developed an internal SNOMED ontology rested on the NCBO BioPortal web services. Results Onco-i2b2 manages data of more than 6,500 patients with breast cancer diagnosis collected between 2001 and 2011 (over 390 of them have at least one biological sample in the cancer biobank), more than 47,000 visits and 96,000 observations over 960 medical concepts. Conclusions Onco-i2b2 is a concrete example of how integrated Information and Communication Technology architecture can be implemented to support translational research. The next steps of our project will involve the extension of its capabilities by implementing new plug-in devoted to bioinformatics data analysis as well as a temporal query module. PMID:22536972

Searching Across the International Space Station Databases

NASA Technical Reports Server (NTRS)

Maluf, David A.; McDermott, William J.; Smith, Ernest E.; Bell, David G.; Gurram, Mohana

2007-01-01

Data access in the enterprise generally requires us to combine data from different sources and different formats. It is advantageous thus to focus on the intersection of the knowledge across sources and domains; keeping irrelevant knowledge around only serves to make the integration more unwieldy and more complicated than necessary. A context search over multiple domain is proposed in this paper to use context sensitive queries to support disciplined manipulation of domain knowledge resources. The objective of a context search is to provide the capability for interrogating many domain knowledge resources, which are largely semantically disjoint. The search supports formally the tasks of selecting, combining, extending, specializing, and modifying components from a diverse set of domains. This paper demonstrates a new paradigm in composition of information for enterprise applications. In particular, it discusses an approach to achieving data integration across multiple sources, in a manner that does not require heavy investment in database and middleware maintenance. This lean approach to integration leads to cost-effectiveness and scalability of data integration with an underlying schemaless object-relational database management system. This highly scalable, information on demand system framework, called NX-Search, which is an implementation of an information system built on NETMARK. NETMARK is a flexible, high-throughput open database integration framework for managing, storing, and searching unstructured or semi-structured arbitrary XML and HTML used widely at the National Aeronautics Space Administration (NASA) and industry.

Integrated radiologist's workstation enabling the radiologist as an effective clinical consultant

NASA Astrophysics Data System (ADS)

McEnery, Kevin W.; Suitor, Charles T.; Hildebrand, Stan; Downs, Rebecca; Thompson, Stephen K.; Shepard, S. Jeff

2002-05-01

Since February 2000, radiologists at the M. D. Anderson Cancer Center have accessed clinical information through an internally developed radiologist's clinical interpretation workstation called RadStation. This project provides a fully integrated digital dictation workstation with clinical data review. RadStation enables the radiologist as an effective clinical consultant with access to pertinent sources of clinical information at the time of dictation. Data sources not only include prior radiology reports from the radiology information system (RIS) but access to pathology data, laboratory data, history and physicals, clinic notes, and operative reports. With integrated clinical information access, a radiologists's interpretation not only comments on morphologic findings but also can enable evaluation of study findings in the context of pertinent clinical presentation and history. Image access is enabled through the integration of an enterprise image archive (Stentor, San Francisco). Database integration is achieved by a combination of real time HL7 messaging and queries to SQL-based legacy databases. A three-tier system architecture accommodates expanding access to additional databases including real-time patient schedule as well as patient medications and allergies.

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

PubMed

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

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33,017,407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. © The Author(s) 2015. Published by Oxford University Press.

Database citation in full text biomedical articles.

PubMed

Kafkas, Şenay; Kim, Jee-Hyub; McEntyre, Johanna R

2013-01-01

Molecular biology and literature databases represent essential infrastructure for life science research. Effective integration of these data resources requires that there are structured cross-references at the level of individual articles and biological records. Here, we describe the current patterns of how database entries are cited in research articles, based on analysis of the full text Open Access articles available from Europe PMC. Focusing on citation of entries in the European Nucleotide Archive (ENA), UniProt and Protein Data Bank, Europe (PDBe), we demonstrate that text mining doubles the number of structured annotations of database record citations supplied in journal articles by publishers. Many thousands of new literature-database relationships are found by text mining, since these relationships are also not present in the set of articles cited by database records. We recommend that structured annotation of database records in articles is extended to other databases, such as ArrayExpress and Pfam, entries from which are also cited widely in the literature. The very high precision and high-throughput of this text-mining pipeline makes this activity possible both accurately and at low cost, which will allow the development of new integrated data services.

Database Citation in Full Text Biomedical Articles

PubMed Central

Kafkas, Şenay; Kim, Jee-Hyub; McEntyre, Johanna R.

2013-01-01

Molecular biology and literature databases represent essential infrastructure for life science research. Effective integration of these data resources requires that there are structured cross-references at the level of individual articles and biological records. Here, we describe the current patterns of how database entries are cited in research articles, based on analysis of the full text Open Access articles available from Europe PMC. Focusing on citation of entries in the European Nucleotide Archive (ENA), UniProt and Protein Data Bank, Europe (PDBe), we demonstrate that text mining doubles the number of structured annotations of database record citations supplied in journal articles by publishers. Many thousands of new literature-database relationships are found by text mining, since these relationships are also not present in the set of articles cited by database records. We recommend that structured annotation of database records in articles is extended to other databases, such as ArrayExpress and Pfam, entries from which are also cited widely in the literature. The very high precision and high-throughput of this text-mining pipeline makes this activity possible both accurately and at low cost, which will allow the development of new integrated data services. PMID:23734176

PIGD: a database for intronless genes in the Poaceae.

PubMed

Yan, Hanwei; Jiang, Cuiping; Li, Xiaoyu; Sheng, Lei; Dong, Qing; Peng, Xiaojian; Li, Qian; Zhao, Yang; Jiang, Haiyang; Cheng, Beijiu

2014-10-01

Intronless genes are a feature of prokaryotes; however, they are widespread and unequally distributed among eukaryotes and represent an important resource to study the evolution of gene architecture. Although many databases on exons and introns exist, there is currently no cohesive database that collects intronless genes in plants into a single database. In this study, we present the Poaceae Intronless Genes Database (PIGD), a user-friendly web interface to explore information on intronless genes from different plants. Five Poaceae species, Sorghum bicolor, Zea mays, Setaria italica, Panicum virgatum and Brachypodium distachyon, are included in the current release of PIGD. Gene annotations and sequence data were collected and integrated from different databases. The primary focus of this study was to provide gene descriptions and gene product records. In addition, functional annotations, subcellular localization prediction and taxonomic distribution are reported. PIGD allows users to readily browse, search and download data. BLAST and comparative analyses are also provided through this online database, which is available at http://pigd.ahau.edu.cn/. PIGD provides a solid platform for the collection, integration and analysis of intronless genes in the Poaceae. As such, this database will be useful for subsequent bio-computational analysis in comparative genomics and evolutionary studies.