MAGA, a new database of gas natural emissions: a collaborative web environment for collecting data.

NASA Astrophysics Data System (ADS)

Cardellini, Carlo; Chiodini, Giovanni; Frigeri, Alessandro; Bagnato, Emanuela; Frondini, Francesco; Aiuppa, Alessandro

2014-05-01

The data on volcanic and non-volcanic gas emissions available online are, as today, are 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 scales. A new and detailed web database (MAGA: MApping GAs emissions) has been developed, and recently improved, to collect data on carbon degassing form volcanic and non-volcanic environments. MAGA database allows 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 with the ingestion in to the database of the data from: i) a literature survey on publications on volcanic gas fluxes 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, and ii) the revision and update of Googas database on non-volcanic emission of the Italian territory (Chiodini et al., 2008), in the framework of the Deep Earth Carbon Degassing (DECADE) research initiative of the Deep Carbon Observatory (DCO). 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 each site. In this phase data can be accessed on the network from a web interface, and data-driven web service, where software clients can request data directly from the database, are planned to be implemented shortly. This way Geographical Information Systems (GIS) and Virtual Globes (e.g., Google Earth) could easily access the database, and data could be exchanged with other database. At the moment the database includes: i) more than 1000 flux data about volcanic plume degassing from Etna and Stromboli volcanoes, ii) data from ~ 30 sites of diffuse soil degassing from Napoletan volcanoes, Azores, Canary, Etna, Stromboli, and Vulcano Island, several data on fumarolic emissions (~ 7 sites) with CO2 fluxes; iii) data from ~ 270 non volcanic gas emission site in Italy. 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

JAMSTEC E-library of Deep-sea Images (J-EDI) Realizes a Virtual Journey to the Earth's Unexplored Deep Ocean

NASA Astrophysics Data System (ADS)

Sasaki, T.; Azuma, S.; Matsuda, S.; Nagayama, A.; Ogido, M.; Saito, H.; Hanafusa, Y.

2016-12-01

The Japan Agency for Marine-Earth Science and Technology (JAMSTEC) archives a large amount of deep-sea research videos and photos obtained by JAMSTEC's research submersibles and vehicles with cameras. The web site "JAMSTEC E-library of Deep-sea Images : J-EDI" (http://www.godac.jamstec.go.jp/jedi/e/) has made videos and photos available to the public via the Internet since 2011. Users can search for target videos and photos by keywords, easy-to-understand icons, and dive information at J-EDI because operating staffs classify videos and photos as to contents, e.g. living organism and geological environment, and add comments to them.Dive survey data including videos and photos are not only valiant academically but also helpful for education and outreach activities. With the aim of the improvement of visibility for broader communities, we added new functions of 3-dimensional display synchronized various dive survey data with videos in this year.New Functions Users can search for dive survey data by 3D maps with plotted dive points using the WebGL virtual map engine "Cesium". By selecting a dive point, users can watch deep-sea videos and photos and associated environmental data, e.g. water temperature, salinity, rock and biological sample photos, obtained by the dive survey. Users can browse a dive track visualized in 3D virtual spaces using the WebGL JavaScript library. By synchronizing this virtual dive track with videos, users can watch deep-sea videos recorded at a point on a dive track. Users can play an animation which a submersible-shaped polygon automatically traces a 3D virtual dive track and displays of dive survey data are synchronized with tracing a dive track. Users can directly refer to additional information of other JAMSTEC data sites such as marine biodiversity database, marine biological sample database, rock sample database, and cruise and dive information database, on each page which a 3D virtual dive track is displayed. A 3D visualization of a dive track makes users experience a virtual dive survey. In addition, by synchronizing a virtual dive track with videos, it is easy to understand living organisms and geological environments of a dive point. Therefore, these functions will visually support understanding of deep-sea environments in lectures and educational activities.

The Deep Impact Network Experiment Operations Center Monitor and Control System

NASA Technical Reports Server (NTRS)

Wang, Shin-Ywan (Cindy); Torgerson, J. Leigh; Schoolcraft, Joshua; Brenman, Yan

2009-01-01

The Interplanetary Overlay Network (ION) software at JPL is an implementation of Delay/Disruption Tolerant Networking (DTN) which has been proposed as an interplanetary protocol to support space communication. The JPL Deep Impact Network (DINET) is a technology development experiment intended to increase the technical readiness of the JPL implemented ION suite. The DINET Experiment Operations Center (EOC) developed by JPL's Protocol Technology Lab (PTL) was critical in accomplishing the experiment. EOC, containing all end nodes of simulated spaces and one administrative node, exercised publish and subscribe functions for payload data among all end nodes to verify the effectiveness of data exchange over ION protocol stacks. A Monitor and Control System was created and installed on the administrative node as a multi-tiered internet-based Web application to support the Deep Impact Network Experiment by allowing monitoring and analysis of the data delivery and statistics from ION. This Monitor and Control System includes the capability of receiving protocol status messages, classifying and storing status messages into a database from the ION simulation network, and providing web interfaces for viewing the live results in addition to interactive database queries.

DECADE Web Portal: Integrating MaGa, EarthChem and GVP Will Further Our Knowledge on Earth Degassing

NASA Astrophysics Data System (ADS)

Cardellini, C.; Frigeri, A.; Lehnert, K. A.; Ash, J.; McCormick, B.; Chiodini, G.; Fischer, T. P.; Cottrell, E.

2014-12-01

The release of gases from the Earth's interior to the exosphere takes place in both volcanic and non-volcanic areas of the planet. Fully understanding this complex process requires the integration of geochemical, petrological and volcanological data. At present, major online data repositories relevant to studies of degassing are not linked and interoperable. We are developing interoperability between three of those, which will support more powerful synoptic studies of degassing. The three data systems that will make their data accessible via the DECADE portal are: (1) the Smithsonian Institution's Global Volcanism Program database (GVP) of volcanic activity data, (2) EarthChem databases for geochemical and geochronological data of rocks and melt inclusions, and (3) the MaGa database (Mapping Gas emissions) which contains compositional and flux data of gases released at volcanic and non-volcanic degassing sites. These databases are developed and maintained by institutions or groups of experts in a specific field, and data are archived in formats specific to these databases. In the framework of the Deep Earth Carbon Degassing (DECADE) initiative of the Deep Carbon Observatory (DCO), we are developing a web portal that will create a powerful search engine of these databases from a single entry point. The portal will return comprehensive multi-component datasets, based on the search criteria selected by the user. For example, a single geographic or temporal search will return data relating to compositions of emitted gases and erupted products, the age of the erupted products, and coincident activity at the volcano. The development of this level of capability for the DECADE Portal requires complete synergy between these databases, including availability of standard-based web services (WMS, WFS) at all data systems. Data and metadata can thus be extracted from each system without interfering with each database's local schema or being replicated to achieve integration at the DECADE web portal. The DECADE portal will enable new synoptic perspectives on the Earth degassing process. Other data systems can be easily plugged in using the existing framework. Our vision is to explore Earth degassing related datasets over previously unexplored spatial or temporal ranges.

Federated or cached searches: Providing expected performance from multiple invasive species databases

NASA Astrophysics Data System (ADS)

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-06-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search "deep" web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

DEEP: Database of Energy Efficiency Performance

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

Hong, Tianzhen; Piette, Mary; Lee, Sang Hoon

A database of energy efficiency performance (DEEP) is a presimulated database to enable quick and accurate assessment of energy retrofit of commercial buildings. DEEP was compiled from results of about 10 million EnergyPlus simulations. DEEP provides energy savings for screening and evaluation of retrofit measures targeting the small and medium-sized office and retail buildings in California. The prototype building models are developed for a comprehensive assessment of building energy performance based on DOE commercial reference buildings and the California DEER [sic] prototype buildings. The prototype buildings represent seven building types across six vintages of constructions and 16 California climate zones.more » DEEP uses these prototypes to evaluate energy performance of about 100 energy conservation measures covering envelope, lighting, heating, ventilation, air conditioning, plug loads, and domestic hot war. DEEP consists the energy simulation results for individual retrofit measures as well as packages of measures to consider interactive effects between multiple measures. The large scale EnergyPlus simulations are being conducted on the super computers at the National Energy Research Scientific Computing Center (NERSC) of Lawrence Berkeley National Laboratory. The pre-simulation database is a part of the CEC PIER project to develop a web-based retrofit toolkit for small and medium-sized commercial buildings in California, which provides real-time energy retrofit feedback by querying DEEP with recommended measures, estimated energy savings and financial payback period based on users' decision criteria of maximizing energy savings, energy cost savings, carbon reduction, or payback of investment. The pre-simulated database and associated comprehensive measure analysis enhances the ability to performance assessments of retrofits to reduce energy use for small and medium buildings and business owners who typically do not have resources to conduct costly building energy audit.« less

MaGa, a web-based collaborative database for gas emissions: a tool to improve the knowledge on Earth degassing

NASA Astrophysics Data System (ADS)

Frigeri, A.; Cardellini, C.; Chiodini, G.; Frondini, F.; Bagnato, E.; Aiuppa, A.; Fischer, T. P.; Lehnert, K. A.

2014-12-01

The study of the main pathways of carbon flux from the deep Earth requires the analysis of a large quantity and variety of data on volcanic and non-volcanic gas emissions. Hence, there is need for common frameworks to aggregate available data and insert new observations. Since 2010 we have been developing the Mapping Gas emissions (MaGa) web-based database to collect data on carbon degassing form volcanic and non-volcanic environments. MaGa uses an Object-relational model, translating the experience of field surveyors into the database schema. The current web interface of MaGa allows users to browse the data in tabular format or by browsing an interactive web-map. Enabled users can insert information as measurement methods, instrument details as well as the actual values collected in the field. Measurements found in the literature can be inserted as well as direct field observations made by human-operated instruments. Currently the database includes fluxes and gas compositions from active craters degassing, diffuse soil degassing and fumaroles both from dormant volcanoes and open-vent volcanoes from literature survey and data about non-volcanic emission of the Italian territory. Currently, MaGa holds more than 1000 volcanic plume degassing fluxes, data from 30 sites of diffuse soil degassing from italian volcanoes, and about 60 measurements from fumarolic and non volcanic emission sites. For each gas emission site, the MaGa holds data, pictures, descriptions on gas sampling, analysis and measurement methods, together with bibliographic references and contacts to researchers having experience on each site. From 2012, MaGa developments started to be focused towards the framework of the Deep Earth Carbon Degassing research initiative of the Deep Carbon Observatory. Whithin the DECADE initiative, there are others data systems, as EarthChem and the Smithsonian Institution's Global Volcanism Program. An interoperable interaction between the DECADE data systems is being planned. MaGa is showing good potentials to improve the knowledge on Earth degassing firstly by making data more accessible and encouraging participation among researchers, and secondly by allowing to observe and explore, for the first time, a gas emission dataset with spatial and temporal extents never analyzed before.

DEEP: A Database of Energy Efficiency Performance to Accelerate Energy Retrofitting of Commercial Buildings

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

Hoon Lee, Sang; Hong, Tianzhen; Sawaya, Geof

The paper presents a method and process to establish a database of energy efficiency performance (DEEP) to enable quick and accurate assessment of energy retrofit of commercial buildings. DEEP was compiled from results of about 35 million EnergyPlus simulations. DEEP provides energy savings for screening and evaluation of retrofit measures targeting the small and medium-sized office and retail buildings in California. The prototype building models are developed for a comprehensive assessment of building energy performance based on DOE commercial reference buildings and the California DEER prototype buildings. The prototype buildings represent seven building types across six vintages of constructions andmore » 16 California climate zones. DEEP uses these prototypes to evaluate energy performance of about 100 energy conservation measures covering envelope, lighting, heating, ventilation, air-conditioning, plug-loads, and domestic hot water. DEEP consists the energy simulation results for individual retrofit measures as well as packages of measures to consider interactive effects between multiple measures. The large scale EnergyPlus simulations are being conducted on the super computers at the National Energy Research Scientific Computing Center of Lawrence Berkeley National Laboratory. The pre-simulation database is a part of an on-going project to develop a web-based retrofit toolkit for small and medium-sized commercial buildings in California, which provides real-time energy retrofit feedback by querying DEEP with recommended measures, estimated energy savings and financial payback period based on users’ decision criteria of maximizing energy savings, energy cost savings, carbon reduction, or payback of investment. The pre-simulated database and associated comprehensive measure analysis enhances the ability to performance assessments of retrofits to reduce energy use for small and medium buildings and business owners who typically do not have resources to conduct costly building energy audit. DEEP will be migrated into the DEnCity - DOE’s Energy City, which integrates large-scale energy data for multi-purpose, open, and dynamic database leveraging diverse source of existing simulation data.« less

CMO: Cruise Metadata Organizer for JAMSTEC Research Cruises

NASA Astrophysics Data System (ADS)

Fukuda, K.; Saito, H.; Hanafusa, Y.; Vanroosebeke, A.; Kitayama, T.

2011-12-01

JAMSTEC's Data Research Center for Marine-Earth Sciences manages and distributes a wide variety of observational data and samples obtained from JAMSTEC research vessels and deep sea submersibles. Generally, metadata are essential to identify data and samples were obtained. In JAMSTEC, cruise metadata include cruise information such as cruise ID, name of vessel, research theme, and diving information such as dive number, name of submersible and position of diving point. They are submitted by chief scientists of research cruises in the Microsoft Excel° spreadsheet format, and registered into a data management database to confirm receipt of observational data files, cruise summaries, and cruise reports. The cruise metadata are also published via "JAMSTEC Data Site for Research Cruises" within two months after end of cruise. Furthermore, these metadata are distributed with observational data, images and samples via several data and sample distribution websites after a publication moratorium period. However, there are two operational issues in the metadata publishing process. One is that duplication efforts and asynchronous metadata across multiple distribution websites due to manual metadata entry into individual websites by administrators. The other is that differential data types or representation of metadata in each website. To solve those problems, we have developed a cruise metadata organizer (CMO) which allows cruise metadata to be connected from the data management database to several distribution websites. CMO is comprised of three components: an Extensible Markup Language (XML) database, an Enterprise Application Integration (EAI) software, and a web-based interface. The XML database is used because of its flexibility for any change of metadata. Daily differential uptake of metadata from the data management database to the XML database is automatically processed via the EAI software. Some metadata are entered into the XML database using the web-based interface by a metadata editor in CMO as needed. Then daily differential uptake of metadata from the XML database to databases in several distribution websites is automatically processed using a convertor defined by the EAI software. Currently, CMO is available for three distribution websites: "Deep Sea Floor Rock Sample Database GANSEKI", "Marine Biological Sample Database", and "JAMSTEC E-library of Deep-sea Images". CMO is planned to provide "JAMSTEC Data Site for Research Cruises" with metadata in the future.

Prototype of web-based database of surface wave investigation results for site classification

NASA Astrophysics Data System (ADS)

Hayashi, K.; Cakir, R.; Martin, A. J.; Craig, M. S.; Lorenzo, J. M.

2016-12-01

As active and passive surface wave methods are getting popular for evaluating site response of earthquake ground motion, demand on the development of database for investigation results is also increasing. Seismic ground motion not only depends on 1D velocity structure but also on 2D and 3D structures so that spatial information of S-wave velocity must be considered in ground motion prediction. The database can support to construct 2D and 3D underground models. Inversion of surface wave processing is essentially non-unique so that other information must be combined into the processing. The database of existed geophysical, geological and geotechnical investigation results can provide indispensable information to improve the accuracy and reliability of investigations. Most investigations, however, are carried out by individual organizations and investigation results are rarely stored in the unified and organized database. To study and discuss appropriate database and digital standard format for the surface wave investigations, we developed a prototype of web-based database to store observed data and processing results of surface wave investigations that we have performed at more than 400 sites in U.S. and Japan. The database was constructed on a web server using MySQL and PHP so that users can access to the database through the internet from anywhere with any device. All data is registered in the database with location and users can search geophysical data through Google Map. The database stores dispersion curves, horizontal to vertical spectral ratio and S-wave velocity profiles at each site that was saved in XML files as digital data so that user can review and reuse them. The database also stores a published 3D deep basin and crustal structure and user can refer it during the processing of surface wave data.

NOAA Operational Tsunameter Support for Research

NASA Astrophysics Data System (ADS)

Bouchard, R.; Stroker, K.

2008-12-01

In March 2008, the National Oceanic and Atmospheric Administration's (NOAA) National Data Buoy Center (NDBC) completed the deployment of the last of the 39-station network of deep-sea tsunameters. As part of NOAA's effort to strengthen tsunami warning capabilities, NDBC expanded the network from 6 to 39 stations and upgraded all stations to the second generation Deep-ocean Assessment and Reporting of Tsunamis technology (DART II). Consisting of a bottom pressure recorder (BPR) and a surface buoy, the tsunameters deliver water-column heights, estimated from pressure measurements at the sea floor, to Tsunami Warning Centers in less than 3 minutes. This network provides coastal communities in the Pacific, Atlantic, Caribbean, and the Gulf of Mexico with faster and more accurate tsunami warnings. In addition, both the coarse resolution real-time data and the high resolution (15-second) recorded data provide invaluable contributions to research, such as the detection of the 2004 Sumatran tsunami in the Northeast Pacific (Gower and González, 2006) and the experimental tsunami forecast system (Bernard et al., 2007). NDBC normally recovers the BPRs every 24 months and sends the recovered high resolution data to NOAA's National Geophysical Data Center (NGDC) for archive and distribution. NGDC edits and processes this raw binary format to obtain research-quality data. NGDC provides access to retrospective BPR data from 1986 to the present. The DART database includes pressure and temperature data from the ocean floor, stored in a relational database, enabling data integration with the global tsunami and significant earthquake databases. All data are accessible via the Web as tables, reports, interactive maps, OGC Web Map Services (WMS), and Web Feature Services (WFS) to researchers around the world. References: Gower, J. and F. González, 2006. U.S. Warning System Detected the Sumatra Tsunami, Eos Trans. AGU, 87(10). Bernard, E. N., C. Meinig, and A. Hilton, 2007. Deep Ocean Tsunami Detection: Third Generation DART, Eos Trans. AGU, 88(52), Fall Meet. Suppl., Abstract S51C-03.

DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data.

PubMed

Yang, Jian-Hua; Qu, Liang-Hu

2012-01-01

Recent advances in high-throughput deep-sequencing technology have produced large numbers of short and long RNA sequences and enabled the detection and profiling of known and novel microRNAs (miRNAs) and other noncoding RNAs (ncRNAs) at unprecedented sensitivity and depth. In this chapter, we describe the use of deepBase, a database that we have developed to integrate all public deep-sequencing data and to facilitate the comprehensive annotation and discovery of miRNAs and other ncRNAs from these data. deepBase provides an integrative, interactive, and versatile web graphical interface to evaluate miRBase-annotated miRNA genes and other known ncRNAs, explores the expression patterns of miRNAs and other ncRNAs, and discovers novel miRNAs and other ncRNAs from deep-sequencing data. deepBase also provides a deepView genome browser to comparatively analyze these data at multiple levels. deepBase is available at http://deepbase.sysu.edu.cn/.

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data.

PubMed

Arango-Argoty, Gustavo; Garner, Emily; Pruden, Amy; Heath, Lenwood S; Vikesland, Peter; Zhang, Liqing

2018-02-01

Growing concerns about increasing rates of antibiotic resistance call for expanded and comprehensive global monitoring. Advancing methods for monitoring of environmental media (e.g., wastewater, agricultural waste, food, and water) is especially needed for identifying potential resources of novel antibiotic resistance genes (ARGs), hot spots for gene exchange, and as pathways for the spread of ARGs and human exposure. Next-generation sequencing now enables direct access and profiling of the total metagenomic DNA pool, where ARGs are typically identified or predicted based on the "best hits" of sequence searches against existing databases. Unfortunately, this approach produces a high rate of false negatives. To address such limitations, we propose here a deep learning approach, taking into account a dissimilarity matrix created using all known categories of ARGs. Two deep learning models, DeepARG-SS and DeepARG-LS, were constructed for short read sequences and full gene length sequences, respectively. Evaluation of the deep learning models over 30 antibiotic resistance categories demonstrates that the DeepARG models can predict ARGs with both high precision (> 0.97) and recall (> 0.90). The models displayed an advantage over the typical best hit approach, yielding consistently lower false negative rates and thus higher overall recall (> 0.9). As more data become available for under-represented ARG categories, the DeepARG models' performance can be expected to be further enhanced due to the nature of the underlying neural networks. Our newly developed ARG database, DeepARG-DB, encompasses ARGs predicted with a high degree of confidence and extensive manual inspection, greatly expanding current ARG repositories. The deep learning models developed here offer more accurate antimicrobial resistance annotation relative to current bioinformatics practice. DeepARG does not require strict cutoffs, which enables identification of a much broader diversity of ARGs. The DeepARG models and database are available as a command line version and as a Web service at http://bench.cs.vt.edu/deeparg .

Named Entity Recognition in a Hungarian NL Based QA System

NASA Astrophysics Data System (ADS)

Tikkl, Domonkos; Szidarovszky, P. Ferenc; Kardkovacs, Zsolt T.; Magyar, Gábor

In WoW project our purpose is to create a complex search interface with the following features: search in the deep web content of contracted partners' databases, processing Hungarian natural language (NL) questions and transforming them to SQL queries for database access, image search supported by a visual thesaurus that describes in a structural form the visual content of images (also in Hungarian). This paper primarily focuses on a particular problem of question processing task: the entity recognition. Before going into details we give a short overview of the project's aims.

The MIND PALACE: A Multi-Spectral Imaging and Spectroscopy Database for Planetary Science

NASA Astrophysics Data System (ADS)

Eshelman, E.; Doloboff, I.; Hara, E. K.; Uckert, K.; Sapers, H. M.; Abbey, W.; Beegle, L. W.; Bhartia, R.

2017-12-01

The Multi-Instrument Database (MIND) is the web-based home to a well-characterized set of analytical data collected by a suite of deep-UV fluorescence/Raman instruments built at the Jet Propulsion Laboratory (JPL). Samples derive from a growing body of planetary surface analogs, mineral and microbial standards, meteorites, spacecraft materials, and other astrobiologically relevant materials. In addition to deep-UV spectroscopy, datasets stored in MIND are obtained from a variety of analytical techniques obtained over multiple spatial and spectral scales including electron microscopy, optical microscopy, infrared spectroscopy, X-ray fluorescence, and direct fluorescence imaging. Multivariate statistical analysis techniques, primarily Principal Component Analysis (PCA), are used to guide interpretation of these large multi-analytical spectral datasets. Spatial co-referencing of integrated spectral/visual maps is performed using QGIS (geographic information system software). Georeferencing techniques transform individual instrument data maps into a layered co-registered data cube for analysis across spectral and spatial scales. The body of data in MIND is intended to serve as a permanent, reliable, and expanding database of deep-UV spectroscopy datasets generated by this unique suite of JPL-based instruments on samples of broad planetary science interest.

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

Automating Mid- and Long-Range Scheduling for the NASA Deep Space Network

NASA Technical Reports Server (NTRS)

Johnston, Mark D.; Tran, Daniel

2012-01-01

NASA has recently deployed a new mid-range scheduling system for the antennas of the Deep Space Network (DSN), called Service Scheduling Software, or S(sup 3). This system was designed and deployed as a modern web application containing a central scheduling database integrated with a collaborative environment, exploiting the same technologies as social web applications but applied to a space operations context. This is highly relevant to the DSN domain since the network schedule of operations is developed in a peer-to-peer negotiation process among all users of the DSN. These users represent not only NASA's deep space missions, but also international partners and ground-based science and calibration users. The initial implementation of S(sup 3) is complete and the system has been operational since July 2011. This paper describes some key aspects of the S(sup 3) system and on the challenges of modeling complex scheduling requirements and the ongoing extension of S(sup 3) to encompass long-range planning, downtime analysis, and forecasting, as the next step in developing a single integrated DSN scheduling tool suite to cover all time ranges.

Stratification-Based Outlier Detection over the Deep Web.

PubMed

Xian, Xuefeng; Zhao, Pengpeng; Sheng, Victor S; Fang, Ligang; Gu, Caidong; Yang, Yuanfeng; Cui, Zhiming

2016-01-01

For many applications, finding rare instances or outliers can be more interesting than finding common patterns. Existing work in outlier detection never considers the context of deep web. In this paper, we argue that, for many scenarios, it is more meaningful to detect outliers over deep web. In the context of deep web, users must submit queries through a query interface to retrieve corresponding data. Therefore, traditional data mining methods cannot be directly applied. The primary contribution of this paper is to develop a new data mining method for outlier detection over deep web. In our approach, the query space of a deep web data source is stratified based on a pilot sample. Neighborhood sampling and uncertainty sampling are developed in this paper with the goal of improving recall and precision based on stratification. Finally, a careful performance evaluation of our algorithm confirms that our approach can effectively detect outliers in deep web.

Stratification-Based Outlier Detection over the Deep Web

PubMed Central

Xian, Xuefeng; Zhao, Pengpeng; Sheng, Victor S.; Fang, Ligang; Gu, Caidong; Yang, Yuanfeng; Cui, Zhiming

2016-01-01

For many applications, finding rare instances or outliers can be more interesting than finding common patterns. Existing work in outlier detection never considers the context of deep web. In this paper, we argue that, for many scenarios, it is more meaningful to detect outliers over deep web. In the context of deep web, users must submit queries through a query interface to retrieve corresponding data. Therefore, traditional data mining methods cannot be directly applied. The primary contribution of this paper is to develop a new data mining method for outlier detection over deep web. In our approach, the query space of a deep web data source is stratified based on a pilot sample. Neighborhood sampling and uncertainty sampling are developed in this paper with the goal of improving recall and precision based on stratification. Finally, a careful performance evaluation of our algorithm confirms that our approach can effectively detect outliers in deep web. PMID:27313603

Commercial Building Energy Saver, API

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

Hong, Tianzhen; Piette, Mary; Lee, Sang Hoon

2015-08-27

The CBES API provides Application Programming Interface to a suite of functions to improve energy efficiency of buildings, including building energy benchmarking, preliminary retrofit analysis using a pre-simulation database DEEP, and detailed retrofit analysis using energy modeling with the EnergyPlus simulation engine. The CBES API is used to power the LBNL CBES Web App. It can be adopted by third party developers and vendors into their software tools and platforms.

CrossCheck: an open-source web tool for high-throughput screen data analysis.

PubMed

Najafov, Jamil; Najafov, Ayaz

2017-07-19

Modern high-throughput screening methods allow researchers to generate large datasets that potentially contain important biological information. However, oftentimes, picking relevant hits from such screens and generating testable hypotheses requires training in bioinformatics and the skills to efficiently perform database mining. There are currently no tools available to general public that allow users to cross-reference their screen datasets with published screen datasets. To this end, we developed CrossCheck, an online platform for high-throughput screen data analysis. CrossCheck is a centralized database that allows effortless comparison of the user-entered list of gene symbols with 16,231 published datasets. These datasets include published data from genome-wide RNAi and CRISPR screens, interactome proteomics and phosphoproteomics screens, cancer mutation databases, low-throughput studies of major cell signaling mediators, such as kinases, E3 ubiquitin ligases and phosphatases, and gene ontological information. Moreover, CrossCheck includes a novel database of predicted protein kinase substrates, which was developed using proteome-wide consensus motif searches. CrossCheck dramatically simplifies high-throughput screen data analysis and enables researchers to dig deep into the published literature and streamline data-driven hypothesis generation. CrossCheck is freely accessible as a web-based application at http://proteinguru.com/crosscheck.

Efficacy and Safety of Pedunculopontine Nuclei (PPN) Deep Brain Stimulation in the Treatment of Gait Disorders: A Meta-Analysis of Clinical Studies.

PubMed

Golestanirad, Laleh; Elahi, Behzad; Graham, Simon J; Das, Sunit; Wald, Lawrence L

2016-01-01

Pedunculopontine nucleus (PPN) has complex reciprocal connections with basal ganglia, especially with internal globus pallidus and substantia nigra, and it has been postulated that PPN stimulation may improve gait instability and freezing of gait. In this meta-analysis, we will assess the evidence for PPN deep brain stimulation in treatment of gait and motor abnormalities especially focusing on Parkinson disease patients. PubMed and Scopus electronic databases were searched for related studies published before February 2014. Medline (1966-2014), Embase (1974-2010), CINAHL, Web of Science, Scopus bibliographic, and Google Scholar databases (1960-2014) were also searched for studies investigating effect of PPN deep brain stimulation in treatment of postural and postural instability and total of ten studies met the inclusion criteria for this analysis. Our findings showed a significant improvement in postural instability (p<0.001) and motor symptoms of Parkinson disease on and off medications (p<0.05), but failed to show improvement in freezing of gait. Despite significant improvement in postural instability observed in included studies, evidence from current literature is not sufficient to generalize these findings to the majority of patients.

WEB-GIS Decision Support System for CO2 storage

NASA Astrophysics Data System (ADS)

Gaitanaru, Dragos; Leonard, Anghel; Radu Gogu, Constantin; Le Guen, Yvi; Scradeanu, Daniel; Pagnejer, Mihaela

2013-04-01

Environmental decision support systems (DSS) paradigm evolves and changes as more knowledge and technology become available to the environmental community. Geographic Information Systems (GIS) can be used to extract, assess and disseminate some types of information, which are otherwise difficult to access by traditional methods. In the same time, with the help of the Internet and accompanying tools, creating and publishing online interactive maps has become easier and rich with options. The Decision Support System (MDSS) developed for the MUSTANG (A MUltiple Space and Time scale Approach for the quaNtification of deep saline formations for CO2 storaGe) project is a user friendly web based application that uses the GIS capabilities. MDSS can be exploited by the experts for CO2 injection and storage in deep saline aquifers. The main objective of the MDSS is to help the experts to take decisions based large structured types of data and information. In order to achieve this objective the MDSS has a geospatial objected-orientated database structure for a wide variety of data and information. The entire application is based on several principles leading to a series of capabilities and specific characteristics: (i) Open-Source - the entire platform (MDSS) is based on open-source technologies - (1) database engine, (2) application server, (3) geospatial server, (4) user interfaces, (5) add-ons, etc. (ii) Multiple database connections - MDSS is capable to connect to different databases that are located on different server machines. (iii)Desktop user experience - MDSS architecture and design follows the structure of a desktop software. (iv)Communication - the server side and the desktop are bound together by series functions that allows the user to upload, use, modify and download data within the application. The architecture of the system involves one database and a modular application composed by: (1) a visualization module, (2) an analysis module, (3) a guidelines module, and (4) a risk assessment module. The Database component is build by using the PostgreSQL and PostGIS open source technology. The visualization module allows the user to view data of CO2 injection sites in different ways: (1) geospatial visualization, (2) table view, (3) 3D visualization. The analysis module will allow the user to perform certain analysis like Injectivity, Containment and Capacity analysis. The Risk Assessment module focus on the site risk matrix approach. The Guidelines module contains the methodologies of CO2 injection and storage into deep saline aquifers guidelines.

Dealing with an information overload of health science data: structured utilisation of libraries, distributed knowledge in databases and Web content.

PubMed

Hoelzer, Simon; Schweiger, Ralf K; Rieger, Joerg; Meyer, Michael

2006-01-01

The organizational structures of web contents and electronic information resources must adapt to the demands of a growing volume of information and user requirements. Otherwise the information society will be threatened by disinformation. The biomedical sciences are especially vulnerable in this regard, since they are strongly oriented toward text-based knowledge sources. Here sustainable improvement can only be achieved by using a comprehensive, integrated approach that not only includes data management but also specifically incorporates the editorial processes, including structuring information sources and publication. The technical resources needed to effectively master these tasks are already available in the form of the data standards and tools of the Semantic Web. They include Rich Site Summaries (RSS), which have become an established means of distributing and syndicating conventional news messages and blogs. They can also provide access to the contents of the previously mentioned information sources, which are conventionally classified as 'deep web' content.

77 FR 39269 - Submission for OMB Review, Comment Request, Proposed Collection: IMLS Museum Web Database...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-02

..., Proposed Collection: IMLS Museum Web Database: MuseumsCount.gov AGENCY: Institute of Museum and Library... general public. Information such as name, address, phone, email, Web site, staff size, program details... Museum Web Database: MuseumsCount.gov collection. The 60-day notice for the IMLS Museum Web Database...

Software for Allocating Resources in the Deep Space Network

NASA Technical Reports Server (NTRS)

Wang, Yeou-Fang; Borden, Chester; Zendejas, Silvino; Baldwin, John

2003-01-01

TIGRAS 2.0 is a computer program designed to satisfy a need for improved means for analyzing the tracking demands of interplanetary space-flight missions upon the set of ground antenna resources of the Deep Space Network (DSN) and for allocating those resources. Written in Microsoft Visual C++, TIGRAS 2.0 provides a single rich graphical analysis environment for use by diverse DSN personnel, by connecting to various data sources (relational databases or files) based on the stages of the analyses being performed. Notable among the algorithms implemented by TIGRAS 2.0 are a DSN antenna-load-forecasting algorithm and a conflict-aware DSN schedule-generating algorithm. Computers running TIGRAS 2.0 can also be connected using SOAP/XML to a Web services server that provides analysis services via the World Wide Web. TIGRAS 2.0 supports multiple windows and multiple panes in each window for users to view and use information, all in the same environment, to eliminate repeated switching among various application programs and Web pages. TIGRAS 2.0 enables the use of multiple windows for various requirements, trajectory-based time intervals during which spacecraft are viewable, ground resources, forecasts, and schedules. Each window includes a time navigation pane, a selection pane, a graphical display pane, a list pane, and a statistics pane.

A Tactical Framework for Cyberspace Situational Awareness

DTIC Science & Technology

2010-06-01

Command & Control 1. VOIP Telephone 2. Internet Chat 3. Web App ( TBMCS ) 4. Email 5. Web App (PEX) 6. Database (CAMS) 7. Database (ARMS) 8...Database (LogMod) 9. Resource (WWW) 10. Application (PFPS) Mission Planning 1. Application (PFPS) 2. Email 3. Web App ( TBMCS ) 4. Internet Chat...1. Web App (PEX) 2. Database (ARMS) 3. Web App ( TBMCS ) 4. Email 5. Database (CAMS) 6. VOIP Telephone 7. Application (PFPS) 8. Internet Chat 9

An insight into the deep web; why it matters for addiction psychiatry?

PubMed

Orsolini, Laura; Papanti, Duccio; Corkery, John; Schifano, Fabrizio

2017-05-01

Nowadays, the web is rapidly spreading, playing a significant role in the marketing or sale or distribution of "quasi" legal drugs, hence facilitating continuous changes in drug scenarios. The easily renewable and anarchic online drug-market is gradually transforming indeed the drug market itself, from a "street" to a "virtual" one, with customers being able to shop with a relative anonymity in a 24-hr marketplace. The hidden "deep web" is facilitating this phenomenon. The paper aims at providing an overview to mental health's and addiction's professionals on current knowledge about prodrug activities on the deep web. A nonparticipant netnographic qualitative study of a list of prodrug websites (blogs, fora, and drug marketplaces) located into the surface web was here carried out. A systematic Internet search was conducted on Duckduckgo® and Google® whilst including the following keywords: "drugs" or "legal highs" or "Novel Psychoactive Substances" or "NPS" combined with the word deep web. Four themes (e.g., "How to access into the deepweb"; "Darknet and the online drug trading sites"; "Grams-search engine for the deep web"; and "Cryptocurrencies") and 14 categories were here generated and properly discussed. This paper represents a complete or systematical guideline about the deep web, specifically focusing on practical information on online drug marketplaces, useful for addiction's professionals. Copyright © 2017 John Wiley & Sons, Ltd.

SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

PubMed

Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

2014-08-15

Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

mirEX: a platform for comparative exploration of plant pri-miRNA expression data.

PubMed

Bielewicz, Dawid; Dolata, Jakub; Zielezinski, Andrzej; Alaba, Sylwia; Szarzynska, Bogna; Szczesniak, Michal W; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia; Karlowski, Wojciech M

2012-01-01

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT-qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. A web-based mirEX interface can be accessed at http://bioinfo.amu.edu.pl/mirex.

Just-in-time Database-Driven Web Applications

PubMed Central

2003-01-01

"Just-in-time" database-driven Web applications are inexpensive, quickly-developed software that can be put to many uses within a health care organization. Database-driven Web applications garnered 73873 hits on our system-wide intranet in 2002. They enabled collaboration and communication via user-friendly Web browser-based interfaces for both mission-critical and patient-care-critical functions. Nineteen database-driven Web applications were developed. The application categories that comprised 80% of the hits were results reporting (27%), graduate medical education (26%), research (20%), and bed availability (8%). The mean number of hits per application was 3888 (SD = 5598; range, 14-19879). A model is described for just-in-time database-driven Web application development and an example given with a popular HTML editor and database program. PMID:14517109

AggNet: Deep Learning From Crowds for Mitosis Detection in Breast Cancer Histology Images.

PubMed

Albarqouni, Shadi; Baur, Christoph; Achilles, Felix; Belagiannis, Vasileios; Demirci, Stefanie; Navab, Nassir

2016-05-01

The lack of publicly available ground-truth data has been identified as the major challenge for transferring recent developments in deep learning to the biomedical imaging domain. Though crowdsourcing has enabled annotation of large scale databases for real world images, its application for biomedical purposes requires a deeper understanding and hence, more precise definition of the actual annotation task. The fact that expert tasks are being outsourced to non-expert users may lead to noisy annotations introducing disagreement between users. Despite being a valuable resource for learning annotation models from crowdsourcing, conventional machine-learning methods may have difficulties dealing with noisy annotations during training. In this manuscript, we present a new concept for learning from crowds that handle data aggregation directly as part of the learning process of the convolutional neural network (CNN) via additional crowdsourcing layer (AggNet). Besides, we present an experimental study on learning from crowds designed to answer the following questions. 1) Can deep CNN be trained with data collected from crowdsourcing? 2) How to adapt the CNN to train on multiple types of annotation datasets (ground truth and crowd-based)? 3) How does the choice of annotation and aggregation affect the accuracy? Our experimental setup involved Annot8, a self-implemented web-platform based on Crowdflower API realizing image annotation tasks for a publicly available biomedical image database. Our results give valuable insights into the functionality of deep CNN learning from crowd annotations and prove the necessity of data aggregation integration.

A Magnetic Petrology Database for Satellite Magnetic Anomaly Interpretations

NASA Astrophysics Data System (ADS)

Nazarova, K.; Wasilewski, P.; Didenko, A.; Genshaft, Y.; Pashkevich, I.

2002-05-01

A Magnetic Petrology Database (MPDB) is now being compiled at NASA/Goddard Space Flight Center in cooperation with Russian and Ukrainian Institutions. The purpose of this database is to provide the geomagnetic community with a comprehensive and user-friendly method of accessing magnetic petrology data via Internet for more realistic interpretation of satellite magnetic anomalies. Magnetic Petrology Data had been accumulated in NASA/Goddard Space Flight Center, United Institute of Physics of the Earth (Russia) and Institute of Geophysics (Ukraine) over several decades and now consists of many thousands of records of data in our archives. The MPDB was, and continues to be in big demand especially since recent launching in near Earth orbit of the mini-constellation of three satellites - Oersted (in 1999), Champ (in 2000), and SAC-C (in 2000) which will provide lithospheric magnetic maps with better spatial and amplitude resolution (about 1 nT). The MPDB is focused on lower crustal and upper mantle rocks and will include data on mantle xenoliths, serpentinized ultramafic rocks, granulites, iron quartzites and rocks from Archean-Proterozoic metamorphic sequences from all around the world. A substantial amount of data is coming from the area of unique Kursk Magnetic Anomaly and Kola Deep Borehole (which recovered 12 km of continental crust). A prototype MPDB can be found on the Geodynamics Branch web server of Goddard Space Flight Center at http://core2.gsfc.nasa.gov/terr_mag/magnpetr.html. The MPDB employs a searchable relational design and consists of 7 interrelated tables. The schema of database is shown at http://core2.gsfc.nasa.gov/terr_mag/doc.html. MySQL database server was utilized to implement MPDB. The SQL (Structured Query Language) is used to query the database. To present the results of queries on WEB and for WEB programming we utilized PHP scripting language and CGI scripts. The prototype MPDB is designed to search database by major satellite magnetic anomaly, tectonic structure, geographical location, rock type, magnetic properties, chemistry and reference, see http://core2.gsfc.nasa.gov/terr_mag/query1.html. The output of database is HTML structured table, text file, and downloadable file. This database will be very useful for studies of lithospheric satellite magnetic anomalies on the Earth and other terrestrial planets.

76 FR 1137 - Publicly Available Consumer Product Safety Information Database: Notice of Public Web Conferences

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-07

...: Notice of Public Web Conferences AGENCY: Consumer Product Safety Commission. ACTION: Notice. SUMMARY: The Consumer Product Safety Commission (``Commission,'' ``CPSC,'' or ``we'') is announcing two Web conferences... database (``Database''). The Web conferences will be webcast live from the Commission's headquarters in...

76 FR 54807 - Notice of Proposed Information Collection: IMLS Museum Web Database: MuseumsCount.gov

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-02

...: IMLS Museum Web Database: MuseumsCount.gov AGENCY: Institute of Museum and Library Services, National..., and the general public. Information such as name, address, phone, e-mail, Web site, congressional...: IMLS Museum Web Database, MuseumsCount.gov . OMB Number: To be determined. Agency Number: 3137...

Commercial Building Energy Saver, Web App

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

Hong, Tianzhen; Piette, Mary; Lee, Sang Hoon

The CBES App is a web-based toolkit for use by small businesses and building owners and operators of small and medium size commercial buildings to perform energy benchmarking and retrofit analysis for buildings. The CBES App analyzes the energy performance of user's building for pre-and posto-retrofit, in conjunction with user's input data, to identify recommended retrofit measures, energy savings and economic analysis for the selected measures. The CBES App provides energy benchmarking, including getting an EnergyStar score using EnergyStar API and benchmarking against California peer buildings using the EnergyIQ API. The retrofit analysis includes a preliminary analysis by looking upmore » retrofit measures from a pre-simulated database DEEP, and a detailed analysis creating and running EnergyPlus models to calculate energy savings of retrofit measures. The CBES App builds upon the LBNL CBES API.« less

Discrepancy Reporting Management System

NASA Technical Reports Server (NTRS)

Cooper, Tonja M.; Lin, James C.; Chatillon, Mark L.

2004-01-01

Discrepancy Reporting Management System (DRMS) is a computer program designed for use in the stations of NASA's Deep Space Network (DSN) to help establish the operational history of equipment items; acquire data on the quality of service provided to DSN customers; enable measurement of service performance; provide early insight into the need to improve processes, procedures, and interfaces; and enable the tracing of a data outage to a change in software or hardware. DRMS is a Web-based software system designed to include a distributed database and replication feature to achieve location-specific autonomy while maintaining a consistent high quality of data. DRMS incorporates commercial Web and database software. DRMS collects, processes, replicates, communicates, and manages information on spacecraft data discrepancies, equipment resets, and physical equipment status, and maintains an internal station log. All discrepancy reports (DRs), Master discrepancy reports (MDRs), and Reset data are replicated to a master server at NASA's Jet Propulsion Laboratory; Master DR data are replicated to all the DSN sites; and Station Logs are internal to each of the DSN sites and are not replicated. Data are validated according to several logical mathematical criteria. Queries can be performed on any combination of data.

omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data.

PubMed

Müller, Sören; Rycak, Lukas; Winter, Peter; Kahl, Günter; Koch, Ina; Rotter, Björn

2013-10-15

Small RNA deep sequencing is widely used to characterize non-coding RNAs (ncRNAs) differentially expressed between two conditions, e.g. healthy and diseased individuals and to reveal insights into molecular mechanisms underlying condition-specific phenotypic traits. The ncRNAome is composed of a multitude of RNAs, such as transfer RNA, small nucleolar RNA and microRNA (miRNA), to name few. Here we present omiRas, a Web server for the annotation, comparison and visualization of interaction networks of ncRNAs derived from next-generation sequencing experiments of two different conditions. The Web tool allows the user to submit raw sequencing data and results are presented as: (i) static annotation results including length distribution, mapping statistics, alignments and quantification tables for each library as well as lists of differentially expressed ncRNAs between conditions and (ii) an interactive network visualization of user-selected miRNAs and their target genes based on the combination of several miRNA-mRNA interaction databases. The omiRas Web server is implemented in Python, PostgreSQL, R and can be accessed at: http://tools.genxpro.net/omiras/.

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

The Mendeleev-Meyer force project.

PubMed

Santos, Sergio; Lai, Chia-Yun; Amadei, Carlo A; Gadelrab, Karim R; Tang, Tzu-Chieh; Verdaguer, Albert; Barcons, Victor; Font, Josep; Colchero, Jaime; Chiesa, Matteo

2016-10-14

Here we present the Mendeleev-Meyer Force Project which aims at tabulating all materials and substances in a fashion similar to the periodic table. The goal is to group and tabulate substances using nanoscale force footprints rather than atomic number or electronic configuration as in the periodic table. The process is divided into: (1) acquiring nanoscale force data from materials, (2) parameterizing the raw data into standardized input features to generate a library, (3) feeding the standardized library into an algorithm to generate, enhance or exploit a model to identify a material or property. We propose producing databases mimicking the Materials Genome Initiative, the Medical Literature Analysis and Retrieval System Online (MEDLARS) or the PRoteomics IDEntifications database (PRIDE) and making these searchable online via search engines mimicking Pubmed or the PRIDE web interface. A prototype exploiting deep learning algorithms, i.e. multilayer neural networks, is presented.

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

PubMed Central

Turner, Brian; Razick, Sabry; Turinsky, Andrei L.; Vlasblom, James; Crowdy, Edgard K.; Cho, Emerson; Morrison, Kyle; Wodak, Shoshana J.

2010-01-01

We present iRefWeb, a web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins and cited publications. Through links to source databases and supporting evidence, researchers may gauge the reliability of an interaction using simple criteria, such as the detection methods, the scale of the study (high- or low-throughput) or the number of cited publications. Furthermore, iRefWeb compares the information extracted from the same publication by different databases, and offers means to follow-up possible inconsistencies. We provide an overview of the consolidated protein–protein interaction landscape and show how it can be automatically cropped to aid the generation of meaningful organism-specific interactomes. iRefWeb can be accessed at: http://wodaklab.org/iRefWeb. Database URL: http://wodaklab.org/iRefWeb/ PMID:20940177

Business Faculty Research: Satisfaction with the Web versus Library Databases

ERIC Educational Resources Information Center

Dewald, Nancy H.; Silvius, Matthew A.

2005-01-01

Business faculty members teaching at undergraduate campuses of the Pennsylvania State University were surveyed in order to assess their satisfaction with free Web sources and with subscription databases for their professional research. Although satisfaction with the Web's ease of use was higher than that for databases, overall satisfaction for…

A Web-Based Database for Nurse Led Outreach Teams (NLOT) in Toronto.

PubMed

Li, Shirley; Kuo, Mu-Hsing; Ryan, David

2016-01-01

A web-based system can provide access to real-time data and information. Healthcare is moving towards digitizing patients' medical information and securely exchanging it through web-based systems. In one of Ontario's health regions, Nurse Led Outreach Teams (NLOT) provide emergency mobile nursing services to help reduce unnecessary transfers from long-term care homes to emergency departments. Currently the NLOT team uses a Microsoft Access database to keep track of the health information on the residents that they serve. The Access database lacks scalability, portability, and interoperability. The objective of this study is the development of a web-based database using Oracle Application Express that is easily accessible from mobile devices. The web-based database will allow NLOT nurses to enter and access resident information anytime and from anywhere.

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

PubMed

Wollbrett, Julien; Larmande, Pierre; de Lamotte, Frédéric; Ruiz, Manuel

2013-04-15

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

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

PubMed Central

2013-01-01

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

Automating Mid- and Long-Range Scheduling for NASA's Deep Space Network

NASA Technical Reports Server (NTRS)

Johnston, Mark D.; Tran, Daniel; Arroyo, Belinda; Sorensen, Sugi; Tay, Peter; Carruth, Butch; Coffman, Adam; Wallace, Mike

2012-01-01

NASA has recently deployed a new mid-range scheduling system for the antennas of the Deep Space Network (DSN), called Service Scheduling Software, or S(sup 3). This system is architected as a modern web application containing a central scheduling database integrated with a collaborative environment, exploiting the same technologies as social web applications but applied to a space operations context. This is highly relevant to the DSN domain since the network schedule of operations is developed in a peer-to-peer negotiation process among all users who utilize the DSN (representing 37 projects including international partners and ground-based science and calibration users). The initial implementation of S(sup 3) is complete and the system has been operational since July 2011. S(sup 3) has been used for negotiating schedules since April 2011, including the baseline schedules for three launching missions in late 2011. S(sup 3) supports a distributed scheduling model, in which changes can potentially be made by multiple users based on multiple schedule "workspaces" or versions of the schedule. This has led to several challenges in the design of the scheduling database, and of a change proposal workflow that allows users to concur with or to reject proposed schedule changes, and then counter-propose with alternative or additional suggested changes. This paper describes some key aspects of the S(sup 3) system and lessons learned from its operational deployment to date, focusing on the challenges of multi-user collaborative scheduling in a practical and mission-critical setting. We will also describe the ongoing project to extend S(sup 3) to encompass long-range planning, downtime analysis, and forecasting, as the next step in developing a single integrated DSN scheduling tool suite to cover all time ranges.

Facilitating Collaboration, Knowledge Construction and Communication with Web-Enabled Databases.

ERIC Educational Resources Information Center

McNeil, Sara G.; Robin, Bernard R.

This paper presents an overview of World Wide Web-enabled databases that dynamically generate Web materials and focuses on the use of this technology to support collaboration, knowledge construction, and communication. Database applications have been used in classrooms to support learning activities for over a decade, but, although business and…

Implementing a Dynamic Database-Driven Course Using LAMP

ERIC Educational Resources Information Center

Laverty, Joseph Packy; Wood, David; Turchek, John

2011-01-01

This paper documents the formulation of a database driven open source architecture web development course. The design of a web-based curriculum faces many challenges: a) relative emphasis of client and server-side technologies, b) choice of a server-side language, and c) the cost and efficient delivery of a dynamic web development, database-driven…

A Tutorial in Creating Web-Enabled Databases with Inmagic DB/TextWorks through ODBC.

ERIC Educational Resources Information Center

Breeding, Marshall

2000-01-01

Explains how to create Web-enabled databases. Highlights include Inmagic's DB/Text WebPublisher product called DB/TextWorks; ODBC (Open Database Connectivity) drivers; Perl programming language; HTML coding; Structured Query Language (SQL); Common Gateway Interface (CGI) programming; and examples of HTML pages and Perl scripts. (LRW)

Web Database Development: Implications for Academic Publishing.

ERIC Educational Resources Information Center

Fernekes, Bob

This paper discusses the preliminary planning, design, and development of a pilot project to create an Internet accessible database and search tool for locating and distributing company data and scholarly work. Team members established four project objectives: (1) to develop a Web accessible database and decision tool that creates Web pages on the…

Do-It-Yourself: A Special Library's Approach to Creating Dynamic Web Pages Using Commercial Off-The-Shelf Applications

NASA Technical Reports Server (NTRS)

Steeman, Gerald; Connell, Christopher

2000-01-01

Many librarians may feel that dynamic Web pages are out of their reach, financially and technically. Yet we are reminded in library and Web design literature that static home pages are a thing of the past. This paper describes how librarians at the Institute for Defense Analyses (IDA) library developed a database-driven, dynamic intranet site using commercial off-the-shelf applications. Administrative issues include surveying a library users group for interest and needs evaluation; outlining metadata elements; and, committing resources from managing time to populate the database and training in Microsoft FrontPage and Web-to-database design. Technical issues covered include Microsoft Access database fundamentals, lessons learned in the Web-to-database process (including setting up Database Source Names (DSNs), redesigning queries to accommodate the Web interface, and understanding Access 97 query language vs. Standard Query Language (SQL)). This paper also offers tips on editing Active Server Pages (ASP) scripting to create desired results. A how-to annotated resource list closes out the paper.

Userscripts for the life sciences.

PubMed

Willighagen, Egon L; O'Boyle, Noel M; Gopalakrishnan, Harini; Jiao, Dazhi; Guha, Rajarshi; Steinbeck, Christoph; Wild, David J

2007-12-21

The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources. Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts. This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity.

Userscripts for the Life Sciences

PubMed Central

Willighagen, Egon L; O'Boyle, Noel M; Gopalakrishnan, Harini; Jiao, Dazhi; Guha, Rajarshi; Steinbeck, Christoph; Wild, David J

2007-01-01

Background The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources. Results Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts. Conclusion This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity. PMID:18154664

WebEAV: automatic metadata-driven generation of web interfaces to entity-attribute-value databases.

PubMed

Nadkarni, P M; Brandt, C M; Marenco, L

2000-01-01

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples.

49 CFR 630.4 - Requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.4 Requirements. (a) National Transit Database Reporting System... from the National Transit Database Web site located at http://www.ntdprogram.gov. These reference... Transit Database Web site and a notice of any significant changes to the reporting requirements specified...

49 CFR 630.4 - Requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.4 Requirements. (a) National Transit Database Reporting System... from the National Transit Database Web site located at http://www.ntdprogram.gov. These reference... Transit Database Web site and a notice of any significant changes to the reporting requirements specified...

49 CFR 630.4 - Requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.4 Requirements. (a) National Transit Database Reporting System... from the National Transit Database Web site located at http://www.ntdprogram.gov. These reference... Transit Database Web site and a notice of any significant changes to the reporting requirements specified...

49 CFR 630.4 - Requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.4 Requirements. (a) National Transit Database Reporting System... from the National Transit Database Web site located at http://www.ntdprogram.gov. These reference... Transit Database Web site and a notice of any significant changes to the reporting requirements specified...

49 CFR 630.4 - Requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... TRANSPORTATION NATIONAL TRANSIT DATABASE § 630.4 Requirements. (a) National Transit Database Reporting System... from the National Transit Database Web site located at http://www.ntdprogram.gov. These reference... Transit Database Web site and a notice of any significant changes to the reporting requirements specified...

Use of a secure Internet Web site for collaborative medical research.

PubMed

Marshall, W W; Haley, R W

2000-10-11

Researchers who collaborate on clinical research studies from diffuse locations need a convenient, inexpensive, secure way to record and manage data. The Internet, with its World Wide Web, provides a vast network that enables researchers with diverse types of computers and operating systems anywhere in the world to log data through a common interface. Development of a Web site for scientific data collection can be organized into 10 steps, including planning the scientific database, choosing a database management software system, setting up database tables for each collaborator's variables, developing the Web site's screen layout, choosing a middleware software system to tie the database software to the Web site interface, embedding data editing and calculation routines, setting up the database on the central server computer, obtaining a unique Internet address and name for the Web site, applying security measures to the site, and training staff who enter data. Ensuring the security of an Internet database requires limiting the number of people who have access to the server, setting up the server on a stand-alone computer, requiring user-name and password authentication for server and Web site access, installing a firewall computer to prevent break-ins and block bogus information from reaching the server, verifying the identity of the server and client computers with certification from a certificate authority, encrypting information sent between server and client computers to avoid eavesdropping, establishing audit trails to record all accesses into the Web site, and educating Web site users about security techniques. When these measures are carefully undertaken, in our experience, information for scientific studies can be collected and maintained on Internet databases more efficiently and securely than through conventional systems of paper records protected by filing cabinets and locked doors. JAMA. 2000;284:1843-1849.

Geoinformatics in the public service: building a cyberinfrastructure across the geological surveys

USGS Publications Warehouse

Allison, M. Lee; Gundersen, Linda C.; Richard, Stephen M.; Keller, G. Randy; Baru, Chaitanya

2011-01-01

Advanced information technology infrastructure is increasingly being employed in the Earth sciences to provide researchers with efficient access to massive central databases and to integrate diversely formatted information from a variety of sources. These geoinformatics initiatives enable manipulation, modeling and visualization of data in a consistent way, and are helping to develop integrated Earth models at various scales, and from the near surface to the deep interior. This book uses a series of case studies to demonstrate computer and database use across the geosciences. Chapters are thematically grouped into sections that cover data collection and management; modeling and community computational codes; visualization and data representation; knowledge management and data integration; and web services and scientific workflows. Geoinformatics is a fascinating and accessible introduction to this emerging field for readers across the solid Earth sciences and an invaluable reference for researchers interested in initiating new cyberinfrastructure projects of their own.

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.

Applying World Wide Web technology to the study of patients with rare diseases.

PubMed

de Groen, P C; Barry, J A; Schaller, W J

1998-07-15

Randomized, controlled trials of sporadic diseases are rarely conducted. Recent developments in communication technology, particularly the World Wide Web, allow efficient dissemination and exchange of information. However, software for the identification of patients with a rare disease and subsequent data entry and analysis in a secure Web database are currently not available. To study cholangiocarcinoma, a rare cancer of the bile ducts, we developed a computerized disease tracing system coupled with a database accessible on the Web. The tracing system scans computerized information systems on a daily basis and forwards demographic information on patients with bile duct abnormalities to an electronic mailbox. If informed consent is given, the patient's demographic and preexisting medical information available in medical database servers are electronically forwarded to a UNIX research database. Information from further patient-physician interactions and procedures is also entered into this database. The database is equipped with a Web user interface that allows data entry from various platforms (PC-compatible, Macintosh, and UNIX workstations) anywhere inside or outside our institution. To ensure patient confidentiality and data security, the database includes all security measures required for electronic medical records. The combination of a Web-based disease tracing system and a database has broad applications, particularly for the integration of clinical research within clinical practice and for the coordination of multicenter trials.

High Temperature Superconducting Materials Database

National Institute of Standards and Technology Data Gateway

SRD 62 NIST High Temperature Superconducting Materials Database (Web, free access)   The NIST High Temperature Superconducting Materials Database (WebHTS) provides evaluated thermal, mechanical, and superconducting property data for oxides and other nonconventional superconductors.

What Do They Tell Their Students? Business Faculty Acceptance of the Web and Library Databases for Student Research

ERIC Educational Resources Information Center

Dewald, Nancy H.

2005-01-01

Business faculty were surveyed as to their use of free Web resources and subscription databases for their own and their students' research. A much higher percentage of respondents either require or encourage Web use by their students than require or encourage database use, though most also advise use of multiple sources.

deepTools2: a next generation web server for deep-sequencing data analysis.

PubMed

Ramírez, Fidel; Ryan, Devon P; Grüning, Björn; Bhardwaj, Vivek; Kilpert, Fabian; Richter, Andreas S; Heyne, Steffen; Dündar, Friederike; Manke, Thomas

2016-07-08

We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

deepTools: a flexible platform for exploring deep-sequencing data.

PubMed

Ramírez, Fidel; Dündar, Friederike; Diehl, Sarah; Grüning, Björn A; Manke, Thomas

2014-07-01

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structural Ceramics Database

National Institute of Standards and Technology Data Gateway

SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

Traditional Chinese and western medicine for the prevention of deep venous thrombosis after lower extremity orthopedic surgery: a meta-analysis of randomized controlled trials.

PubMed

Zhu, Shibai; Song, Yi; Chen, Xi; Qian, Wenwei

2018-04-10

Chinese herbal medicine has traditionally been considered to promote blood circulation to remove obstruction in the channels and clear pathogenic heat to drain dampness effects. We conducted this meta-analysis to evaluate its benefits for the prevention of deep venous thrombosis (DVT) after lower extremity orthopedic surgery. Relevant, published studies were identified using the following keywords: lower extremity orthopedic surgery, arthroplasty, joint replacement, fracture, traditional Chinese and western medicine, Chinese herbal medicine, deep venous thrombosis (DVT), and Venous thromboembolism (VTE). The following databases were used to identify the literature consisting of RCTs with a date of search of 31 May 2017: PubMed, Cochrane Library, Web of knowledge, the Chinese National Knowledge Infrastructure Database, the Chongqing VIP Database, the Chinese Biomedical Database, and the Wanfang Database (including three English and four Chinese databases). All relevant data were collected from studies meeting the inclusion criteria. The outcome variables were the incidence rate of DVT, activated partial thromboplastin time (APTT), prothrombin time (PT), and D-dimer; subcutaneous hematoma; and other reported outcomes. RevMan5.2. software was adopted for the meta-analysis. A total of 20 published studies (1862 cases) met the inclusion criteria. The experimental group, 910 patients (48.87%), received the Chinese herbal medicine or traditional Chinese and western medicine for prevention of DVT; the control group, 952 patients (51.13%), received the standard western treatment. The meta-analysis showed that traditional Chinese and western medicine therapy reduced the incidence rates of DVT significantly when compared with controls (risk ratio [RR] = 0.40; 95% CI, 0.30 to 0.54; P < 0.00001), and the D-dimer was lower in the experimental group (P = 0.01). Besides, the incidence rate of subcutaneous hematoma was lower in the experimental group (P < 0.0001). However, no significant difference was found in the PT (P = 0.98) and APTT (P = 0.75) in two groups. No serious adverse events were reported. Traditional Chinese and western medicine therapy may be a safe, effective prevention modality for DVT after lower extremity orthopedic surgery. Further rigorously designed, randomized trials are warranted.

Magnetic Fields for All: The GPIPS Community Web-Access Portal

NASA Astrophysics Data System (ADS)

Carveth, Carol; Clemens, D. P.; Pinnick, A.; Pavel, M.; Jameson, K.; Taylor, B.

2007-12-01

The new GPIPS website portal provides community users with an intuitive and powerful interface to query the data products of the Galactic Plane Infrared Polarization Survey. The website, which was built using PHP for the front end and MySQL for the database back end, allows users to issue queries based on galactic or equatorial coordinates, GPIPS-specific identifiers, polarization information, magnitude information, and several other attributes. The returns are presented in HTML tables, with the added option of either downloading or being emailed an ASCII file including the same or more information from the database. Other functionalities of the website include providing details of the status of the Survey (which fields have been observed or are planned to be observed), techniques involved in data collection and analysis, and descriptions of the database contents and names. For this initial launch of the website, users may access the GPIPS polarization point source catalog and the deep coadd photometric point source catalog. Future planned developments include a graphics-based method for querying the database, as well as tools to combine neighboring GPIPS images into larger image files for both polarimetry and photometry. This work is partially supported by NSF grant AST-0607500.

Ocean Drilling Program: Janus Web Database

Science.gov Websites

in Janus Data Types and Examples Leg 199, sunrise. Janus Web Database ODP and IODP data are stored in as time permits (see Database Overview for available data). Data are available to everyone. There are

DSAP: deep-sequencing small RNA analysis pipeline.

PubMed

Huang, Po-Jung; Liu, Yi-Chung; Lee, Chi-Ching; Lin, Wei-Chen; Gan, Richie Ruei-Chi; Lyu, Ping-Chiang; Tang, Petrus

2010-07-01

DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log(2)-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw.

Solution Kinetics Database on the Web

National Institute of Standards and Technology Data Gateway

SRD 40 NDRL/NIST Solution Kinetics Database on the Web (Web, free access)   Data for free radical processes involving primary radicals from water, inorganic radicals and carbon-centered radicals in solution, and singlet oxygen and organic peroxyl radicals in various solvents.

Ocean Drilling Program: Privacy Policy

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main web site ODP/TAMU Science Operator Home Ocean Drilling Program Privacy Policy The following is the privacy policy for the www-odp.tamu.edu web site. 1. Cookies are used in the Database portion of the web

Discrepancies among Scopus, Web of Science, and PubMed coverage of funding information in medical journal articles.

PubMed

Kokol, Peter; Vošner, Helena Blažun

2018-01-01

The overall aim of the present study was to compare the coverage of existing research funding information for articles indexed in Scopus, Web of Science, and PubMed databases. The numbers of articles with funding information published in 2015 were identified in the three selected databases and compared using bibliometric analysis of a sample of twenty-eight prestigious medical journals. Frequency analysis of the number of articles with funding information showed statistically significant differences between Scopus, Web of Science, and PubMed databases. The largest proportion of articles with funding information was found in Web of Science (29.0%), followed by PubMed (14.6%) and Scopus (7.7%). The results show that coverage of funding information differs significantly among Scopus, Web of Science, and PubMed databases in a sample of the same medical journals. Moreover, we found that, currently, funding data in PubMed is more difficult to obtain and analyze compared with that in the other two databases.

A web-based genomic sequence database for the Streptomycetaceae: a tool for systematics and genome mining

USDA-ARS?s Scientific Manuscript database

The ARS Microbial Genome Sequence Database (http://199.133.98.43), a web-based database server, was established utilizing the BIGSdb (Bacterial Isolate Genomics Sequence Database) software package, developed at Oxford University, as a tool to manage multi-locus sequence data for the family Streptomy...

Collection Fusion Using Bayesian Estimation of a Linear Regression Model in Image Databases on the Web.

ERIC Educational Resources Information Center

Kim, Deok-Hwan; Chung, Chin-Wan

2003-01-01

Discusses the collection fusion problem of image databases, concerned with retrieving relevant images by content based retrieval from image databases distributed on the Web. Focuses on a metaserver which selects image databases supporting similarity measures and proposes a new algorithm which exploits a probabilistic technique using Bayesian…

The Web-Database Connection Tools for Sharing Information on the Campus Intranet.

ERIC Educational Resources Information Center

Thibeault, Nancy E.

This paper evaluates four tools for creating World Wide Web pages that interface with Microsoft Access databases: DB Gateway, Internet Database Assistant (IDBA), Microsoft Internet Database Connector (IDC), and Cold Fusion. The system requirements and features of each tool are discussed. A sample application, "The Virtual Help Desk"…

An Overview of ARL’s Multimodal Signatures Database and Web Interface

DTIC Science & Technology

2007-12-01

ActiveX components, which hindered distribution due to license agreements and run-time license software to use such components. g. Proprietary...Overview The database consists of multimodal signature data files in the HDF5 format. Generally, each signature file contains all the ancillary...only contains information in the database, Web interface, and signature files that is releasable to the public. The Web interface consists of static

Analysis and Development of a Web-Enabled Planning and Scheduling Database Application

DTIC Science & Technology

2013-09-01

establishes an entity—relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web- enabled interface for...development, develop, design, process, re- engineering, reengineering, MySQL , structured query language, SQL, myPHPadmin. 15. NUMBER OF PAGES 107 16...relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web-enabled interface for the population of

Vision science literature of Nepal in the database "Web of Science".

PubMed

Risal, S; Prasad, H N

2012-01-01

Vision Science is considered to be a quite developed discipline in Nepal, with much research currently in progress. Though the results of these endeavors are published in scientific journals, formal citation analyses have not been performed on works contributed by Nepalese vision scientists. To study Nepal's contribution to vision science literature in the database "Web of Science". The primary data source of this paper was Web of Science, a citation database of Thomas Reuters. All bibliometric analyses were performed with the help of Web of Science analysis service. In the current database of vision science literature, Nepalese authors contributed 112 publications to Web of Science, 95 of which were original articles. Pokharel GP had the highest number of citations among contributing authors of Nepal. Hennig A contributed the highest number of article as a first author. The Nepal Eye Hospital contributed the highest number of articles as an institution to the field of Vision Science. Currently, only two journals from Nepal including Journal of Nepal Medical Association (JAMA) are indexed in the Web of Science database (Sieving, 2012). To evaluate the total productivity of vision science literature from Nepal, total publication counts from national journals and articles indexed in other databases such as PubMed and Scopus must also be considered. © NEPjOPH.

Cyanide Suicide After Deep Web Shopping: A Case Report.

PubMed

Le Garff, Erwan; Delannoy, Yann; Mesli, Vadim; Allorge, Delphine; Hédouin, Valéry; Tournel, Gilles

2016-09-01

Cyanide is a product that is known for its use in industrial or laboratory processes, as well as for intentional intoxication. The toxicity of cyanide is well described in humans with rapid inhibition of cellular aerobic metabolism after ingestion or inhalation, leading to severe clinical effects that are frequently lethal. We report the case of a young white man found dead in a hotel room after self-poisoning with cyanide ordered in the deep Web. This case shows a probable complex suicide kit use including cyanide, as a lethal tool, and dextromethorphan, as a sedative and anxiolytic substance. This case is an original example of the emerging deep Web shopping in illegal drug procurement.

Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies.

PubMed

Huang, Yu S; Horton, Matthew; Vilhjálmsson, Bjarni J; Seren, Umit; Meng, Dazhe; Meyer, Christopher; Ali Amer, Muhammad; Borevitz, Justin O; Bergelson, Joy; Nordborg, Magnus

2011-01-01

With large-scale genomic data becoming the norm in biological studies, the storing, integrating, viewing and searching of such data have become a major challenge. In this article, we describe the development of an Arabidopsis thaliana database that hosts the geographic information and genetic polymorphism data for over 6000 accessions and genome-wide association study (GWAS) results for 107 phenotypes representing the largest collection of Arabidopsis polymorphism data and GWAS results to date. Taking advantage of a series of the latest web 2.0 technologies, such as Ajax (Asynchronous JavaScript and XML), GWT (Google-Web-Toolkit), MVC (Model-View-Controller) web framework and Object Relationship Mapper, we have created a web-based application (web app) for the database, that offers an integrated and dynamic view of geographic information, genetic polymorphism and GWAS results. Essential search functionalities are incorporated into the web app to aid reverse genetics research. The database and its web app have proven to be a valuable resource to the Arabidopsis community. The whole framework serves as an example of how biological data, especially GWAS, can be presented and accessed through the web. In the end, we illustrate the potential to gain new insights through the web app by two examples, showcasing how it can be used to facilitate forward and reverse genetics research. Database URL: http://arabidopsis.usc.edu/

Web data mining

NASA Astrophysics Data System (ADS)

Wibonele, Kasanda J.; Zhang, Yanqing

2002-03-01

A web data mining system using granular computing and ASP programming is proposed. This is a web based application, which allows web users to submit survey data for many different companies. This survey is a collection of questions that will help these companies develop and improve their business and customer service with their clients by analyzing survey data. This web application allows users to submit data anywhere. All the survey data is collected into a database for further analysis. An administrator of this web application can login to the system and view all the data submitted. This web application resides on a web server, and the database resides on the MS SQL server.

Mining a Web Citation Database for Author Co-Citation Analysis.

ERIC Educational Resources Information Center

He, Yulan; Hui, Siu Cheung

2002-01-01

Proposes a mining process to automate author co-citation analysis based on the Web Citation Database, a data warehouse for storing citation indices of Web publications. Describes the use of agglomerative hierarchical clustering for author clustering and multidimensional scaling for displaying author cluster maps, and explains PubSearch, a…

Database of Novel and Emerging Adsorbent Materials

National Institute of Standards and Technology Data Gateway

SRD 205 NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials (Web, free access)   The NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials is a free, web-based catalog of adsorbent materials and measured adsorption properties of numerous materials obtained from article entries from the scientific literature. Search fields for the database include adsorbent material, adsorbate gas, experimental conditions (pressure, temperature), and bibliographic information (author, title, journal), and results from queries are provided as a list of articles matching the search parameters. The database also contains adsorption isotherms digitized from the cataloged articles, which can be compared visually online in the web application or exported for offline analysis.

THE ECOTOX DATABASE AND ECOLOGICAL SOIL SCREENING LEVEL (ECO-SSL) WEB SITES

EPA Science Inventory

The EPA's ECOTOX database (http://www.epa.gov/ecotox/) provides a web browser search interface for locating aquatic and terrestrial toxic effects information. Data on more than 8100 chemicals and 5700 terrestrial and aquatic species are included in the database. Information is ...

Dark Web 101

DTIC Science & Technology

2016-07-21

Todays internet has multiple webs. The surface web is what Google and other search engines index and pull based on links. Essentially, the surface...financial records, research and development), and personal data (medical records or legal documents). These are all deep web. Standard search engines dont

Evaluation of the content and accessibility of web sites for accredited orthopaedic sports medicine fellowships.

PubMed

Mulcahey, Mary K; Gosselin, Michelle M; Fadale, Paul D

2013-06-19

The Internet is a common source of information for orthopaedic residents applying for sports medicine fellowships, with the web sites of the American Orthopaedic Society for Sports Medicine (AOSSM) and the San Francisco Match serving as central databases. We sought to evaluate the web sites for accredited orthopaedic sports medicine fellowships with regard to content and accessibility. We reviewed the existing web sites of the ninety-five accredited orthopaedic sports medicine fellowships included in the AOSSM and San Francisco Match databases from February to March 2012. A Google search was performed to determine the overall accessibility of program web sites and to supplement information obtained from the AOSSM and San Francisco Match web sites. The study sample consisted of the eighty-seven programs whose web sites connected to information about the fellowship. Each web site was evaluated for its informational value. Of the ninety-five programs, fifty-one (54%) had links listed in the AOSSM database. Three (3%) of all accredited programs had web sites that were linked directly to information about the fellowship. Eighty-eight (93%) had links listed in the San Francisco Match database; however, only five (5%) had links that connected directly to information about the fellowship. Of the eighty-seven programs analyzed in our study, all eighty-seven web sites (100%) provided a description of the program and seventy-six web sites (87%) included information about the application process. Twenty-one web sites (24%) included a list of current fellows. Fifty-six web sites (64%) described the didactic instruction, seventy (80%) described team coverage responsibilities, forty-seven (54%) included a description of cases routinely performed by fellows, forty-one (47%) described the role of the fellow in seeing patients in the office, eleven (13%) included call responsibilities, and seventeen (20%) described a rotation schedule. Two Google searches identified direct links for 67% to 71% of all accredited programs. Most accredited orthopaedic sports medicine fellowships lack easily accessible or complete web sites in the AOSSM or San Francisco Match databases. Improvement in the accessibility and quality of information on orthopaedic sports medicine fellowship web sites would facilitate the ability of applicants to obtain useful information.

[A systematic evaluation of application of the web-based cancer database].

PubMed

Huang, Tingting; Liu, Jialin; Li, Yong; Zhang, Rui

2013-10-01

In order to support the theory and practice of the web-based cancer database development in China, we applied a systematic evaluation to assess the development condition of the web-based cancer databases at home and abroad. We performed computer-based retrieval of the Ovid-MEDLINE, Springerlink, EBSCOhost, Wiley Online Library and CNKI databases, the papers of which were published between Jan. 1995 and Dec. 2011, and retrieved the references of these papers by hand. We selected qualified papers according to the pre-established inclusion and exclusion criteria, and carried out information extraction and analysis of the papers. Eventually, searching the online database, we obtained 1244 papers, and checking the reference lists, we found other 19 articles. Thirty-one articles met the inclusion and exclusion criteria and we extracted the proofs and assessed them. Analyzing these evidences showed that the U.S.A. counted for 26% in the first place. Thirty-nine percent of these web-based cancer databases are comprehensive cancer databases. As for single cancer databases, breast cancer and prostatic cancer are on the top, both counting for 10% respectively. Thirty-two percent of the cancer database are associated with cancer gene information. For the technical applications, MySQL and PHP applied most widely, nearly 23% each.

75 FR 78236 - Lock+TM

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-15

...-foot-wide, 20-foot-deep excavated power canal; (2) a 55-foot-long, 65-foot-wide, 8-foot-deep excavated... 18 CFR 385.2001(a)(1)(iii) and the instructions on the Commission's Web site http://www.ferc.gov/docs... Web site at http://www.ferc.gov/docs-filing/elibrary.asp . Enter the docket number (P-13743-000, 13753...

Deep pelagic food web structure as revealed by in situ feeding observations.

PubMed

Choy, C Anela; Haddock, Steven H D; Robison, Bruce H

2017-12-06

Food web linkages, or the feeding relationships between species inhabiting a shared ecosystem, are an ecological lens through which ecosystem structure and function can be assessed, and thus are fundamental to informing sustainable resource management. Empirical feeding datasets have traditionally been painstakingly generated from stomach content analysis, direct observations and from biochemical trophic markers (stable isotopes, fatty acids, molecular tools). Each approach carries inherent biases and limitations, as well as advantages. Here, using 27 years (1991-2016) of in situ feeding observations collected by remotely operated vehicles (ROVs), we quantitatively characterize the deep pelagic food web of central California within the California Current, complementing existing studies of diet and trophic interactions with a unique perspective. Seven hundred and forty-three independent feeding events were observed with ROVs from near-surface waters down to depths approaching 4000 m, involving an assemblage of 84 different predators and 82 different prey types, for a total of 242 unique feeding relationships. The greatest diversity of prey was consumed by narcomedusae, followed by physonect siphonophores, ctenophores and cephalopods. We highlight key interactions within the poorly understood 'jelly web', showing the importance of medusae, ctenophores and siphonophores as key predators, whose ecological significance is comparable to large fish and squid species within the central California deep pelagic food web. Gelatinous predators are often thought to comprise relatively inefficient trophic pathways within marine communities, but we build upon previous findings to document their substantial and integral roles in deep pelagic food webs. © 2017 The Authors.

A simple method for serving Web hypermaps with dynamic database drill-down

PubMed Central

Boulos, Maged N Kamel; Roudsari, Abdul V; Carson, Ewart R

2002-01-01

Background HealthCyberMap aims at mapping parts of health information cyberspace in novel ways to deliver a semantically superior user experience. This is achieved through "intelligent" categorisation and interactive hypermedia visualisation of health resources using metadata, clinical codes and GIS. HealthCyberMap is an ArcView 3.1 project. WebView, the Internet extension to ArcView, publishes HealthCyberMap ArcView Views as Web client-side imagemaps. The basic WebView set-up does not support any GIS database connection, and published Web maps become disconnected from the original project. A dedicated Internet map server would be the best way to serve HealthCyberMap database-driven interactive Web maps, but is an expensive and complex solution to acquire, run and maintain. This paper describes HealthCyberMap simple, low-cost method for "patching" WebView to serve hypermaps with dynamic database drill-down functionality on the Web. Results The proposed solution is currently used for publishing HealthCyberMap GIS-generated navigational information maps on the Web while maintaining their links with the underlying resource metadata base. Conclusion The authors believe their map serving approach as adopted in HealthCyberMap has been very successful, especially in cases when only map attribute data change without a corresponding effect on map appearance. It should be also possible to use the same solution to publish other interactive GIS-driven maps on the Web, e.g., maps of real world health problems. PMID:12437788

[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.

Ocean Drilling Program: TAMU Staff Directory

Science.gov Websites

products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main web site Employment Opportunities ODP | Search | Database | Drilling | Publications | Science | Cruise Info | Public

SNPversity: a web-based tool for visualizing diversity

PubMed Central

Schott, David A; Vinnakota, Abhinav G; Portwood, John L; Andorf, Carson M

2018-01-01

Abstract Many stand-alone desktop software suites exist to visualize single nucleotide polymorphism (SNP) diversity, but web-based software that can be easily implemented and used for biological databases is absent. SNPversity was created to answer this need by building an open-source visualization tool that can be implemented on a Unix-like machine and served through a web browser that can be accessible worldwide. SNPversity consists of a HDF5 database back-end for SNPs, a data exchange layer powered by TASSEL libraries that represent data in JSON format, and an interface layer using PHP to visualize SNP information. SNPversity displays data in real-time through a web browser in grids that are color-coded according to a given SNP’s allelic status and mutational state. SNPversity is currently available at MaizeGDB, the maize community’s database, and will be soon available at GrainGenes, the clade-oriented database for Triticeae and Avena species, including wheat, barley, rye, and oat. The code and documentation are uploaded onto github, and they are freely available to the public. We expect that the tool will be highly useful for other biological databases with a similar need to display SNP diversity through their web interfaces. Database URL: https://www.maizegdb.org/snpversity PMID:29688387

Development of Database for Accident Analysis in Indian Mines

NASA Astrophysics Data System (ADS)

Tripathy, Debi Prasad; Guru Raghavendra Reddy, K.

2016-10-01

Mining is a hazardous industry and high accident rates associated with underground mining is a cause of deep concern. Technological developments notwithstanding, rate of fatal accidents and reportable incidents have not shown corresponding levels of decline. This paper argues that adoption of appropriate safety standards by both mine management and the government may result in appreciable reduction in accident frequency. This can be achieved by using the technology in improving the working conditions, sensitising workers and managers about causes and prevention of accidents. Inputs required for a detailed analysis of an accident include information on location, time, type, cost of accident, victim, nature of injury, personal and environmental factors etc. Such information can be generated from data available in the standard coded accident report form. This paper presents a web based application for accident analysis in Indian mines during 2001-2013. An accident database (SafeStat) prototype based on Intranet of the TCP/IP agreement, as developed by the authors, is also discussed.

Construction of a Linux based chemical and biological information system.

PubMed

Molnár, László; Vágó, István; Fehér, András

2003-01-01

A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

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

The system is developed to collect, process, store and present the information provided by the radio frequency identification (RFID) devices. The system contains three parts, the application software, the database and the web page. The application software manages multiple RFID devices, such as readers and portals, simultaneously. It communicates with the devices through application programming interface (API) provided by the device vendor. The application software converts data collected by the RFID readers and portals to readable information. It is capable of encrypting data using 256 bits advanced encryption standard (AES). The application software has a graphical user interface (GUI). Themore » GUI mimics the configurations of the nucler material storage sites or transport vehicles. The GUI gives the user and system administrator an intuitive way to read the information and/or configure the devices. The application software is capable of sending the information to a remote, dedicated and secured web and database server. Two captured screen samples, one for storage and transport, are attached. The database is constructed to handle a large number of RFID tag readers and portals. A SQL server is employed for this purpose. An XML script is used to update the database once the information is sent from the application software. The design of the web page imitates the design of the application software. The web page retrieves data from the database and presents it in different panels. The user needs a user name combined with a password to access the web page. The web page is capable of sending e-mail and text messages based on preset criteria, such as when alarm thresholds are excceeded. A captured screen sample is attached. The application software is designed to be installed on a local computer. The local computer is directly connected to the RFID devices and can be controlled locally or remotely. There are multiple local computers managing different sites or transport vehicles. The control from remote sites and information transmitted to a central database server is through secured internet. The information stored in the central databaser server is shown on the web page. The users can view the web page on the internet. A dedicated and secured web and database server (https) is used to provide information security.« less

Ionic Liquids Database- (ILThermo)

National Institute of Standards and Technology Data Gateway

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

FirstSearch and NetFirst--Web and Dial-up Access: Plus Ca Change, Plus C'est la Meme Chose?

ERIC Educational Resources Information Center

Koehler, Wallace; Mincey, Danielle

1996-01-01

Compares and evaluates the differences between OCLC's dial-up and World Wide Web FirstSearch access methods and their interfaces with the underlying databases. Also examines NetFirst, OCLC's new Internet catalog, the only Internet tracking database from a "traditional" database service. (Author/PEN)

Ocean Drilling Program: Web Site Access Statistics

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main See statistics for JOIDES members. See statistics for Janus database. 1997 October November December accessible only on www-odp.tamu.edu. ** End of ODP, start of IODP. Privacy Policy ODP | Search | Database

XCOM: Photon Cross Sections Database

National Institute of Standards and Technology Data Gateway

SRD 8 XCOM: Photon Cross Sections Database (Web, free access)   A web database is provided which can be used to calculate photon cross sections for scattering, photoelectric absorption and pair production, as well as total attenuation coefficients, for any element, compound or mixture (Z <= 100) at energies from 1 keV to 100 GeV.

Dining in the Deep: The Feeding Ecology of Deep-Sea Fishes

NASA Astrophysics Data System (ADS)

Drazen, Jeffrey C.; Sutton, Tracey T.

2017-01-01

Deep-sea fishes inhabit ˜75% of the biosphere and are a critical part of deep-sea food webs. Diet analysis and more recent trophic biomarker approaches, such as stable isotopes and fatty-acid profiles, have enabled the description of feeding guilds and an increased recognition of the vertical connectivity in food webs in a whole-water-column sense, including benthic-pelagic coupling. Ecosystem modeling requires data on feeding rates; the available estimates indicate that deep-sea fishes have lower per-individual feeding rates than coastal and epipelagic fishes, but the overall predation impact may be high. A limited number of studies have measured the vertical flux of carbon by mesopelagic fishes, which appears to be substantial. Anthropogenic activities are altering deep-sea ecosystems and their services, which are mediated by trophic interactions. We also summarize outstanding data gaps.

Transition to a Unified System: Using Perl To Drive Library Databases and Enhance Web Site Functionality.

ERIC Educational Resources Information Center

Fagan, Judy Condit

2001-01-01

Discusses the need for libraries to routinely redesign their Web sites, and presents a case study that describes how a Perl-driven database at Southern Illinois University's library improved Web site organization and patron access, simplified revisions, and allowed staff unfamiliar with HTML to update content. (Contains 56 references.) (Author/LRW)

ITS-90 Thermocouple Database

National Institute of Standards and Technology Data Gateway

SRD 60 NIST ITS-90 Thermocouple Database (Web, free access)   Web version of Standard Reference Database 60 and NIST Monograph 175. The database gives temperature -- electromotive force (emf) reference functions and tables for the letter-designated thermocouple types B, E, J, K, N, R, S and T. These reference functions have been adopted as standards by the American Society for Testing and Materials (ASTM) and the International Electrotechnical Commission (IEC).

A comparative study of six European databases of medically oriented Web resources.

PubMed

Abad García, Francisca; González Teruel, Aurora; Bayo Calduch, Patricia; de Ramón Frias, Rosa; Castillo Blasco, Lourdes

2005-10-01

The paper describes six European medically oriented databases of Web resources, pertaining to five quality-controlled subject gateways, and compares their performance. The characteristics, coverage, procedure for selecting Web resources, record structure, searching possibilities, and existence of user assistance were described for each database. Performance indicators for each database were obtained by means of searches carried out using the key words, "myocardial infarction." Most of the databases originated in the 1990s in an academic or library context and include all types of Web resources of an international nature. Five databases use Medical Subject Headings. The number of fields per record varies between three and nineteen. The language of the search interfaces is mostly English, and some of them allow searches in other languages. In some databases, the search can be extended to Pubmed. Organizing Medical Networked Information, Catalogue et Index des Sites Médicaux Francophones, and Diseases, Disorders and Related Topics produced the best results. The usefulness of these databases as quick reference resources is clear. In addition, their lack of content overlap means that, for the user, they complement each other. Their continued survival faces three challenges: the instability of the Internet, maintenance costs, and lack of use in spite of their potential usefulness.

THGS: a web-based database of Transmembrane Helices in Genome Sequences

PubMed Central

Fernando, S. A.; Selvarani, P.; Das, Soma; Kumar, Ch. Kiran; Mondal, Sukanta; Ramakumar, S.; Sekar, K.

2004-01-01

Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome Database (GDB). The proposed database has provision to search sequence motifs in transmembrane and globular proteins. In addition, the motif can be searched in the other sequence databases (Swiss-Prot and PIR) or in the macromolecular structure database, Protein Data Bank (PDB). Further, the 3D structure of the corresponding queried motif, if it is available in the solved protein structures deposited in the Protein Data Bank, can also be visualized using the widely used graphics package RASMOL. All the sequence databases used in the present work are updated frequently and hence the results produced are up to date. The database THGS is freely available via the world wide web and can be accessed at http://pranag.physics.iisc.ernet.in/thgs/ or http://144.16.71.10/thgs/. PMID:14681375

[Oncologic gynecology and the Internet].

PubMed

Gizler, Robert; Bielanów, Tomasz; Kulikiewicz, Krzysztof

2002-11-01

The strategy of World Wide Web searching for medical sites was presented in this article. The "deep web" and "surface web" resources were searched. The 10 best sites connected with the gynecological oncology, according to authors' opinion, were presented.

NNDC Data Services

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

Tuli, J.K.; Sonzogni,A.

The National Nuclear Data Center has provided remote access to some of its resources since 1986. The major databases and other resources available currently through NNDC Web site are summarized. The National Nuclear Data Center (NNDC) has provided remote access to the nuclear physics databases it maintains and to other resources since 1986. With considerable innovation access is now mostly through the Web. The NNDC Web pages have been modernized to provide a consistent state-of-the-art style. The improved database services and other resources available from the NNOC site at www.nndc.bnl.govwill be described.

Annotations of Mexican bullfighting videos for semantic index

NASA Astrophysics Data System (ADS)

Montoya Obeso, Abraham; Oropesa Morales, Lester Arturo; Fernando Vázquez, Luis; Cocolán Almeda, Sara Ivonne; Stoian, Andrei; García Vázquez, Mireya Saraí; Zamudio Fuentes, Luis Miguel; Montiel Perez, Jesús Yalja; de la O Torres, Saul; Ramírez Acosta, Alejandro Alvaro

2015-09-01

The video annotation is important for web indexing and browsing systems. Indeed, in order to evaluate the performance of video query and mining techniques, databases with concept annotations are required. Therefore, it is necessary generate a database with a semantic indexing that represents the digital content of the Mexican bullfighting atmosphere. This paper proposes a scheme to make complex annotations in a video in the frame of multimedia search engine project. Each video is partitioned using our segmentation algorithm that creates shots of different length and different number of frames. In order to make complex annotations about the video, we use ELAN software. The annotations are done in two steps: First, we take note about the whole content in each shot. Second, we describe the actions as parameters of the camera like direction, position and deepness. As a consequence, we obtain a more complete descriptor of every action. In both cases we use the concepts of the TRECVid 2014 dataset. We also propose new concepts. This methodology allows to generate a database with the necessary information to create descriptors and algorithms capable to detect actions to automatically index and classify new bullfighting multimedia content.

Comparing Unique Title Coverage of Web of Science and Scopus in Earth and Atmospheric Sciences

ERIC Educational Resources Information Center

Barnett, Philip; Lascar, Claudia

2012-01-01

The current journal titles in earth and atmospheric sciences, that are unique to each of two databases, Web of Science and Scopus, were identified using different methods. Comparing by subject category shows that Scopus has hundreds of unique titles, and Web of Science just 16. The titles unique to each database have low SCImago Journal Rank…

Keeping Research Data from the Continental Deep Drilling Programme (KTB) Accessible and Taking First Steps Towards Digital Preservation

NASA Astrophysics Data System (ADS)

Klump, J. F.; Ulbricht, D.; Conze, R.

2014-12-01

The Continental Deep Drilling Programme (KTB) was a scientific drilling project from 1987 to 1995 near Windischeschenbach, Bavaria. The main super-deep borehole reached a depth of 9,101 meters into the Earth's continental crust. The project used the most current equipment for data capture and processing. After the end of the project key data were disseminated through the web portal of the International Continental Scientific Drilling Program (ICDP). The scientific reports were published as printed volumes. As similar projects have also experienced, it becomes increasingly difficult to maintain a data portal over a long time. Changes in software and underlying hardware make a migration of the entire system inevitable. Around 2009 the data presented on the ICDP web portal were migrated to the Scientific Drilling Database (SDDB) and published through DataCite using Digital Object Identifiers (DOI) as persistent identifiers. The SDDB portal used a relational database with a complex data model to store data and metadata. A PHP-based Content Management System with custom modifications made it possible to navigate and browse datasets using the metadata and then download datasets. The data repository software eSciDoc allows storing self-contained packages consistent with the OAIS reference model. Each package consists of binary data files and XML-metadata. Using a REST-API the packages can be stored in the eSciDoc repository and can be searched using the XML-metadata. During the last maintenance cycle of the SDDB the data and metadata were migrated into the eSciDoc repository. Discovery metadata was generated following the GCMD-DIF, ISO19115 and DataCite schemas. The eSciDoc repository allows to store an arbitrary number of XML-metadata records with each data object. In addition to descriptive metadata each data object may contain pointers to related materials, such as IGSN-metadata to link datasets to physical specimens, or identifiers of literature interpreting the data. Datasets are presented by XSLT-stylesheet transformation using the stored metadata. The presentation shows several migration cycles of data and metadata, which were driven by aging software systems. Currently the datasets reside as self-contained entities in a repository system that is ready for digital preservation.

Generic HTML Form Processor: A versatile PHP script to save web-collected data into a MySQL database.

PubMed

Göritz, Anja S; Birnbaum, Michael H

2005-11-01

The customizable PHP script Generic HTML Form Processor is intended to assist researchers and students in quickly setting up surveys and experiments that can be administered via the Web. This script relieves researchers from the burdens of writing new CGI scripts and building databases for each Web study. Generic HTML Form Processor processes any syntactically correct HTML forminput and saves it into a dynamically created open-source database. We describe five modes for usage of the script that allow increasing functionality but require increasing levels of knowledge of PHP and Web servers: The first two modes require no previous knowledge, and the fifth requires PHP programming expertise. Use of Generic HTML Form Processor is free for academic purposes, and its Web address is www.goeritz.net/brmic.

Turning Access into a web-enabled secure information system for clinical trials.

PubMed

Dongquan Chen; Chen, Wei-Bang; Soong, Mayhue; Soong, Seng-Jaw; Orthner, Helmuth F

2009-08-01

Organizations that have limited resources need to conduct clinical studies in a cost-effective, but secure way. Clinical data residing in various individual databases need to be easily accessed and secured. Although widely available, digital certification, encryption, and secure web server, have not been implemented as widely, partly due to a lack of understanding of needs and concerns over issues such as cost and difficulty in implementation. The objective of this study was to test the possibility of centralizing various databases and to demonstrate ways of offering an alternative to a large-scale comprehensive and costly commercial product, especially for simple phase I and II trials, with reasonable convenience and security. We report a working procedure to transform and develop a standalone Access database into a secure Web-based secure information system. For data collection and reporting purposes, we centralized several individual databases; developed, and tested a web-based secure server using self-issued digital certificates. The system lacks audit trails. The cost of development and maintenance may hinder its wide application. The clinical trial databases scattered in various departments of an institution could be centralized into a web-enabled secure information system. The limitations such as the lack of a calendar and audit trail can be partially addressed with additional programming. The centralized Web system may provide an alternative to a comprehensive clinical trial management system.

A Web-based open-source database for the distribution of hyperspectral signatures

NASA Astrophysics Data System (ADS)

Ferwerda, J. G.; Jones, S. D.; Du, Pei-Jun

2006-10-01

With the coming of age of field spectroscopy as a non-destructive means to collect information on the physiology of vegetation, there is a need for storage of signatures, and, more importantly, their metadata. Without the proper organisation of metadata, the signatures itself become limited. In order to facilitate re-distribution of data, a database for the storage & distribution of hyperspectral signatures and their metadata was designed. The database was built using open-source software, and can be used by the hyperspectral community to share their data. Data is uploaded through a simple web-based interface. The database recognizes major file-formats by ASD, GER and International Spectronics. The database source code is available for download through the hyperspectral.info web domain, and we happily invite suggestion for additions & modification for the database to be submitted through the online forums on the same website.

Moby and Moby 2: creatures of the deep (web).

PubMed

Vandervalk, Ben P; McCarthy, E Luke; Wilkinson, Mark D

2009-03-01

Facile and meaningful integration of data from disparate resources is the 'holy grail' of bioinformatics. Some resources have begun to address this problem by providing their data using Semantic Web standards, specifically the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare. In response, we have seen the emergence of centralized 'semantic warehouses' that collect public data from third parties, integrate it, translate it into OWL/RDF and provide it to the community as a unified and queryable resource. One limitation of the warehouse approach is that queries are confined to the resources that have been selected for inclusion. A related problem, perhaps of greater concern, is that the majority of bioinformatics data exists in the 'Deep Web'-that is, the data does not exist until an application or analytical tool is invoked, and therefore does not have a predictable Web address. The inability to utilize Uniform Resource Identifiers (URIs) to address this data is a barrier to its accessibility via URI-centric Semantic Web technologies. Here we examine 'The State of the Union' for the adoption of Semantic Web standards in the health care and life sciences domain by key bioinformatics resources, explore the nature and connectivity of several community-driven semantic warehousing projects, and report on our own progress with the CardioSHARE/Moby-2 project, which aims to make the resources of the Deep Web transparently accessible through SPARQL queries.

76 FR 38383 - Ballville Hydroelectric Group, LLC; Notice of Preliminary Permit Application Accepted for Filing...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-30

... wide by 50 feet long by 30 feet deep; (3) the existing 50-foot-long by 20-foot-wide by 30-foot- deep... Commission's Web site ( http://www.ferc.gov/docs-filing/ferconline.asp ) under the ``eFiling'' link. For a... 20426. For more information on how to submit these types of filings please go to the Commission's Web...

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

PubMed

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

2018-05-08

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

Accessibility and quality of online information for pediatric orthopaedic surgery fellowships.

PubMed

Davidson, Austin R; Murphy, Robert F; Spence, David D; Kelly, Derek M; Warner, William C; Sawyer, Jeffrey R

2014-12-01

Pediatric orthopaedic fellowship applicants commonly use online-based resources for information on potential programs. Two primary sources are the San Francisco Match (SF Match) database and the Pediatric Orthopaedic Society of North America (POSNA) database. We sought to determine the accessibility and quality of information that could be obtained by using these 2 sources. The online databases of the SF Match and POSNA were reviewed to determine the availability of embedded program links or external links for the included programs. If not available in the SF Match or POSNA data, Web sites for listed programs were located with a Google search. All identified Web sites were analyzed for accessibility, content volume, and content quality. At the time of online review, 50 programs, offering 68 positions, were listed in the SF Match database. Although 46 programs had links included with their information, 36 (72%) of them simply listed http://www.sfmatch.org as their unique Web site. Ten programs (20%) had external links listed, but only 2 (4%) linked directly to the fellowship web page. The POSNA database does not list any links to the 47 programs it lists, which offer 70 positions. On the basis of a Google search of the 50 programs listed in the SF Match database, web pages were found for 35. Of programs with independent web pages, all had a description of the program and 26 (74%) described their application process. Twenty-nine (83%) listed research requirements, 22 (63%) described the rotation schedule, and 12 (34%) discussed the on-call expectations. A contact telephone number and/or email address was provided by 97% of programs. Twenty (57%) listed both the coordinator and fellowship director, 9 (26%) listed the coordinator only, 5 (14%) listed the fellowship director only, and 1 (3%) had no contact information given. The SF Match and POSNA databases provide few direct links to fellowship Web sites, and individual program Web sites either do not exist or do not effectively convey information about the programs. Improved accessibility and accurate information online would allow potential applicants to obtain information about pediatric fellowships in a more efficient manner.

Structure and navigation for electronic publishing

NASA Astrophysics Data System (ADS)

Tillinghast, John; Beretta, Giordano B.

1998-01-01

The sudden explosion of the World Wide Web as a new publication medium has given a dramatic boost to the electronic publishing industry, which previously was a limited market centered around CD-ROMs and on-line databases. While the phenomenon has parallels to the advent of the tabloid press in the middle of last century, the electronic nature of the medium brings with it the typical characteristic of 4th wave media, namely the acceleration in its propagation speed and the volume of information. Consequently, e-publications are even flatter than print media; Shakespeare's Romeo and Juliet share the same computer screen with a home-made plagiarized copy of Deep Throat. The most touted tool for locating useful information on the World Wide Web is the search engine. However, due to the medium's flatness, sought information is drowned in a sea of useless information. A better solution is to build tools that allow authors to structure information so that it can easily be navigated. We experimented with the use of ontologies as a tool to formulate structures for information about a specific topic, so that related concepts are placed in adjacent locations and can easily be navigated using simple and ergonomic user models. We describe our effort in building a World Wide Web based photo album that is shared among a small network of people.

WebEAV

PubMed Central

Nadkarni, Prakash M.; Brandt, Cynthia M.; Marenco, Luis

2000-01-01

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples. PMID:10887163

TryTransDB: A web-based resource for transport proteins in Trypanosomatidae.

PubMed

Sonar, Krushna; Kabra, Ritika; Singh, Shailza

2018-03-12

TryTransDB is a web-based resource that stores transport protein data which can be retrieved using a standalone BLAST tool. We have attempted to create an integrated database that can be a one-stop shop for the researchers working with transport proteins of Trypanosomatidae family. TryTransDB (Trypanosomatidae Transport Protein Database) is a web based comprehensive resource that can fire a BLAST search against most of the transport protein sequences (protein and nucleotide) from Trypanosomatidae family organisms. This web resource further allows to compute a phylogenetic tree by performing multiple sequence alignment (MSA) using CLUSTALW suite embedded in it. Also, cross-linking to other databases helps in gathering more information for a certain transport protein in a single website.

Global Tsunami Database: Adding Geologic Deposits, Proxies, and Tools

NASA Astrophysics Data System (ADS)

Brocko, V. R.; Varner, J.

2007-12-01

A result of collaboration between NOAA's National Geophysical Data Center (NGDC) and the Cooperative Institute for Research in the Environmental Sciences (CIRES), the Global Tsunami Database includes instrumental records, human observations, and now, information inferred from the geologic record. Deep Ocean Assessment and Reporting of Tsunamis (DART) data, historical reports, and information gleaned from published tsunami deposit research build a multi-faceted view of tsunami hazards and their history around the world. Tsunami history provides clues to what might happen in the future, including frequency of occurrence and maximum wave heights. However, instrumental and written records commonly span too little time to reveal the full range of a region's tsunami hazard. The sedimentary deposits of tsunamis, identified with the aid of modern analogs, increasingly complement instrumental and human observations. By adding the component of tsunamis inferred from the geologic record, the Global Tsunami Database extends the record of tsunamis backward in time. Deposit locations, their estimated age and descriptions of the deposits themselves fill in the tsunami record. Tsunamis inferred from proxies, such as evidence for coseismic subsidence, are included to estimate recurrence intervals, but are flagged to highlight the absence of a physical deposit. Authors may submit their own descriptions and upload digital versions of publications. Users may sort by any populated field, including event, location, region, age of deposit, author, publication type (extract information from peer reviewed publications only, if you wish), grain size, composition, presence/absence of plant material. Users may find tsunami deposit references for a given location, event or author; search for particular properties of tsunami deposits; and even identify potential collaborators. Users may also download public-domain documents. Data and information may be viewed using tools designed to extract and display data from the Oracle database (selection forms, Web Map Services, and Web Feature Services). In addition, the historic tsunami archive (along with related earthquakes and volcanic eruptions) is available in KML (Keyhole Markup Language) format for use with Google Earth and similar geo-viewers.

Using Web Database Tools To Facilitate the Construction of Knowledge in Online Courses.

ERIC Educational Resources Information Center

McNeil, Sara G.; Robin, Bernard R.

This paper presents an overview of database tools that dynamically generate World Wide Web materials and focuses on the use of these tools to support research activities, as well as teaching and learning. Database applications have been used in classrooms to support learning activities for over a decade, but, although business and e-commerce have…

Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses.

PubMed

Falagas, Matthew E; Pitsouni, Eleni I; Malietzis, George A; Pappas, Georgios

2008-02-01

The evolution of the electronic age has led to the development of numerous medical databases on the World Wide Web, offering search facilities on a particular subject and the ability to perform citation analysis. We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar. The official Web pages of the databases were used to extract information on the range of journals covered, search facilities and restrictions, and update frequency. We used the example of a keyword search to evaluate the usefulness of these databases in biomedical information retrieval and a specific published article to evaluate their utility in performing citation analysis. All databases were practical in use and offered numerous search facilities. PubMed and Google Scholar are accessed for free. The keyword search with PubMed offers optimal update frequency and includes online early articles; other databases can rate articles by number of citations, as an index of importance. For citation analysis, Scopus offers about 20% more coverage than Web of Science, whereas Google Scholar offers results of inconsistent accuracy. PubMed remains an optimal tool in biomedical electronic research. Scopus covers a wider journal range, of help both in keyword searching and citation analysis, but it is currently limited to recent articles (published after 1995) compared with Web of Science. Google Scholar, as for the Web in general, can help in the retrieval of even the most obscure information but its use is marred by inadequate, less often updated, citation information.

Database Organisation in a Web-Enabled Free and Open-Source Software (foss) Environment for Spatio-Temporal Landslide Modelling

NASA Astrophysics Data System (ADS)

Das, I.; Oberai, K.; Sarathi Roy, P.

2012-07-01

Landslides exhibit themselves in different mass movement processes and are considered among the most complex natural hazards occurring on the earth surface. Making landslide database available online via WWW (World Wide Web) promotes the spreading and reaching out of the landslide information to all the stakeholders. The aim of this research is to present a comprehensive database for generating landslide hazard scenario with the help of available historic records of landslides and geo-environmental factors and make them available over the Web using geospatial Free & Open Source Software (FOSS). FOSS reduces the cost of the project drastically as proprietary software's are very costly. Landslide data generated for the period 1982 to 2009 were compiled along the national highway road corridor in Indian Himalayas. All the geo-environmental datasets along with the landslide susceptibility map were served through WEBGIS client interface. Open source University of Minnesota (UMN) mapserver was used as GIS server software for developing web enabled landslide geospatial database. PHP/Mapscript server-side application serve as a front-end application and PostgreSQL with PostGIS extension serve as a backend application for the web enabled landslide spatio-temporal databases. This dynamic virtual visualization process through a web platform brings an insight into the understanding of the landslides and the resulting damage closer to the affected people and user community. The landslide susceptibility dataset is also made available as an Open Geospatial Consortium (OGC) Web Feature Service (WFS) which can be accessed through any OGC compliant open source or proprietary GIS Software.

Metadata tables to enable dynamic data modeling and web interface design: the SEER example.

PubMed

Weiner, Mark; Sherr, Micah; Cohen, Abigail

2002-04-01

A wealth of information addressing health status, outcomes and resource utilization is compiled and made available by various government agencies. While exploration of the data is possible using existing tools, in general, would-be users of the resources must acquire CD-ROMs or download data from the web, and upload the data into their own database. Where web interfaces exist, they are highly structured, limiting the kinds of queries that can be executed. This work develops a web-based database interface engine whose content and structure is generated through interaction with a metadata table. The result is a dynamically generated web interface that can easily accommodate changes in the underlying data model by altering the metadata table, rather than requiring changes to the interface code. This paper discusses the background and implementation of the metadata table and web-based front end and provides examples of its use with the NCI's Surveillance, Epidemiology and End-Results (SEER) database.

CUNY+ Web: Usability Study of the Web-Based GUI Version of the Bibliographic Database of the City University of New York (CUNY).

ERIC Educational Resources Information Center

Oulanov, Alexei; Pajarillo, Edmund J. Y.

2002-01-01

Describes the usability evaluation of the CUNY (City University of New York) information system in Web and Graphical User Interface (GUI) versions. Compares results to an earlier usability study of the basic information database available on CUNY's wide-area network and describes the applicability of the previous usability instrument to this…

DEEPWATER AND NEARSHORE FOOD WEB CHARACTERIZATIONS IN LAKE SUPERIOR

EPA Science Inventory

Due to the difficulty associated with sampling deep aquatic systems, food web relationships among deepwater fauna are often poorly known. We are characterizing nearshore versus offshore habitats in the Great Lakes and investigating food web linkages among profundal, pelagic, and ...

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.

Dancing girl flap: a new flap suitable for web release.

PubMed

Shinya, K

1999-12-01

To create a deep web, a flap must be designed to have a high elongation effect in one direction along the mid-lateral line of the finger and also to have a shortening effect in the other direction, crossing at a right angle to the mid-lateral line. The dancing girl flap is a modification of a four-flap Z-plasty with two additional Z-plasties. It has a high elongation effect in one direction (>550%) and a shortening effect in the other direction at a right angle (<33%), creating a deep, U-shaped surface. This new flap can be used to release severe scar contracture with a web, and is most suitable for incomplete syndactyly with webs as high as the proximal interphalangeal joint.

Domain-specific Web Service Discovery with Service Class Descriptions

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

Rocco, D; Caverlee, J; Liu, L

2005-02-14

This paper presents DynaBot, a domain-specific web service discovery system. The core idea of the DynaBot service discovery system is to use domain-specific service class descriptions powered by an intelligent Deep Web crawler. In contrast to current registry-based service discovery systems--like the several available UDDI registries--DynaBot promotes focused crawling of the Deep Web of services and discovers candidate services that are relevant to the domain of interest. It uses intelligent filtering algorithms to match services found by focused crawling with the domain-specific service class descriptions. We demonstrate the capability of DynaBot through the BLAST service discovery scenario and describe ourmore » initial experience with DynaBot.« less

A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

PubMed

Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

2012-07-01

The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

Structural modeling of G-protein coupled receptors: An overview on automatic web-servers.

PubMed

Busato, Mirko; Giorgetti, Alejandro

2016-08-01

Despite the significant efforts and discoveries during the last few years in G protein-coupled receptor (GPCR) expression and crystallization, the receptors with known structures to date are limited only to a small fraction of human GPCRs. The lack of experimental three-dimensional structures of the receptors represents a strong limitation that hampers a deep understanding of their function. Computational techniques are thus a valid alternative strategy to model three-dimensional structures. Indeed, recent advances in the field, together with extraordinary developments in crystallography, in particular due to its ability to capture GPCRs in different activation states, have led to encouraging results in the generation of accurate models. This, prompted the community of modelers to render their methods publicly available through dedicated databases and web-servers. Here, we present an extensive overview on these services, focusing on their advantages, drawbacks and their role in successful applications. Future challenges in the field of GPCR modeling, such as the predictions of long loop regions and the modeling of receptor activation states are presented as well. Copyright © 2016 Elsevier Ltd. All rights reserved.

Deep pelagic food web structure as revealed by in situ feeding observations

PubMed Central

Haddock, Steven H. D.; Robison, Bruce H.

2017-01-01

Food web linkages, or the feeding relationships between species inhabiting a shared ecosystem, are an ecological lens through which ecosystem structure and function can be assessed, and thus are fundamental to informing sustainable resource management. Empirical feeding datasets have traditionally been painstakingly generated from stomach content analysis, direct observations and from biochemical trophic markers (stable isotopes, fatty acids, molecular tools). Each approach carries inherent biases and limitations, as well as advantages. Here, using 27 years (1991–2016) of in situ feeding observations collected by remotely operated vehicles (ROVs), we quantitatively characterize the deep pelagic food web of central California within the California Current, complementing existing studies of diet and trophic interactions with a unique perspective. Seven hundred and forty-three independent feeding events were observed with ROVs from near-surface waters down to depths approaching 4000 m, involving an assemblage of 84 different predators and 82 different prey types, for a total of 242 unique feeding relationships. The greatest diversity of prey was consumed by narcomedusae, followed by physonect siphonophores, ctenophores and cephalopods. We highlight key interactions within the poorly understood ‘jelly web’, showing the importance of medusae, ctenophores and siphonophores as key predators, whose ecological significance is comparable to large fish and squid species within the central California deep pelagic food web. Gelatinous predators are often thought to comprise relatively inefficient trophic pathways within marine communities, but we build upon previous findings to document their substantial and integral roles in deep pelagic food webs. PMID:29212727

Digital hand atlas and computer-aided bone age assessment via the Web

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

1999-07-01

A frequently used assessment method of bone age is atlas matching by a radiological examination of a hand image against a reference set of atlas patterns of normal standards. We are in a process of developing a digital hand atlas with a large standard set of normal hand and wrist images that reflect the skeletal maturity, race and sex difference, and current child development. The digital hand atlas will be used for a computer-aided bone age assessment via Web. We have designed and partially implemented a computer-aided diagnostic (CAD) system for Web-based bone age assessment. The system consists of a digital hand atlas, a relational image database and a Web-based user interface. The digital atlas is based on a large standard set of normal hand an wrist images with extracted bone objects and quantitative features. The image database uses a content- based indexing to organize the hand images and their attributes and present to users in a structured way. The Web-based user interface allows users to interact with the hand image database from browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, will be extracted and compared with patterns from the atlas database to assess the bone age. The relevant reference imags and the final assessment report will be sent back to the user's browser via Web. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. In this paper, we present the system design and Web-based client-server model for computer-assisted bone age assessment and our initial implementation of the digital atlas database.

Long-term survival and vitality outcomes of permanent teeth following deep caries treatment with step-wise and partial-caries-removal: A Systematic Review.

PubMed

Hoefler, Vaughan; Nagaoka, Hiroko; Miller, Craig S

2016-11-01

A systematic review was performed to compare the long-term survival of deep dentine caries-affected permanent teeth treated with partial-caries-removal (PCR) versus similar teeth treated with stepwise-caries-removal techniques (SWT). Clinical studies investigating long-term PCR and SWT outcomes in unrestored permanent teeth with deep dentine caries were evaluated. Failures were defined as loss of pulp vitality or restorative failures following treatment. PubMed, Web of Science, Dentistry and Oral Sciences Source, and Central databases were systematically searched. From 136 potentially relevant articles, 9 publications utilizing data from 5 studies (2 RCTs, and 3 observational case-series) reporting outcomes for 426 permanent teeth over two to ten years were analyzed. Regarding restorative failures, >88% success at two years for both techniques was reported. For loss of pulp vitality, observational studies reported >96% vitality at two years for each technique, while one RCT reported significantly higher vitality (p<0.05) at three years for PCR (96%) compared to SWT (83%). Risk of bias was high in all studies. Successful vitality and restorative outcomes for both PCR and SWT have been demonstrated at two years and beyond in permanent teeth with deep dentine caries. Partial-caries-removal may result in fewer pulpal complications over a three year period than SWT, although claims of a therapeutic advantage are based on very few, limited-quality studies. Partial-caries-removal and SWT are deep caries management techniques that reduce pulp exposure risk. Permanent teeth with deep dentine caries treated with either technique have a high likelihood for survival beyond two years. Copyright © 2016 Elsevier Ltd. All rights reserved.

The National Deep-Sea Coral and Sponge Database: A Comprehensive Resource for United States Deep-Sea Coral and Sponge Records

NASA Astrophysics Data System (ADS)

Dornback, M.; Hourigan, T.; Etnoyer, P.; McGuinn, R.; Cross, S. L.

2014-12-01

Research on deep-sea corals has expanded rapidly over the last two decades, as scientists began to realize their value as long-lived structural components of high biodiversity habitats and archives of environmental information. The NOAA Deep Sea Coral Research and Technology Program's National Database for Deep-Sea Corals and Sponges is a comprehensive resource for georeferenced data on these organisms in U.S. waters. The National Database currently includes more than 220,000 deep-sea coral records representing approximately 880 unique species. Database records from museum archives, commercial and scientific bycatch, and from journal publications provide baseline information with relatively coarse spatial resolution dating back as far as 1842. These data are complemented by modern, in-situ submersible observations with high spatial resolution, from surveys conducted by NOAA and NOAA partners. Management of high volumes of modern high-resolution observational data can be challenging. NOAA is working with our data partners to incorporate this occurrence data into the National Database, along with images and associated information related to geoposition, time, biology, taxonomy, environment, provenance, and accuracy. NOAA is also working to link associated datasets collected by our program's research, to properly archive them to the NOAA National Data Centers, to build a robust metadata record, and to establish a standard protocol to simplify the process. Access to the National Database is provided through an online mapping portal. The map displays point based records from the database. Records can be refined by taxon, region, time, and depth. The queries and extent used to view the map can also be used to download subsets of the database. The database, map, and website is already in use by NOAA, regional fishery management councils, and regional ocean planning bodies, but we envision it as a model that can expand to accommodate data on a global scale.

DeepLoc: prediction of protein subcellular localization using deep learning.

PubMed

Almagro Armenteros, José Juan; Sønderby, Casper Kaae; Sønderby, Søren Kaae; Nielsen, Henrik; Winther, Ole

2017-11-01

The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of them, predictions rely on annotation of homologues from knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effects of sequence variants, it is desirable to have methods for predicting protein properties from sequence information only. Here, we present a prediction algorithm using deep neural networks to predict protein subcellular localization relying only on sequence information. At its core, the prediction model uses a recurrent neural network that processes the entire protein sequence and an attention mechanism identifying protein regions important for the subcellular localization. The model was trained and tested on a protein dataset extracted from one of the latest UniProt releases, in which experimentally annotated proteins follow more stringent criteria than previously. We demonstrate that our model achieves a good accuracy (78% for 10 categories; 92% for membrane-bound or soluble), outperforming current state-of-the-art algorithms, including those relying on homology information. The method is available as a web server at http://www.cbs.dtu.dk/services/DeepLoc. Example code is available at https://github.com/JJAlmagro/subcellular_localization. The dataset is available at http://www.cbs.dtu.dk/services/DeepLoc/data.php. jjalma@dtu.dk. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

DeepSite: protein-binding site predictor using 3D-convolutional neural networks.

PubMed

Jiménez, J; Doerr, S; Martínez-Rosell, G; Rose, A S; De Fabritiis, G

2017-10-01

An important step in structure-based drug design consists in the prediction of druggable binding sites. Several algorithms for detecting binding cavities, those likely to bind to a small drug compound, have been developed over the years by clever exploitation of geometric, chemical and evolutionary features of the protein. Here we present a novel knowledge-based approach that uses state-of-the-art convolutional neural networks, where the algorithm is learned by examples. In total, 7622 proteins from the scPDB database of binding sites have been evaluated using both a distance and a volumetric overlap approach. Our machine-learning based method demonstrates superior performance to two other competitive algorithmic strategies. DeepSite is freely available at www.playmolecule.org. Users can submit either a PDB ID or PDB file for pocket detection to our NVIDIA GPU-equipped servers through a WebGL graphical interface. gianni.defabritiis@upf.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

The deep lymphatic anatomy of the hand.

PubMed

Ma, Chuan-Xiang; Pan, Wei-Ren; Liu, Zhi-An; Zeng, Fan-Qiang; Qiu, Zhi-Qiang

2018-07-01

The deep lymphatic anatomy of the hand still remains the least described in medical literature. Eight hands were harvested from four nonembalmed human cadavers amputated above the wrist. A small amount of 6% hydrogen peroxide was employed to detect the lymphatic vessels around the superficial and deep palmar vascular arches, in webs from the index to little fingers, the thenar and hypothenar areas. A 30-gauge needle was inserted into the vessels and injected with a barium sulphate compound. Each specimen was dissected, photographed and radiographed to demonstrate deep lymphatic distribution of the hand. Five groups of deep collecting lymph vessels were found in the hand: superficial palmar arch lymph vessel (SPALV); deep palmar arch lymph vessel (DPALV); thenar lymph vessel (TLV); hypothenar lymph vessel (HTLV); deep finger web lymph vessel (DFWLV). Each group of vessels drained in different directions first, then all turned and ran towards the wrist in different layers. The deep lymphatic drainage of the hand has been presented. The results will provide an anatomical basis for clinical management, educational reference and scientific research. Copyright © 2018 Elsevier GmbH. All rights reserved.

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

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.

COMPUTER-AIDED SCIENCE POLICY ANALYSIS AND RESEARCH (WEBCASPAR)

EPA Science Inventory

WebCASPAR is a database system containing information about academic science and engineering resources and is available on the World Wide Web. Included in the database is information from several of SRS's academic surveys plus information from a variety of other sources, includin...

EpiCollect: linking smartphones to web applications for epidemiology, ecology and community data collection.

PubMed

Aanensen, David M; Huntley, Derek M; Feil, Edward J; al-Own, Fada'a; Spratt, Brian G

2009-09-16

Epidemiologists and ecologists often collect data in the field and, on returning to their laboratory, enter their data into a database for further analysis. The recent introduction of mobile phones that utilise the open source Android operating system, and which include (among other features) both GPS and Google Maps, provide new opportunities for developing mobile phone applications, which in conjunction with web applications, allow two-way communication between field workers and their project databases. Here we describe a generic framework, consisting of mobile phone software, EpiCollect, and a web application located within www.spatialepidemiology.net. Data collected by multiple field workers can be submitted by phone, together with GPS data, to a common web database and can be displayed and analysed, along with previously collected data, using Google Maps (or Google Earth). Similarly, data from the web database can be requested and displayed on the mobile phone, again using Google Maps. Data filtering options allow the display of data submitted by the individual field workers or, for example, those data within certain values of a measured variable or a time period. Data collection frameworks utilising mobile phones with data submission to and from central databases are widely applicable and can give a field worker similar display and analysis tools on their mobile phone that they would have if viewing the data in their laboratory via the web. We demonstrate their utility for epidemiological data collection and display, and briefly discuss their application in ecological and community data collection. Furthermore, such frameworks offer great potential for recruiting 'citizen scientists' to contribute data easily to central databases through their mobile phone.

Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases

PubMed Central

Ahmadi, Maryam; Sarabi, Roghayeh Ershad; Orak, Roohangiz Jamshidi; Bahaadinbeigy, Kambiz

2015-01-01

Background and Aims: The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field. Methods: Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated. Results: The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases. Conclusion: PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles. PMID:26236086

Protein Information Resource: a community resource for expert annotation of protein data

PubMed Central

Barker, Winona C.; Garavelli, John S.; Hou, Zhenglin; Huang, Hongzhan; Ledley, Robert S.; McGarvey, Peter B.; Mewes, Hans-Werner; Orcutt, Bruce C.; Pfeiffer, Friedhelm; Tsugita, Akira; Vinayaka, C. R.; Xiao, Chunlin; Yeh, Lai-Su L.; Wu, Cathy

2001-01-01

The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database. To provide timely and high quality annotation and promote database interoperability, the PIR-International employs rule-based and classification-driven procedures based on controlled vocabulary and standard nomenclature and includes status tags to distinguish experimentally determined from predicted protein features. The database contains about 200 000 non-redundant protein sequences, which are classified into families and superfamilies and their domains and motifs identified. Entries are extensively cross-referenced to other sequence, classification, genome, structure and activity databases. The PIR web site features search engines that use sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. The PIR-Inter­national databases and search tools are accessible on the PIR web site at http://pir.georgetown.edu/ and at the MIPS web site at http://www.mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP. PMID:11125041

Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases.

PubMed

Ahmadi, Maryam; Sarabi, Roghayeh Ershad; Orak, Roohangiz Jamshidi; Bahaadinbeigy, Kambiz

2015-06-01

The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field. Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated. The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases. PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles.

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.

PubMed

Yang, Jian-Hua; Li, Jun-Hao; Jiang, Shan; Zhou, Hui; Qu, Liang-Hu

2013-01-01

Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) represent two classes of important non-coding RNAs in eukaryotes. Although these non-coding RNAs have been implicated in organismal development and in various human diseases, surprisingly little is known about their transcriptional regulation. Recent advances in chromatin immunoprecipitation with next-generation DNA sequencing (ChIP-Seq) have provided methods of detecting transcription factor binding sites (TFBSs) with unprecedented sensitivity. In this study, we describe ChIPBase (http://deepbase.sysu.edu.cn/chipbase/), a novel database that we have developed to facilitate the comprehensive annotation and discovery of transcription factor binding maps and transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. The current release of ChIPBase includes high-throughput sequencing data that were generated by 543 ChIP-Seq experiments in diverse tissues and cell lines from six organisms. By analysing millions of TFBSs, we identified tens of thousands of TF-lncRNA and TF-miRNA regulatory relationships. Furthermore, two web-based servers were developed to annotate and discover transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. In addition, we developed two genome browsers, deepView and genomeView, to provide integrated views of multidimensional data. Moreover, our web implementation supports diverse query types and the exploration of TFs, lncRNAs, miRNAs, gene ontologies and pathways.

Construction and validation of a web-based epidemiological database for inflammatory bowel diseases in Europe An EpiCom study.

PubMed

Burisch, Johan; Cukovic-Cavka, Silvija; Kaimakliotis, Ioannis; Shonová, Olga; Andersen, Vibeke; Dahlerup, Jens F; Elkjaer, Margarita; Langholz, Ebbe; Pedersen, Natalia; Salupere, Riina; Kolho, Kaija-Leena; Manninen, Pia; Lakatos, Peter Laszlo; Shuhaibar, Mary; Odes, Selwyn; Martinato, Matteo; Mihu, Ion; Magro, Fernando; Belousova, Elena; Fernandez, Alberto; Almer, Sven; Halfvarson, Jonas; Hart, Ailsa; Munkholm, Pia

2011-08-01

The EpiCom-study investigates a possible East-West-gradient in Europe in the incidence of IBD and the association with environmental factors. A secured web-based database is used to facilitate and centralize data registration. To construct and validate a web-based inception cohort database available in both English and Russian language. The EpiCom database has been constructed in collaboration with all 34 participating centers. The database was translated into Russian using forward translation, patient questionnaires were translated by simplified forward-backward translation. Data insertion implies fulfillment of international diagnostic criteria, disease activity, medical therapy, quality of life, work productivity and activity impairment, outcome of pregnancy, surgery, cancer and death. Data is secured by the WinLog3 System, developed in cooperation with the Danish Data Protection Agency. Validation of the database has been performed in two consecutive rounds, each followed by corrections in accordance with comments. The EpiCom database fulfills the requirements of the participating countries' local data security agencies by being stored at a single location. The database was found overall to be "good" or "very good" by 81% of the participants after the second validation round and the general applicability of the database was evaluated as "good" or "very good" by 77%. In the inclusion period January 1st -December 31st 2010 1336 IBD patients have been included in the database. A user-friendly, tailor-made and secure web-based inception cohort database has been successfully constructed, facilitating remote data input. The incidence of IBD in 23 European countries can be found at www.epicom-ecco.eu. Copyright © 2011 European Crohn's and Colitis Organisation. All rights reserved.

Distributed Episodic Exploratory Planning (DEEP)

DTIC Science & Technology

2008-12-01

API). For DEEP, Hibernate offered the following advantages: • Abstracts SQL by utilizing HQL so any database with a Java Database Connectivity... Hibernate SQL ICCRTS International Command and Control Research and Technology Symposium JDB Java Distributed Blackboard JDBC Java Database Connectivity...selected because of its opportunistic reasoning capabilities and implemented in Java for platform independence. Java was chosen for ease of

Upgrades to the TPSX Material Properties Database

NASA Technical Reports Server (NTRS)

Squire, T. H.; Milos, F. S.; Partridge, Harry (Technical Monitor)

2001-01-01

The TPSX Material Properties Database is a web-based tool that serves as a database for properties of advanced thermal protection materials. TPSX provides an easy user interface for retrieving material property information in a variety of forms, both graphical and text. The primary purpose and advantage of TPSX is to maintain a high quality source of often used thermal protection material properties in a convenient, easily accessible form, for distribution to government and aerospace industry communities. Last year a major upgrade to the TPSX web site was completed. This year, through the efforts of researchers at several NASA centers, the Office of the Chief Engineer awarded funds to update and expand the databases in TPSX. The FY01 effort focuses on updating correcting the Ames and Johnson thermal protection materials databases. In this session we will summarize the improvements made to the web site last year, report on the status of the on-going database updates, describe the planned upgrades for FY02 and FY03, and provide a demonstration of TPSX.

Village Green Project: Web-accessible Database

EPA Science Inventory

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

The Brainomics/Localizer database.

PubMed

Papadopoulos Orfanos, Dimitri; Michel, Vincent; Schwartz, Yannick; Pinel, Philippe; Moreno, Antonio; Le Bihan, Denis; Frouin, Vincent

2017-01-01

The Brainomics/Localizer database exposes part of the data collected by the in-house Localizer project, which planned to acquire four types of data from volunteer research subjects: anatomical MRI scans, functional MRI data, behavioral and demographic data, and DNA sampling. Over the years, this local project has been collecting such data from hundreds of subjects. We had selected 94 of these subjects for their complete datasets, including all four types of data, as the basis for a prior publication; the Brainomics/Localizer database publishes the data associated with these 94 subjects. Since regulatory rules prevent us from making genetic data available for download, the database serves only anatomical MRI scans, functional MRI data, behavioral and demographic data. To publish this set of heterogeneous data, we use dedicated software based on the open-source CubicWeb semantic web framework. Through genericity in the data model and flexibility in the display of data (web pages, CSV, JSON, XML), CubicWeb helps us expose these complex datasets in original and efficient ways. Copyright © 2015 Elsevier Inc. All rights reserved.

Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

PubMed Central

Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

2012-01-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

CREDO: a structural interactomics database for drug discovery

PubMed Central

Schreyer, Adrian M.; Blundell, Tom L.

2013-01-01

CREDO is a unique relational database storing all pairwise atomic interactions of inter- as well as intra-molecular contacts between small molecules and macromolecules found in experimentally determined structures from the Protein Data Bank. These interactions are integrated with further chemical and biological data. The database implements useful data structures and algorithms such as cheminformatics routines to create a comprehensive analysis platform for drug discovery. The database can be accessed through a web-based interface, downloads of data sets and web services at http://www-cryst.bioc.cam.ac.uk/credo. Database URL: http://www-cryst.bioc.cam.ac.uk/credo PMID:23868908

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.

Content and Accessibility of Shoulder and Elbow Fellowship Web Sites in the United States.

PubMed

Young, Bradley L; Oladeji, Lasun O; Cichos, Kyle; Ponce, Brent

2016-01-01

Increasing numbers of training physicians are using the Internet to gather information about graduate medical education programs. The content and accessibility of web sites that provide this information have been demonstrated to influence applicants' decisions. Assessments of orthopedic fellowship web sites including sports medicine, pediatrics, hand and spine have found varying degrees of accessibility and material. The purpose of this study was to evaluate the accessibility and content of the American Shoulder and Elbow Surgeons (ASES) fellowship web sites (SEFWs). A complete list of ASES programs was obtained from a database on the ASES web site. The accessibility of each SEFWs was assessed by the existence of a functioning link found in the database and through Google®. Then, the following content areas of each SEFWs were evaluated: fellow education, faculty/previous fellow information, and recruitment. At the time of the study, 17 of the 28 (60.7%) ASES programs had web sites accessible through Google®, and only five (17.9%) had functioning links in the ASES database. Nine programs lacked a web site. Concerning web site content, the majority of SEFWs contained information regarding research opportunities, research requirements, case descriptions, meetings and conferences, teaching responsibilities, attending faculty, the application process, and a program description. Fewer than half of the SEFWs provided information regarding rotation schedules, current fellows, previous fellows, on-call expectations, journal clubs, medical school of current fellows, residency of current fellows, employment of previous fellows, current research, and previous research. A large portion of ASES fellowship programs lacked functioning web sites, and even fewer provided functioning links through the ASES database. Valuable information for potential applicants was largely inadequate across present SEFWs.

Accessing the SEED genome databases via Web services API: tools for programmers.

PubMed

Disz, Terry; Akhter, Sajia; Cuevas, Daniel; Olson, Robert; Overbeek, Ross; Vonstein, Veronika; Stevens, Rick; Edwards, Robert A

2010-06-14

The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

Web application for detailed real-time database transaction monitoring for CMS condition data

NASA Astrophysics Data System (ADS)

de Gruttola, Michele; Di Guida, Salvatore; Innocente, Vincenzo; Pierro, Antonio

2012-12-01

In the upcoming LHC era, database have become an essential part for the experiments collecting data from LHC, in order to safely store, and consistently retrieve, a wide amount of data, which are produced by different sources. In the CMS experiment at CERN, all this information is stored in ORACLE databases, allocated in several servers, both inside and outside the CERN network. In this scenario, the task of monitoring different databases is a crucial database administration issue, since different information may be required depending on different users' tasks such as data transfer, inspection, planning and security issues. We present here a web application based on Python web framework and Python modules for data mining purposes. To customize the GUI we record traces of user interactions that are used to build use case models. In addition the application detects errors in database transactions (for example identify any mistake made by user, application failure, unexpected network shutdown or Structured Query Language (SQL) statement error) and provides warning messages from the different users' perspectives. Finally, in order to fullfill the requirements of the CMS experiment community, and to meet the new development in many Web client tools, our application was further developed, and new features were deployed.

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

Comparisons of citations in Web of Science, Scopus, and Google Scholar for articles published in general medical journals.

PubMed

Kulkarni, Abhaya V; Aziz, Brittany; Shams, Iffat; Busse, Jason W

2009-09-09

Until recently, Web of Science was the only database available to track citation counts for published articles. Other databases are now available, but their relative performance has not been established. To compare the citation count profiles of articles published in general medical journals among the citation databases of Web of Science, Scopus, and Google Scholar. Cohort study of 328 articles published in JAMA, Lancet, or the New England Journal of Medicine between October 1, 1999, and March 31, 2000. Total citation counts for each article up to June 2008 were retrieved from Web of Science, Scopus, and Google Scholar. Article characteristics were analyzed in linear regression models to determine interaction with the databases. Number of citations received by an article since publication and article characteristics associated with citation in databases. Google Scholar and Scopus retrieved more citations per article with a median of 160 (interquartile range [IQR], 83 to 324) and 149 (IQR, 78 to 289), respectively, than Web of Science (median, 122; IQR, 66 to 241) (P < .001 for both comparisons). Compared with Web of Science, Scopus retrieved more citations from non-English-language sources (median, 10.2% vs 4.1%) and reviews (30.8% vs 18.2%), and fewer citations from articles (57.2% vs 70.5%), editorials (2.1% vs 5.9%), and letters (0.8% vs 2.6%) (all P < .001). On a log(10)-transformed scale, fewer citations were found in Google Scholar to articles with declared industry funding (nonstandardized regression coefficient, -0.09; 95% confidence interval [CI], -0.15 to -0.03), reporting a study of a drug or medical device (-0.05; 95% CI, -0.11 to 0.01), or with group authorship (-0.29; 95% CI, -0.35 to -0.23). In multivariable analysis, group authorship was the only characteristic that differed among the databases; Google Scholar had significantly fewer citations to group-authored articles (-0.30; 95% CI, -0.36 to -0.23) compared with Web of Science. Web of Science, Scopus, and Google Scholar produced quantitatively and qualitatively different citation counts for articles published in 3 general medical journals.

A radiology department intranet: development and applications.

PubMed

Willing, S J; Berland, L L

1999-01-01

An intranet is a "private Internet" that uses the protocols of the World Wide Web to share information resources within a company or with the company's business partners and clients. The hardware requirements for an intranet begin with a dedicated Web server permanently connected to the departmental network. The heart of a Web server is the hypertext transfer protocol (HTTP) service, which receives a page request from a client's browser and transmits the page back to the client. Although knowledge of hypertext markup language (HTML) is not essential for authoring a Web page, a working familiarity with HTML is useful, as is knowledge of programming and database management. Security can be ensured by using scripts to write information in hidden fields or by means of "cookies." Interfacing databases and database management systems with the Web server and conforming the user interface to HTML syntax can be achieved by means of the common gateway interface (CGI), Active Server Pages (ASP), or other methods. An intranet in a radiology department could include the following types of content: on-call schedules, work schedules and a calendar, a personnel directory, resident resources, memorandums and discussion groups, software for a radiology information system, and databases.

BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers.

PubMed

Meyer, Michael J; Geske, Philip; Yu, Haiyuan

2016-05-15

Biological sequence databases are integral to efforts to characterize and understand biological molecules and share biological data. However, when analyzing these data, scientists are often left holding disparate biological currency-molecular identifiers from different databases. For downstream applications that require converting the identifiers themselves, there are many resources available, but analyzing associated loci and variants can be cumbersome if data is not given in a form amenable to particular analyses. Here we present BISQUE, a web server and customizable command-line tool for converting molecular identifiers and their contained loci and variants between different database conventions. BISQUE uses a graph traversal algorithm to generalize the conversion process for residues in the human genome, genes, transcripts and proteins, allowing for conversion across classes of molecules and in all directions through an intuitive web interface and a URL-based web service. BISQUE is freely available via the web using any major web browser (http://bisque.yulab.org/). Source code is available in a public GitHub repository (https://github.com/hyulab/BISQUE). haiyuan.yu@cornell.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A community effort to construct a gravity database for the United States and an associated Web portal

USGS Publications Warehouse

Keller, Gordon R.; Hildenbrand, T.G.; Kucks, R.; Webring, M.; Briesacher, A.; Rujawitz, K.; Hittleman, A.M.; Roman, D.R.; Winester, D.; Aldouri, R.; Seeley, J.; Rasillo, J.; Torres, R.; Hinze, W. J.; Gates, A.; Kreinovich, V.; Salayandia, L.

2006-01-01

Potential field data (gravity and magnetic measurements) are both useful and costeffective tools for many geologic investigations. Significant amounts of these data are traditionally in the public domain. A new magnetic database for North America was released in 2002, and as a result, a cooperative effort between government agencies, industry, and universities to compile an upgraded digital gravity anomaly database, grid, and map for the conterminous United States was initiated and is the subject of this paper. This database is being crafted into a data system that is accessible through a Web portal. This data system features the database, software tools, and convenient access. The Web portal will enhance the quality and quantity of data contributed to the gravity database that will be a shared community resource. The system's totally digital nature ensures that it will be flexible so that it can grow and evolve as new data, processing procedures, and modeling and visualization tools become available. Another goal of this Web-based data system is facilitation of the efforts of researchers and students who wish to collect data from regions currently not represented adequately in the database. The primary goal of upgrading the United States gravity database and this data system is to provide more reliable data that support societal and scientific investigations of national importance. An additional motivation is the international intent to compile an enhanced North American gravity database, which is critical to understanding regional geologic features, the tectonic evolution of the continent, and other issues that cross national boundaries. ?? 2006 Geological Society of America. All rights reserved.

Combined application versus topical and intravenous application of tranexamic acid following primary total hip arthroplasty: a meta-analysis.

PubMed

Zhang, Pei; Liang, Yuan; Chen, Pengtao; Fang, Yongchao; He, Jinshan; Wang, Jingcheng

2017-02-21

The use of intravenous (IV) or topical tranexamic acid (TXA) in total hip arthroplasty has been proven to be effective and safe in total hip arthroplasty. However, which of these two administration routes is better has not been determined. The combined administration of TXA has been used in total knee arthroplasty with satisfactory results. We hypothesized that combined application of TXA may be the most effective way without increased rate of thrombotic events such as deep vein thrombosis (DVT) and pulmonary embolisms (PE) in patients subjected to primary total hip replacement (THA). A meta-analysis was conducted to compare the efficacy and safety of the combined use of tranexamic acid (TXA) relative to topical or intravenous (IV) use alone for treatment of primary THA. The outcomes included total blood loss, postoperative hemoglobin decline, transfusion rates, and the incidence rates of deep vein thrombosis (DVT) and pulmonary embolisms (PE). We searched electronic databases including PubMed, EMBASE, the Cochrane Library, Web of Science, the Chinese Biomedical Literature database, the CNKI database, and Wanfang Data until September 2016. The references of the included articles were also checked for additional potentially relevant studies. There were no language restrictions for the search. The data of the included studies were analyzed using RevMan 5.3 software. Seven studies met the inclusion criteria, encompassing a total of 1762 patients. Our meta-analysis demonstrated that total blood loss, postoperative hemoglobin decline, and transfusion rates were significantly lower for patients that received the combined treatment compared to patients that received either topical or intravenous administration of TXA. No statistical differences were found in the incidence of deep venous thrombosis (DVT) or pulmonary embolism (PE). The group that received the combined treatment had lower total blood loss, postoperative hemoglobin decline, and transfusion rates without an increased rate of thrombotic events (DVT or PE). The topical or intravenous use of TXA in primary THA is generally considered to be safe and effective. This meta-analysis demonstrated that combined TXA application may be superior to topical or intravenous application of TXA alone. However, larger, high-quality randomized control trials are required for greater confidence in this finding.

7 CFR 3430.55 - Technical reporting.

Code of Federal Regulations, 2010 CFR

2010-01-01

... the Current Research Information System (CRIS). (b) Initial Documentation in the CRIS Database... identification of equipment purchased with any Federal funds under the award and any subsequent use of such equipment. (e) CRIS Web Site Via Internet. The CRIS database is available to the public on the worldwide web...

Online Islamic Organizations and Measuring Web Effectiveness

DTIC Science & Technology

2004-12-01

Internet Research 13 (2003) : 17-26. Retrived from ProQuest online database on 15 May 2004. Lee, Jae-Kwan. “A model for monitoring public sector...Web site strategy.” Internet Research : Electronic Networking Applications and Policy 13 (2003) : 259-266. Retrieved from Emerad online database on

CliniWeb: managing clinical information on the World Wide Web.

PubMed

Hersh, W R; Brown, K E; Donohoe, L C; Campbell, E M; Horacek, A E

1996-01-01

The World Wide Web is a powerful new way to deliver on-line clinical information, but several problems limit its value to health care professionals: content is highly distributed and difficult to find, clinical information is not separated from non-clinical information, and the current Web technology is unable to support some advanced retrieval capabilities. A system called CliniWeb has been developed to address these problems. CliniWeb is an index to clinical information on the World Wide Web, providing a browsing and searching interface to clinical content at the level of the health care student or provider. Its database contains a list of clinical information resources on the Web that are indexed by terms from the Medical Subject Headings disease tree and retrieved with the assistance of SAPHIRE. Limitations of the processes used to build the database are discussed, together with directions for future research.

Information System through ANIS at CeSAM

NASA Astrophysics Data System (ADS)

Moreau, C.; Agneray, F.; Gimenez, S.

2015-09-01

ANIS (AstroNomical Information System) is a web generic tool developed at CeSAM to facilitate and standardize the implementation of astronomical data of various kinds through private and/or public dedicated Information Systems. The architecture of ANIS is composed of a database server which contains the project data, a web user interface template which provides high level services (search, extract and display imaging and spectroscopic data using a combination of criteria, an object list, a sql query module or a cone search interfaces), a framework composed of several packages, and a metadata database managed by a web administration entity. The process to implement a new ANIS instance at CeSAM is easy and fast : the scientific project has to submit data or a data secure access, the CeSAM team installs the new instance (web interface template and the metadata database), and the project administrator can configure the instance with the web ANIS-administration entity. Currently, the CeSAM offers through ANIS a web access to VO compliant Information Systems for different projects (HeDaM, HST-COSMOS, CFHTLS-ZPhots, ExoDAT,...).

Analysis Tool Web Services from the EMBL-EBI.

PubMed

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-07-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

Analysis Tool Web Services from the EMBL-EBI

PubMed Central

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-01-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods. PMID:23671338

GALT protein database, a bioinformatics resource for the management and analysis of structural features of a galactosemia-related protein and its mutants.

PubMed

d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

2009-06-01

We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-1-phosphate uridyltransferase (GALT) involved in the genetic disease named galactosemia type I. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http://bioinformatica.isa.cnr.it/GALT/.

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

PubMed

Miao, Zhichao; Westhof, Eric

2016-07-08

RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on: http://ahsoka.u-strasbg.fr/rbscorenbench/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

S/MARt DB: a database on scaffold/matrix attached regions.

PubMed

Liebich, Ines; Bode, Jürgen; Frisch, Matthias; Wingender, Edgar

2002-01-01

S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct submissions is also available. S/MARt DB is closely linked to the TRANSFAC database on transcription factors and their binding sites. It is freely accessible through the World Wide Web (http://transfac.gbf.de/SMARtDB/) for non-profit research.

Working with Data: Discovering Knowledge through Mining and Analysis; Systematic Knowledge Management and Knowledge Discovery; Text Mining; Methodological Approach in Discovering User Search Patterns through Web Log Analysis; Knowledge Discovery in Databases Using Formal Concept Analysis; Knowledge Discovery with a Little Perspective.

ERIC Educational Resources Information Center

Qin, Jian; Jurisica, Igor; Liddy, Elizabeth D.; Jansen, Bernard J; Spink, Amanda; Priss, Uta; Norton, Melanie J.

2000-01-01

These six articles discuss knowledge discovery in databases (KDD). Topics include data mining; knowledge management systems; applications of knowledge discovery; text and Web mining; text mining and information retrieval; user search patterns through Web log analysis; concept analysis; data collection; and data structure inconsistency. (LRW)

Corporate Web Sites in Traditional Print Advertisements.

ERIC Educational Resources Information Center

Pardun, Carol J.; Lamb, Larry

1999-01-01

Describes the Web presence in print advertisements to determine how marketers are creating bridges between traditional advertising and the Internet. Content analysis showed Web addresses in print ads; categories of advertisers most likely to link print ads with Web sites; and whether the Web site attempts to develop a database of potential…

The Protein Disease Database of human body fluids: II. Computer methods and data issues.

PubMed

Lemkin, P F; Orr, G A; Goldstein, M P; Creed, G J; Myrick, J E; Merril, C R

1995-01-01

The Protein Disease Database (PDD) is a relational database of proteins and diseases. With this database it is possible to screen for quantitative protein abnormalities associated with disease states. These quantitative relationships use data drawn from the peer-reviewed biomedical literature. Assays may also include those observed in high-resolution electrophoretic gels that offer the potential to quantitate many proteins in a single test as well as data gathered by enzymatic or immunologic assays. We are using the Internet World Wide Web (WWW) and the Web browser paradigm as an access method for wide distribution and querying of the Protein Disease Database. The WWW hypertext transfer protocol and its Common Gateway Interface make it possible to build powerful graphical user interfaces that can support easy-to-use data retrieval using query specification forms or images. The details of these interactions are totally transparent to the users of these forms. Using a client-server SQL relational database, user query access, initial data entry and database maintenance are all performed over the Internet with a Web browser. We discuss the underlying design issues, mapping mechanisms and assumptions that we used in constructing the system, data entry, access to the database server, security, and synthesis of derived two-dimensional gel image maps and hypertext documents resulting from SQL database searches.

Diabetic retinopathy screening using deep neural network.

PubMed

Ramachandran, Nishanthan; Hong, Sheng Chiong; Sime, Mary J; Wilson, Graham A

2017-09-07

There is a burgeoning interest in the use of deep neural network in diabetic retinal screening. To determine whether a deep neural network could satisfactorily detect diabetic retinopathy that requires referral to an ophthalmologist from a local diabetic retinal screening programme and an international database. Retrospective audit. Diabetic retinal photos from Otago database photographed during October 2016 (485 photos), and 1200 photos from Messidor international database. Receiver operating characteristic curve to illustrate the ability of a deep neural network to identify referable diabetic retinopathy (moderate or worse diabetic retinopathy or exudates within one disc diameter of the fovea). Area under the receiver operating characteristic curve, sensitivity and specificity. For detecting referable diabetic retinopathy, the deep neural network had an area under receiver operating characteristic curve of 0.901 (95% confidence interval 0.807-0.995), with 84.6% sensitivity and 79.7% specificity for Otago and 0.980 (95% confidence interval 0.973-0.986), with 96.0% sensitivity and 90.0% specificity for Messidor. This study has shown that a deep neural network can detect referable diabetic retinopathy with sensitivities and specificities close to or better than 80% from both an international and a domestic (New Zealand) database. We believe that deep neural networks can be integrated into community screening once they can successfully detect both diabetic retinopathy and diabetic macular oedema. © 2017 Royal Australian and New Zealand College of Ophthalmologists.

Enhanced DIII-D Data Management Through a Relational Database

NASA Astrophysics Data System (ADS)

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

2000-10-01

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

From Local to EXtreme Environments (FLEXE): Promoting Earth Systems Science Literacy Through Student Inquiry and Real Data

NASA Astrophysics Data System (ADS)

Goehring, E. C.; Carlsen, W.; Larsen, J.; Simms, E.; Smith, M.

2007-12-01

From Local to EXtreme Environments (FLEXE) is an innovative new project of the GLOBE Program that involves middle and high school students in systematic, facilitated analyses and comparisons of real environmental data. Through FLEXE, students collect and analyze data from various sources, including the multi-year GLOBE database, deep-sea scientific research projects, and direct measurements of the local environment collected by students using GLOBE sampling protocols. Initial FLEXE materials and training have focused on student understanding of energy transfer through components of the Earth system, including a comparison of how local environmental conditions differ from those found at deep-sea hydrothermal vent communities. While the importance of data acquisition, accuracy and replication is emphasized, FLEXE is also uniquely structured to deepen students' understanding of multiple aspects of the process and nature of science, including written communication of results and on-line peer review. Analyses of data are facilitated through structured, web-based interactions and culminating activities with at-sea scientists through an online forum. The project benefits from the involvement of a professional evaluator, and as the model is tested and refined, it may serve as a template for the inclusion of additional "extreme" earth systems. FLEXE is a partnership of the international GLOBE web- based education program and the NSF Ridge 2000 mid-ocean ridge and hydrothermal vent research program, and includes the expertise of the Center for Science and the Schools at Penn State University. International collaborators also include the InterRidge and ChEss international research programs.

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

PubMed

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.

PubMed

Ochoa, Rodrigo; Davies, Mark; Papadatos, George; Atkinson, Francis; Overington, John P

2014-01-15

myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

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.

Keeping Dublin Core Simple: Cross-Domain Discovery or Resource Description?; First Steps in an Information Commerce Economy: Digital Rights Management in the Emerging E-Book Environment; Interoperability: Digital Rights Management and the Emerging EBook Environment; Searching the Deep Web: Direct Query Engine Applications at the Department of Energy.

ERIC Educational Resources Information Center

Lagoze, Carl; Neylon, Eamonn; Mooney, Stephen; Warnick, Walter L.; Scott, R. L.; Spence, Karen J.; Johnson, Lorrie A.; Allen, Valerie S.; Lederman, Abe

2001-01-01

Includes four articles that discuss Dublin Core metadata, digital rights management and electronic books, including interoperability; and directed query engines, a type of search engine designed to access resources on the deep Web that is being used at the Department of Energy. (LRW)

Designing a Relational Database for the Basic School; Schools Command Web Enabled Officer and Enlisted Database (Sword)

DTIC Science & Technology

2002-06-01

Student memo for personnel MCLLS . . . . . . . . . . . . . . 75 i. Migrate data to SQL Server...The Web Server is on the same server as the SWORD database in the current version. 4: results set 5: dynamic HTML page 6: dynamic HTML page 3: SQL ...still be supported by Access. SQL Server would be a more viable tool for a fully developed application based on the number of potential users and

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.

Faculty Views of Open Web Resource Use by College Students

ERIC Educational Resources Information Center

Tomaiuolo, Nicholas G.

2005-01-01

This article assesses both the extent of students' use of open Web resources and library subscription databases and professors' satisfaction with that use as reported by a survey of 120 community college and university English faculty. It was concluded that although library budgets allocate significant funds to offer subscription databases,…

A Web-Based Tool to Support Data-Based Early Intervention Decision Making

ERIC Educational Resources Information Center

Buzhardt, Jay; Greenwood, Charles; Walker, Dale; Carta, Judith; Terry, Barbara; Garrett, Matthew

2010-01-01

Progress monitoring and data-based intervention decision making have become key components of providing evidence-based early childhood special education services. Unfortunately, there is a lack of tools to support early childhood service providers' decision-making efforts. The authors describe a Web-based system that guides service providers…

Using Web-based Tutorials To Enhance Library Instruction.

ERIC Educational Resources Information Center

Kocour, Bruce G.

2000-01-01

Describes the development of a Web site for library instruction at Carson-Newman College (TN) and its integration into English composition courses. Describes the use of a virtual tour, a tutorial on database searching, tutorials on specific databases, and library guides to specific disciplines to create an effective mechanism for active learning.…

Development of a Relational Database for Learning Management Systems

ERIC Educational Resources Information Center

Deperlioglu, Omer; Sarpkaya, Yilmaz; Ergun, Ertugrul

2011-01-01

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

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 ...

Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

PubMed

Manyam, Ganiraju; Payton, Michelle A; Roth, Jack A; Abruzzo, Lynne V; Coombes, Kevin R

2012-07-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. Copyright © 2012 Elsevier Inc. All rights reserved.

Footprint Database and web services for the Herschel space observatory

NASA Astrophysics Data System (ADS)

Verebélyi, Erika; Dobos, László; Kiss, Csaba

2015-08-01

Using all telemetry and observational meta-data, we created a searchable database of Herschel observation footprints. Data from the Herschel space observatory is freely available for everyone but no uniformly processed catalog of all observations has been published yet. As a first step, we unified the data model for all three Herschel instruments in all observation modes and compiled a database of sky coverage information. As opposed to methods using a pixellation of the sphere, in our database, sky coverage is stored in exact geometric form allowing for precise area calculations. Indexing of the footprints allows for very fast search among observations based on pointing, time, sky coverage overlap and meta-data. This enables us, for example, to find moving objects easily in Herschel fields. The database is accessible via a web site and also as a set of REST web service functions which makes it usable from program clients like Python or IDL scripts. Data is available in various formats including Virtual Observatory standards.

76 FR 67456 - Common Formats for Patient Safety Data Collection and Event Reporting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-01

... Common Formats, can be accessed electronically at the following HHS Web site: http://www.PSO.AHRQ.gov... Thromboembolism (VTE), which includes Deep Vein Thrombosis (DVT) and Pulmonary Embolism (PE), will apply to both... available at the PSO Privacy Protection Center (PPC) Web site: https://www.psoppc.org/web/patientsafety...

Development of Web-based Distributed Cooperative Development Environmentof Sign-Language Animation System and its Evaluation

NASA Astrophysics Data System (ADS)

Yuizono, Takaya; Hara, Kousuke; Nakayama, Shigeru

A web-based distributed cooperative development environment of sign-language animation system has been developed. We have extended the system from the previous animation system that was constructed as three tiered system which consists of sign-language animation interface layer, sign-language data processing layer, and sign-language animation database. Two components of a web client using VRML plug-in and web servlet are added to the previous system. The systems can support humanoid-model avatar for interoperability, and can use the stored sign language animation data shared on the database. It is noted in the evaluation of this system that the inverse kinematics function of web client improves the sign-language animation making.

Semantic SenseLab: implementing the vision of the Semantic Web in neuroscience

PubMed Central

Samwald, Matthias; Chen, Huajun; Ruttenberg, Alan; Lim, Ernest; Marenco, Luis; Miller, Perry; Shepherd, Gordon; Cheung, Kei-Hoi

2011-01-01

Summary Objective Integrative neuroscience research needs a scalable informatics framework that enables semantic integration of diverse types of neuroscience data. This paper describes the use of the Web Ontology Language (OWL) and other Semantic Web technologies for the representation and integration of molecular-level data provided by several of SenseLab suite of neuroscience databases. Methods Based on the original database structure, we semi-automatically translated the databases into OWL ontologies with manual addition of semantic enrichment. The SenseLab ontologies are extensively linked to other biomedical Semantic Web resources, including the Subcellular Anatomy Ontology, Brain Architecture Management System, the Gene Ontology, BIRNLex and UniProt. The SenseLab ontologies have also been mapped to the Basic Formal Ontology and Relation Ontology, which helps ease interoperability with many other existing and future biomedical ontologies for the Semantic Web. In addition, approaches to representing contradictory research statements are described. The SenseLab ontologies are designed for use on the Semantic Web that enables their integration into a growing collection of biomedical information resources. Conclusion We demonstrate that our approach can yield significant potential benefits and that the Semantic Web is rapidly becoming mature enough to realize its anticipated promises. The ontologies are available online at http://neuroweb.med.yale.edu/senselab/ PMID:20006477

Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience.

PubMed

Samwald, Matthias; Chen, Huajun; Ruttenberg, Alan; Lim, Ernest; Marenco, Luis; Miller, Perry; Shepherd, Gordon; Cheung, Kei-Hoi

2010-01-01

Integrative neuroscience research needs a scalable informatics framework that enables semantic integration of diverse types of neuroscience data. This paper describes the use of the Web Ontology Language (OWL) and other Semantic Web technologies for the representation and integration of molecular-level data provided by several of SenseLab suite of neuroscience databases. Based on the original database structure, we semi-automatically translated the databases into OWL ontologies with manual addition of semantic enrichment. The SenseLab ontologies are extensively linked to other biomedical Semantic Web resources, including the Subcellular Anatomy Ontology, Brain Architecture Management System, the Gene Ontology, BIRNLex and UniProt. The SenseLab ontologies have also been mapped to the Basic Formal Ontology and Relation Ontology, which helps ease interoperability with many other existing and future biomedical ontologies for the Semantic Web. In addition, approaches to representing contradictory research statements are described. The SenseLab ontologies are designed for use on the Semantic Web that enables their integration into a growing collection of biomedical information resources. We demonstrate that our approach can yield significant potential benefits and that the Semantic Web is rapidly becoming mature enough to realize its anticipated promises. The ontologies are available online at http://neuroweb.med.yale.edu/senselab/. 2009 Elsevier B.V. All rights reserved.

Application of the Coastal and Marine Ecological Classification Standard to ROV Video Data for Enhanced Analysis of Deep-Sea Habitats in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Ruby, C.; Skarke, A. D.; Mesick, S.

2016-02-01

The Coastal and Marine Ecological Classification Standard (CMECS) is a network of common nomenclature that provides a comprehensive framework for organizing physical, biological, and chemical information about marine ecosystems. It was developed by the National Oceanic and Atmospheric Administration (NOAA) Coastal Services Center, in collaboration with other feral agencies and academic institutions, as a means for scientists to more easily access, compare, and integrate marine environmental data from a wide range of sources and time frames. CMECS has been endorsed by the Federal Geographic Data Committee (FGDC) as a national metadata standard. The research presented here is focused on the application of CMECS to deep-sea video and environmental data collected by the NOAA ROV Deep Discoverer and the NOAA Ship Okeanos Explorer in the Gulf of Mexico in 2011-2014. Specifically, a spatiotemporal index of the physical, chemical, biological, and geological features observed in ROV video records was developed in order to allow scientist, otherwise unfamiliar with the specific content of existing video data, to rapidly determine the abundance and distribution of features of interest, and thus evaluate the applicability of those video data to their research. CMECS units (setting, component, or modifier) for seafloor images extracted from high-definition ROV video data were established based upon visual assessment as well as analysis of coincident environmental sensor (temperature, conductivity), navigation (ROV position, depth, attitude), and log (narrative dive summary) data. The resulting classification units were integrated into easily searchable textual and geo-databases as well as an interactive web map. The spatial distribution and associations of deep-sea habitats as indicated by CMECS classifications are described and optimized methodological approaches for application of CMECS to deep-sea video and environmental data are presented.

Development of a web database portfolio system with PACS connectivity for undergraduate health education and continuing professional development.

PubMed

Ng, Curtise K C; White, Peter; McKay, Janice C

2009-04-01

Increasingly, the use of web database portfolio systems is noted in medical and health education, and for continuing professional development (CPD). However, the functions of existing systems are not always aligned with the corresponding pedagogy and hence reflection is often lost. This paper presents the development of a tailored web database portfolio system with Picture Archiving and Communication System (PACS) connectivity, which is based on the portfolio pedagogy. Following a pre-determined portfolio framework, a system model with the components of web, database and mail servers, server side scripts, and a Query/Retrieve (Q/R) broker for conversion between Hypertext Transfer Protocol (HTTP) requests and Q/R service class of Digital Imaging and Communication in Medicine (DICOM) standard, is proposed. The system was piloted with seventy-seven volunteers. A tailored web database portfolio system (http://radep.hti.polyu.edu.hk) was developed. Technological arrangements for reinforcing portfolio pedagogy include popup windows (reminders) with guidelines and probing questions of 'collect', 'select' and 'reflect' on evidence of development/experience, limitation in the number of files (evidence) to be uploaded, the 'Evidence Insertion' functionality to link the individual uploaded artifacts with reflective writing, capability to accommodate diversity of contents and convenient interfaces for reviewing portfolios and communication. Evidence to date suggests the system supports users to build their portfolios with sound hypertext reflection under a facilitator's guidance, and with reviewers to monitor students' progress providing feedback and comments online in a programme-wide situation.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

PubMed

Katayama, Toshiaki; Arakawa, Kazuharu; Nakao, Mitsuteru; Ono, Keiichiro; Aoki-Kinoshita, Kiyoko F; Yamamoto, Yasunori; Yamaguchi, Atsuko; Kawashima, Shuichi; Chun, Hong-Woo; Aerts, Jan; Aranda, Bruno; Barboza, Lord Hendrix; Bonnal, Raoul Jp; Bruskiewich, Richard; Bryne, Jan C; Fernández, José M; Funahashi, Akira; Gordon, Paul Mk; Goto, Naohisa; Groscurth, Andreas; Gutteridge, Alex; Holland, Richard; Kano, Yoshinobu; Kawas, Edward A; Kerhornou, Arnaud; Kibukawa, Eri; Kinjo, Akira R; Kuhn, Michael; Lapp, Hilmar; Lehvaslaiho, Heikki; Nakamura, Hiroyuki; Nakamura, Yasukazu; Nishizawa, Tatsuya; Nobata, Chikashi; Noguchi, Tamotsu; Oinn, Thomas M; Okamoto, Shinobu; Owen, Stuart; Pafilis, Evangelos; Pocock, Matthew; Prins, Pjotr; Ranzinger, René; Reisinger, Florian; Salwinski, Lukasz; Schreiber, Mark; Senger, Martin; Shigemoto, Yasumasa; Standley, Daron M; Sugawara, Hideaki; Tashiro, Toshiyuki; Trelles, Oswaldo; Vos, Rutger A; Wilkinson, Mark D; York, William; Zmasek, Christian M; Asai, Kiyoshi; Takagi, Toshihisa

2010-08-21

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

PubMed Central

2010-01-01

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies. PMID:20727200

Java Web Simulation (JWS); a web based database of kinetic models.

PubMed

Snoep, J L; Olivier, B G

2002-01-01

Software to make a database of kinetic models accessible via the internet has been developed and a core database has been set up at http://jjj.biochem.sun.ac.za/. This repository of models, available to everyone with internet access, opens a whole new way in which we can make our models public. Via the database, a user can change enzyme parameters and run time simulations or steady state analyses. The interface is user friendly and no additional software is necessary. The database currently contains 10 models, but since the generation of the program code to include new models has largely been automated the addition of new models is straightforward and people are invited to submit their models to be included in the database.

Citations and the h index of soil researchers and journals in the Web of Science, Scopus, and Google Scholar

PubMed Central

Hartemink, Alfred E.; McBratney, Alex; Jang, Ho-Jun

2013-01-01

Citation metrics and h indices differ using different bibliometric databases. We compiled the number of publications, number of citations, h index and year since the first publication from 340 soil researchers from all over the world. On average, Google Scholar has the highest h index, number of publications and citations per researcher, and the Web of Science the lowest. The number of papers in Google Scholar is on average 2.3 times higher and the number of citations is 1.9 times higher compared to the data in the Web of Science. Scopus metrics are slightly higher than that of the Web of Science. The h index in Google Scholar is on average 1.4 times larger than Web of Science, and the h index in Scopus is on average 1.1 times larger than Web of Science. Over time, the metrics increase in all three databases but fastest in Google Scholar. The h index of an individual soil scientist is about 0.7 times the number of years since his/her first publication. There is a large difference between the number of citations, number of publications and the h index using the three databases. From this analysis it can be concluded that the choice of the database affects widely-used citation and evaluation metrics but that bibliometric transfer functions exist to relate the metrics from these three databases. We also investigated the relationship between journal’s impact factor and Google Scholar’s h5-index. The h5-index is a better measure of a journal’s citation than the 2 or 5 year window impact factor. PMID:24167778

Citations and the h index of soil researchers and journals in the Web of Science, Scopus, and Google Scholar.

PubMed

Minasny, Budiman; Hartemink, Alfred E; McBratney, Alex; Jang, Ho-Jun

2013-01-01

Citation metrics and h indices differ using different bibliometric databases. We compiled the number of publications, number of citations, h index and year since the first publication from 340 soil researchers from all over the world. On average, Google Scholar has the highest h index, number of publications and citations per researcher, and the Web of Science the lowest. The number of papers in Google Scholar is on average 2.3 times higher and the number of citations is 1.9 times higher compared to the data in the Web of Science. Scopus metrics are slightly higher than that of the Web of Science. The h index in Google Scholar is on average 1.4 times larger than Web of Science, and the h index in Scopus is on average 1.1 times larger than Web of Science. Over time, the metrics increase in all three databases but fastest in Google Scholar. The h index of an individual soil scientist is about 0.7 times the number of years since his/her first publication. There is a large difference between the number of citations, number of publications and the h index using the three databases. From this analysis it can be concluded that the choice of the database affects widely-used citation and evaluation metrics but that bibliometric transfer functions exist to relate the metrics from these three databases. We also investigated the relationship between journal's impact factor and Google Scholar's h5-index. The h5-index is a better measure of a journal's citation than the 2 or 5 year window impact factor.

Sea Level Station Metadata for Tsunami Detection, Warning and Research

NASA Astrophysics Data System (ADS)

Stroker, K. J.; Marra, J.; Kari, U. S.; Weinstein, S. A.; Kong, L.

2007-12-01

The devastating earthquake and tsunami of December 26, 2004 has greatly increased recognition of the need for water level data both from the coasts and the deep-ocean. In 2006, the National Oceanic and Atmospheric Administration (NOAA) completed a Tsunami Data Management Report describing the management of data required to minimize the impact of tsunamis in the United States. One of the major gaps defined in this report is the access to global coastal water level data. NOAA's National Geophysical Data Center (NGDC) and National Climatic Data Center (NCDC) are working cooperatively to bridge this gap. NOAA relies on a network of global data, acquired and processed in real-time to support tsunami detection and warning, as well as high-quality global databases of archived data to support research and advanced scientific modeling. In 2005, parties interested in enhancing the access and use of sea level station data united under the NOAA NCDC's Integrated Data and Environmental Applications (IDEA) Center's Pacific Region Integrated Data Enterprise (PRIDE) program to develop a distributed metadata system describing sea level stations (Kari et. al., 2006; Marra et.al., in press). This effort started with pilot activities in a regional framework and is targeted at tsunami detection and warning systems being developed by various agencies. It includes development of the components of a prototype sea level station metadata web service and accompanying Google Earth-based client application, which use an XML-based schema to expose, at a minimum, information in the NOAA National Weather Service (NWS) Pacific Tsunami Warning Center (PTWC) station database needed to use the PTWC's Tide Tool application. As identified in the Tsunami Data Management Report, the need also exists for long-term retention of the sea level station data. NOAA envisions that the retrospective water level data and metadata will also be available through web services, using an XML-based schema. Five high-priority metadata requirements identified at a water level workshop held at the XXIV IUGG Meeting in Perugia will be addressed: consistent, validated, and well defined numbers (e.g. amplitude); exact location of sea level stations; a complete record of sea level data stored in the archive; identifying high-priority sea level stations; and consistent definitions. NOAA's National Geophysical Data Center (NGDC) and co-located World Data Center for Solid Earth Geophysics (including tsunamis) would hold the archive of the sea level station data and distribute the standard metadata. Currently, NGDC is also archiving and distributing the DART buoy deep-ocean water level data and metadata in standards based formats. Kari, Uday S., John J. Marra, Stuart A. Weinstein, 2006 A Tsunami Focused Data Sharing Framework For Integration of Databases that Describe Water Level Station Specifications. AGU Fall Meeting, 2006. San Francisco, California. Marra, John, J., Uday S. Kari, and Stuart A. Weinstein (in press). A Tsunami Detection and Warning-focused Sea Level Station Metadata Web Service. IUGG XXIV, July 2-13, 2007. Perugia, Italy.

The Next Linear Collider Program

Science.gov Websites

Navbar Other Address Books: Laboratory Phone/Email Web Directory SLAC SLAC Phonebook Entire SLAC Web FNAL Telephone Directory Fermilab Search LLNL Phone Book LLNL Web Servers LBNL Directory Services Web Search: A-Z Index KEK E-mail Database Research Projects NLC Website Search: Entire SLAC Web | Help

78 FR 42775 - CGI Federal, Inc., and Custom Applications Management; Transfer of Data

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-17

... develop applications, Web sites, Web pages, web-based applications and databases, in accordance with EPA policies and related Federal standards and procedures. The Contractor will provide [[Page 42776

CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization.

PubMed

Frias, Silvia; Bryan, Kenneth; Brinkman, Fiona S L; Lynn, David J

2015-01-01

CerebralWeb is a light-weight JavaScript plug-in that extends Cytoscape.js to enable fast and interactive visualization of molecular interaction networks stratified based on subcellular localization or other user-supplied annotation. The application is designed to be easily integrated into any website and is configurable to support customized network visualization. CerebralWeb also supports the automatic retrieval of Cerebral-compatible localizations for human, mouse and bovine genes via a web service and enables the automated parsing of Cytoscape compatible XGMML network files. CerebralWeb currently supports embedded network visualization on the InnateDB (www.innatedb.com) and Allergy and Asthma Portal (allergen.innatedb.com) database and analysis resources. Database tool URL: http://www.innatedb.com/CerebralWeb © The Author(s) 2015. Published by Oxford University Press.

Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network

PubMed Central

Sward, Katherine A; Newth, Christopher JL; Khemani, Robinder G; Cryer, Martin E; Thelen, Julie L; Enriquez, Rene; Shaoyu, Su; Pollack, Murray M; Harrison, Rick E; Meert, Kathleen L; Berg, Robert A; Wessel, David L; Shanley, Thomas P; Dalton, Heidi; Carcillo, Joseph; Jenkins, Tammara L; Dean, J Michael

2015-01-01

Objectives To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality. Material and Methods Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers. Results Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation. Conclusions Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes. PMID:25796596

TOPSAN: a dynamic web database for structural genomics.

PubMed

Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John

2011-01-01

The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.

The IVTANTHERMO-Online database for thermodynamic properties of individual substances with web interface

NASA Astrophysics Data System (ADS)

Belov, G. V.; Dyachkov, S. A.; Levashov, P. R.; Lomonosov, I. V.; Minakov, D. V.; Morozov, I. V.; Sineva, M. A.; Smirnov, V. N.

2018-01-01

The database structure, main features and user interface of an IVTANTHERMO-Online system are reviewed. This system continues the series of the IVTANTHERMO packages developed in JIHT RAS. It includes the database for thermodynamic properties of individual substances and related software for analysis of experimental results, data fitting, calculation and estimation of thermodynamical functions and thermochemistry quantities. In contrast to the previous IVTANTHERMO versions it has a new extensible database design, the client-server architecture, a user-friendly web interface with a number of new features for online and offline data processing.

Very Deep Convolutional Neural Networks for Morphologic Classification of Erythrocytes.

PubMed

Durant, Thomas J S; Olson, Eben M; Schulz, Wade L; Torres, Richard

2017-12-01

Morphologic profiling of the erythrocyte population is a widely used and clinically valuable diagnostic modality, but one that relies on a slow manual process associated with significant labor cost and limited reproducibility. Automated profiling of erythrocytes from digital images by capable machine learning approaches would augment the throughput and value of morphologic analysis. To this end, we sought to evaluate the performance of leading implementation strategies for convolutional neural networks (CNNs) when applied to classification of erythrocytes based on morphology. Erythrocytes were manually classified into 1 of 10 classes using a custom-developed Web application. Using recent literature to guide architectural considerations for neural network design, we implemented a "very deep" CNN, consisting of >150 layers, with dense shortcut connections. The final database comprised 3737 labeled cells. Ensemble model predictions on unseen data demonstrated a harmonic mean of recall and precision metrics of 92.70% and 89.39%, respectively. Of the 748 cells in the test set, 23 misclassification errors were made, with a correct classification frequency of 90.60%, represented as a harmonic mean across the 10 morphologic classes. These findings indicate that erythrocyte morphology profiles could be measured with a high degree of accuracy with "very deep" CNNs. Further, these data support future efforts to expand classes and optimize practical performance in a clinical environment as a prelude to full implementation as a clinical tool. © 2017 American Association for Clinical Chemistry.

STEPPE: Supporting collaborative research and education on Earth's deep-time sedimentary crust.

NASA Astrophysics Data System (ADS)

Smith, D. M.

2014-12-01

STEPPE—Sedimentary geology, Time, Environment, Paleontology, Paleoclimate, and Energy—is a National Science Foundation supported consortium whose mission is to promote multidisciplinary research and education on Earth's deep-time sedimentary crust. Deep-time sedimentary crust research includes many specialty areas—biology, geography, ecology, paleontology, sedimentary geology, stratigraphy, geochronology, paleoclimatology, sedimentary geochemistry, and more. In fact, the diversity of disciplines and size of the community (roughly one-third of Earth-science faculty in US universities) itself has been a barrier to the formation of collaborative, multidisciplinary teams in the past. STEPPE has been working to support new research synergies and the development of infrastructure that will encourage the community to think about the big problems that need to be solved and facilitate the formation of collaborative research teams to tackle these problems. Toward this end, STEPPE is providing opportunities for workshops, working groups and professional development training sessions, web-hosting and database services and an online collaboration platform that facilitates interaction among participants, the sharing of documentation and workflows and an ability to push news and reports to group participants and beyond using social media tools. As such, STEPPE is working to provide an interactive space that will serve as both a gathering place and clearinghouse for information, allowing for broader integration of research and education across all STEPPE-related sub disciplines.

Integrating Radar Image Data with Google Maps

NASA Technical Reports Server (NTRS)

Chapman, Bruce D.; Gibas, Sarah

2010-01-01

A public Web site has been developed as a method for displaying the multitude of radar imagery collected by NASA s Airborne Synthetic Aperture Radar (AIRSAR) instrument during its 16-year mission. Utilizing NASA s internal AIRSAR site, the new Web site features more sophisticated visualization tools that enable the general public to have access to these images. The site was originally maintained at NASA on six computers: one that held the Oracle database, two that took care of the software for the interactive map, and three that were for the Web site itself. Several tasks were involved in moving this complicated setup to just one computer. First, the AIRSAR database was migrated from Oracle to MySQL. Then the back-end of the AIRSAR Web site was updated in order to access the MySQL database. To do this, a few of the scripts needed to be modified; specifically three Perl scripts that query that database. The database connections were then updated from Oracle to MySQL, numerous syntax errors were corrected, and a query was implemented that replaced one of the stored Oracle procedures. Lastly, the interactive map was designed, implemented, and tested so that users could easily browse and access the radar imagery through the Google Maps interface.

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

DOE PAGES

Zerkin, V. V.; Pritychenko, B.

2018-02-04

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ~22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented in this paper. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. Finally,more » it is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.« less

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

NASA Astrophysics Data System (ADS)

Zerkin, V. V.; Pritychenko, B.

2018-04-01

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ∼22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. It is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.

ADASS Web Database XML Project

NASA Astrophysics Data System (ADS)

Barg, M. I.; Stobie, E. B.; Ferro, A. J.; O'Neil, E. J.

In the spring of 2000, at the request of the ADASS Program Organizing Committee (POC), we began organizing information from previous ADASS conferences in an effort to create a centralized database. The beginnings of this database originated from data (invited speakers, participants, papers, etc.) extracted from HyperText Markup Language (HTML) documents from past ADASS host sites. Unfortunately, not all HTML documents are well formed and parsing them proved to be an iterative process. It was evident at the beginning that if these Web documents were organized in a standardized way, such as XML (Extensible Markup Language), the processing of this information across the Web could be automated, more efficient, and less error prone. This paper will briefly review the many programming tools available for processing XML, including Java, Perl and Python, and will explore the mapping of relational data from our MySQL database to XML.

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

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

Zerkin, V. V.; Pritychenko, B.

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ~22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented in this paper. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. Finally,more » it is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.« less

76 FR 50171 - Notice of Intent To Prepare an Environmental Impact Statement for the Henrys Fork Salinity...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-12

... following methods: Government-wide rulemaking Web site: http://www.regulations.gov . Follow the instructions... irrigation system improvements outlined in this plan will provide more efficient use of this water. Deep... reduction of excess deep percolation passing below the plant root zone. Deep percolation of irrigation water...

FHWA Deep Foundation Load Test Database Version 2.0 User Manual

DOT National Transportation Integrated Search

2016-09-01

The Federal Highway Administration (FHWA) began the development of the first version of the Deep Foundation Load Test Database (DFLTD) in the 1980s. Over 1,500 load tests were collected and stored for various types of piles and drilled shafts in diff...

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination.

PubMed

Hancock, David; Wilson, Michael; Velarde, Giles; Morrison, Norman; Hayes, Andrew; Hulme, Helen; Wood, A Joseph; Nashar, Karim; Kell, Douglas B; Brass, Andy

2005-11-03

maxdLoad2 is a relational database schema and Java application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool. maxdLoad2 presents an easy-to-use interface to an underlying relational database and provides a full complement of facilities for browsing, searching and editing. There is a tree-based visualization of data connectivity and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them. Its principle novel features are: the flexibility of the meta-data that can be captured, the tools provided for importing data from spreadsheets and other tabular representations, the tools provided for the automatic creation of structured documents, the ability to browse and access the data via web and web-services interfaces. Within maxdLoad2 it is very straightforward to customise the meta-data that is being captured or change the definitions of the meta-data. These meta-data definitions are stored within the database itself allowing client software to connect properly to a modified database without having to be specially configured. The meta-data definitions (configuration file) can also be centralized allowing changes made in response to revisions of standards or terminologies to be propagated to clients without user intervention.maxdBrowse is hosted on a web-server and presents multiple interfaces to the contents of maxd databases. maxdBrowse emulates many of the browse and search features available in the maxdLoad2 application via a web-browser. This allows users who are not familiar with maxdLoad2 to browse and export microarray data from the database for their own analysis. The same browse and search features are also available via command-line and SOAP server interfaces. This both enables scripting of data export for use embedded in data repositories and analysis environments, and allows access to the maxd databases via web-service architectures. maxdLoad2 http://www.bioinf.man.ac.uk/microarray/maxd/ and maxdBrowse http://dbk.ch.umist.ac.uk/maxdBrowse are portable and compatible with all common operating systems and major database servers. They provide a powerful, flexible package for annotation of microarray experiments and a convenient dissemination environment. They are available for download and open sourced under the Artistic License.

Nuclear Science References Database

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

Pritychenko, B., E-mail: pritychenko@bnl.gov; Běták, E.; Singh, B.

2014-06-15

The Nuclear Science References (NSR) database together with its associated Web interface, is the world's only comprehensive source of easily accessible low- and intermediate-energy nuclear physics bibliographic information for more than 210,000 articles since the beginning of nuclear science. The weekly-updated NSR database provides essential support for nuclear data evaluation, compilation and research activities. The principles of the database and Web application development and maintenance are described. Examples of nuclear structure, reaction and decay applications are specifically included. The complete NSR database is freely available at the websites of the National Nuclear Data Center (http://www.nndc.bnl.gov/nsr) and the International Atomic Energymore » Agency (http://www-nds.iaea.org/nsr)« less

A web based relational database management system for filariasis control

PubMed Central

Murty, Upadhyayula Suryanarayana; Kumar, Duvvuri Venkata Rama Satya; Sriram, Kumaraswamy; Rao, Kadiri Madhusudhan; Bhattacharyulu, Chakravarthula Hayageeva Narasimha Venakata; Praveen, Bhoopathi; Krishna, Amirapu Radha

2005-01-01

The present study describes a RDBMS (relational database management system) for the effective management of Filariasis, a vector borne disease. Filariasis infects 120 million people from 83 countries. The possible re-emergence of the disease and the complexity of existing control programs warrant the development of new strategies. A database containing comprehensive data associated with filariasis finds utility in disease control. We have developed a database containing information on the socio-economic status of patients, mosquito collection procedures, mosquito dissection data, filariasis survey report and mass blood data. The database can be searched using a user friendly web interface. Availability http://www.webfil.org (login and password can be obtained from the authors) PMID:17597846

Digital hand atlas for web-based bone age assessment: system design and implementation

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

2000-04-01

A frequently used assessment method of skeletal age is atlas matching by a radiological examination of a hand image against a small set of Greulich-Pyle patterns of normal standards. The method however can lead to significant deviation in age assessment, due to a variety of observers with different levels of training. The Greulich-Pyle atlas based on middle upper class white populations in the 1950s, is also not fully applicable for children of today, especially regarding the standard development in other racial groups. In this paper, we present our system design and initial implementation of a digital hand atlas and computer-aided diagnostic (CAD) system for Web-based bone age assessment. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. The system consists of a hand atlas database, a CAD module and a Java-based Web user interface. The atlas database is based on a large set of clinically normal hand images of diverse ethnic groups. The Java-based Web user interface allows users to interact with the hand image database form browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, is then extracted and compared with patterns from the atlas database to assess the bone age.

Globe Teachers Guide and Photographic Data on the Web

NASA Technical Reports Server (NTRS)

Kowal, Dan

2004-01-01

The task of managing the GLOBE Online Teacher s Guide during this time period focused on transforming the technology behind the delivery system of this document. The web application transformed from a flat file retrieval system to a dynamic database access approach. The new methodology utilizes Java Server Pages (JSP) on the front-end and an Oracle relational database on the backend. This new approach allows users of the web site, mainly teachers, to access content efficiently by grade level and/or by investigation or educational concept area. Moreover, teachers can gain easier access to data sheets and lab and field guides. The new online guide also included updated content for all GLOBE protocols. The GLOBE web management team was given documentation for maintaining the new application. Instructions for modifying the JSP templates and managing database content were included in this document. It was delivered to the team by the end of October, 2003. The National Geophysical Data Center (NGDC) continued to manage the school study site photos on the GLOBE website. 333 study site photo images were added to the GLOBE database and posted on the web during this same time period for 64 schools. Documentation for processing study site photos was also delivered to the new GLOBE web management team. Lastly, assistance was provided in transferring reference applications such as the Cloud and LandSat quizzes and Earth Systems Online Poster from NGDC servers to GLOBE servers along with documentation for maintaining these applications.

Workflow and web application for annotating NCBI BioProject transcriptome data

PubMed Central

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A.; Barrero, Luz S.; Landsman, David

2017-01-01

Abstract The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. Database URL: http://www.ncbi.nlm.nih.gov/projects/physalis/ PMID:28605765

GMODWeb: a web framework for the generic model organism database

PubMed Central

O'Connor, Brian D; Day, Allen; Cain, Scott; Arnaiz, Olivier; Sperling, Linda; Stein, Lincoln D

2008-01-01

The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD project designed to speed the development of model organism database (MOD) websites. Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types. GMODWeb was built using the open source Turnkey web framework and is available from . PMID:18570664

NNDC Stand: Activities and Services of the National Nuclear Data Center

NASA Astrophysics Data System (ADS)

Pritychenko, B.; Arcilla, R.; Burrows, T. W.; Dunford, C. L.; Herman, M. W.; McLane, V.; Obložinský, P.; Sonzogni, A. A.; Tuli, J. K.; Winchell, D. F.

2005-05-01

The National Nuclear Data Center (NNDC) collects, evaluates, and disseminates nuclear physics data for basic nuclear research, applied nuclear technologies including energy, shielding, medical and homeland security. In 2004, to answer the needs of nuclear data users community, NNDC completed a project to modernize data storage and management of its databases and began offering new nuclear data Web services. The principles of database and Web application development as well as related nuclear reaction and structure database services are briefly described.

Accounting Data to Web Interface Using PERL

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

Hargeaves, C

2001-08-13

This document will explain the process to create a web interface for the accounting information generated by the High Performance Storage Systems (HPSS) accounting report feature. The accounting report contains useful data but it is not easily accessed in a meaningful way. The accounting report is the only way to see summarized storage usage information. The first step is to take the accounting data, make it meaningful and store the modified data in persistent databases. The second step is to generate the various user interfaces, HTML pages, that will be used to access the data. The third step is tomore » transfer all required files to the web server. The web pages pass parameters to Common Gateway Interface (CGI) scripts that generate dynamic web pages and graphs. The end result is a web page with specific information presented in text with or without graphs. The accounting report has a specific format that allows the use of regular expressions to verify if a line is storage data. Each storage data line is stored in a detailed database file with a name that includes the run date. The detailed database is used to create a summarized database file that also uses run date in its name. The summarized database is used to create the group.html web page that includes a list of all storage users. Scripts that query the database folder to build a list of available databases generate two additional web pages. A master script that is run monthly as part of a cron job, after the accounting report has completed, manages all of these individual scripts. All scripts are written in the PERL programming language. Whenever possible data manipulation scripts are written as filters. All scripts are written to be single source, which means they will function properly on both the open and closed networks at LLNL. The master script handles the command line inputs for all scripts, file transfers to the web server and records run information in a log file. The rest of the scripts manipulate the accounting data or use the files created to generate HTML pages. Each script will be described in detail herein. The following is a brief description of HPSS taken directly from an HPSS web site. ''HPSS is a major development project, which began in 1993 as a Cooperative Research and Development Agreement (CRADA) between government and industry. The primary objective of HPSS is to move very large data objects between high performance computers, workstation clusters, and storage libraries at speeds many times faster than is possible with today's software systems. For example, HPSS can manage parallel data transfers from multiple network-connected disk arrays at rates greater than 1 Gbyte per second, making it possible to access high definition digitized video in real time.'' The HPSS accounting report is a canned report whose format is controlled by the HPSS developers.« less

Underwater Web Work

ERIC Educational Resources Information Center

Wighting, Mervyn J.; Lucking, Robert A.; Christmann, Edwin P.

2004-01-01

Teachers search for ways to enhance oceanography units in the classroom. There are many online resources available to help one explore the mysteries of the deep. This article describes a collection of Web sites on this topic appropriate for middle level classrooms.

Comprehensive mollusk acute toxicity database improves the use of Interspecies Correlation Estimation (ICE) models to predict toxicity of untested freshwater and endangered mussel species

EPA Science Inventory

Interspecies correlation estimation (ICE) models extrapolate acute toxicity data from surrogate test species to untested taxa. A suite of ICE models developed from a comprehensive database is available on the US Environmental Protection Agency’s web-based application, Web-I...

WaveNet: A Web-Based Metocean Data Access, Processing and Analysis Tool; Part 5 - WW3 Database

DTIC Science & Technology

2015-02-01

Program ( CDIP ); and Part 4 for the Great Lakes Observing System/Coastal Forecasting System (GLOS/GLCFS). Using step-by-step instructions, this Part 5...Demirbilek, Z., L. Lin, and D. Wilson. 2014a. WaveNet: A web-based metocean data access, processing, and analysis tool; part 3– CDIP database

Web-Resources for Astronomical Data in the Ultraviolet

NASA Astrophysics Data System (ADS)

Sachkov, M. E.; Malkov, O. Yu.

2017-12-01

In this paper we describe databases of space projects that are operating or have operated in the ultraviolet spectral region. We give brief descriptions and links to major sources for UV data on the web: archives, space mission sites, databases, catalogues. We pay special attention to the World Space Observatory—Ultraviolet mission that will be launched in 2021.

The Common Gateway Interface (CGI) for Enhancing Access to Database Servers via the World Wide Web (WWW).

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Explains the Common Gateway Interface (CGI) protocol as a set of rules for passing information from a Web server to an external program such as a database search engine. Topics include advantages over traditional client/server solutions, limitations, sample library applications, and sources of information from the Internet. (LRW)

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

ERIC Educational Resources Information Center

Jukic, Nenad; Gray, Paul

2008-01-01

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

40 CFR 60.2235 - In what form can I submit my reports?

Code of Federal Regulations, 2013 CFR

2013-07-01

... with ERT are subject to this requirement to be submitted electronically into EPA's WebFIRE database... tests required by this subpart to EPA's WebFIRE database by using the Compliance and Emissions Data...FIRE Administrator, MD C404-02, 4930 Old Page Rd., Durham, NC 27703. The same ERT file with the CBI...

PathCase-SB architecture and database design

PubMed Central

2011-01-01

Background Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. Description PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database. Conclusions PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world. PMID:22070889

FERN Ethnomedicinal Plant Database: Exploring Fern Ethnomedicinal Plants Knowledge for Computational Drug Discovery.

PubMed

Thakar, Sambhaji B; Ghorpade, Pradnya N; Kale, Manisha V; Sonawane, Kailas D

2015-01-01

Fern plants are known for their ethnomedicinal applications. Huge amount of fern medicinal plants information is scattered in the form of text. Hence, database development would be an appropriate endeavor to cope with the situation. So by looking at the importance of medicinally useful fern plants, we developed a web based database which contains information about several group of ferns, their medicinal uses, chemical constituents as well as protein/enzyme sequences isolated from different fern plants. Fern ethnomedicinal plant database is an all-embracing, content management web-based database system, used to retrieve collection of factual knowledge related to the ethnomedicinal fern species. Most of the protein/enzyme sequences have been extracted from NCBI Protein sequence database. The fern species, family name, identification, taxonomy ID from NCBI, geographical occurrence, trial for, plant parts used, ethnomedicinal importance, morphological characteristics, collected from various scientific literatures and journals available in the text form. NCBI's BLAST, InterPro, phylogeny, Clustal W web source has also been provided for the future comparative studies. So users can get information related to fern plants and their medicinal applications at one place. This Fern ethnomedicinal plant database includes information of 100 fern medicinal species. This web based database would be an advantageous to derive information specifically for computational drug discovery, botanists or botanical interested persons, pharmacologists, researchers, biochemists, plant biotechnologists, ayurvedic practitioners, doctors/pharmacists, traditional medicinal users, farmers, agricultural students and teachers from universities as well as colleges and finally fern plant lovers. This effort would be useful to provide essential knowledge for the users about the adventitious applications for drug discovery, applications, conservation of fern species around the world and finally to create social awareness.

Architecture for biomedical multimedia information delivery on the World Wide Web

NASA Astrophysics Data System (ADS)

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

1997-10-01

Research engineers at the National Library of Medicine are building a prototype system for the delivery of multimedia biomedical information on the World Wide Web. This paper discuses the architecture and design considerations for the system, which will be used initially to make images and text from the third National Health and Nutrition Examination Survey (NHANES) publicly available. We categorized our analysis as follows: (1) fundamental software tools: we analyzed trade-offs among use of conventional HTML/CGI, X Window Broadway, and Java; (2) image delivery: we examined the use of unconventional TCP transmission methods; (3) database manager and database design: we discuss the capabilities and planned use of the Informix object-relational database manager and the planned schema for the HNANES database; (4) storage requirements for our Sun server; (5) user interface considerations; (6) the compatibility of the system with other standard research and analysis tools; (7) image display: we discuss considerations for consistent image display for end users. Finally, we discuss the scalability of the system in terms of incorporating larger or more databases of similar data, and the extendibility of the system for supporting content-based retrieval of biomedical images. The system prototype is called the Web-based Medical Information Retrieval System. An early version was built as a Java applet and tested on Unix, PC, and Macintosh platforms. This prototype used the MiniSQL database manager to do text queries on a small database of records of participants in the second NHANES survey. The full records and associated x-ray images were retrievable and displayable on a standard Web browser. A second version has now been built, also a Java applet, using the MySQL database manager.

Great Basin paleontological database

USGS Publications Warehouse

Zhang, N.; Blodgett, R.B.; Hofstra, A.H.

2008-01-01

The U.S. Geological Survey has constructed a paleontological database for the Great Basin physiographic province that can be served over the World Wide Web for data entry, queries, displays, and retrievals. It is similar to the web-database solution that we constructed for Alaskan paleontological data (www.alaskafossil.org). The first phase of this effort was to compile a paleontological bibliography for Nevada and portions of adjacent states in the Great Basin that has recently been completed. In addition, we are also compiling paleontological reports (Known as E&R reports) of the U.S. Geological Survey, which are another extensive source of l,egacy data for this region. Initial population of the database benefited from a recently published conodont data set and is otherwise focused on Devonian and Mississippian localities because strata of this age host important sedimentary exhalative (sedex) Au, Zn, and barite resources and enormons Carlin-type An deposits. In addition, these strata are the most important petroleum source rocks in the region, and record the transition from extension to contraction associated with the Antler orogeny, the Alamo meteorite impact, and biotic crises associated with global oceanic anoxic events. The finished product will provide an invaluable tool for future geologic mapping, paleontological research, and mineral resource investigations in the Great Basin, making paleontological data acquired over nearly the past 150 yr readily available over the World Wide Web. A description of the structure of the database and the web interface developed for this effort are provided herein. This database is being used ws a model for a National Paleontological Database (which we am currently developing for the U.S. Geological Survey) as well as for other paleontological databases now being developed in other parts of the globe. ?? 2008 Geological Society of America.

Inside the Web: A Look at Digital Libraries and the Invisible/Deep Web

ERIC Educational Resources Information Center

Su, Mila C.

2009-01-01

The evolution of the Internet and the World Wide Web continually exceeds expectations with the "swift pace" of technological innovations. Information is added, and just as quickly becomes outdated at a rapid pace. Researchers have found that Digital materials can provide access to primary source materials and connect the researcher to institutions…

The Influence of Surface and Deep Cues on Primary and Secondary School Students' Assessment of Relevance in Web Menus

ERIC Educational Resources Information Center

Rouet, Jean-Francois; Ros, Christine; Goumi, Antonine; Macedo-Rouet, Monica; Dinet, Jerome

2011-01-01

Two experiments investigated primary and secondary school students' Web menu selection strategies using simulated Web search tasks. It was hypothesized that students' selections of websites depend on their perception and integration of multiple relevance cues. More specifically, students should be able to disentangle superficial cues (e.g.,…

A World Wide Web (WWW) server database engine for an organelle database, MitoDat.

PubMed

Lemkin, P F; Chipperfield, M; Merril, C; Zullo, S

1996-03-01

We describe a simple database search engine "dbEngine" which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relationship database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.

Public Release of Pan-STARRS Data

NASA Astrophysics Data System (ADS)

Flewelling, Heather; Consortium, panstarrs

2015-08-01

Pan-STARRS 1 is a 1.8 meter survey telescope, located on Haleakala, Hawaii, with a 1.4 Gigapixel camera, a 7 square degree field of view, and 5 filters (g,r,i,z,y). The public release of data, which is available to everyone, consists of 4 years of data taken between May 2010 and April 2014. Two of the surveys available in the public release are the 3pi survey and the Medium Deep (MD) survey. The 3pi survey has roughly 60 epochs (12 per filter) covering 3/4 of the sky and everything north of -30 degrees declination. The MD survey consists of 10 fields, observed in a couple of filters each night, usually 8 exposures per filter per field, for about 4000 epochs per MD field. The available data product are accessed through the “Postage Stamp Server” and through the Published Science Products Subsystem (PSPS), both of these are available through the Pan-STARRS Science Interface (PSI). The Postage Stamp Server provides images and catalogs for different stages of processing on single exposures, stack images, difference images, and forced photometry. The PSPS is a SQLServer database that can be queried via script or web interface, with a database for each MD field and a large database for the 3pi survey. This database has relative photometry and astrometry and object associations, making it easy to do searches across the entire sky as well as tools to generate lightcurves of individual objects as a function of time.

Antimicrobial photodynamic therapy as an adjunct for treatment of deep carious lesions-A systematic review.

PubMed

Cieplik, Fabian; Buchalla, Wolfgang; Hellwig, Elmar; Al-Ahmad, Ali; Hiller, Karl-Anton; Maisch, Tim; Karygianni, Lamprini

2017-06-01

For deep carious lesions, a more conservative treatment modality ("selective caries removal") has been proposed, where only the heavily contaminated dentine is removed. In this regard, effective adjuncts for cavity disinfection such as the antimicrobial photodynamic therapy (aPDT) can be valuable clinically prior to definitive restoration. Therefore, the aim of this study was to systematically assess clinical studies on the effectiveness of aPDT as a supplementary tool in the treatment of deep caries lesions. Searches were performed in four databases (PubMed, EMBASE, ISI Web of Science, ClinicalTrials.gov) from 1st January, 2011 until 21st June, 2016 for search terms relevant to the observed parameters, pathological condition, intervention and anatomic entity. The pooled information was evaluated according to PRISMA guidelines. At first, 1651 articles were recovered, of which 1249 full-text articles were evaluated, 270 articles thereof were reviewed for eligibility and finally 6 articles met all inclusion criteria. The aPDT protocols involved Methylene Blue, Toluidine Blue and aluminium-chloride-phthalocyanine as photosensitizers and diode lasers, light-emitting diodes and halogen light-sources. The data from five reports, utilizing both culture-dependent and -independent methods, disclosed significant reduction of cariogenic bacterial load after mechanical caries removal with adjunct aPDT. As these studies exhibit some methodological limitations, e.g. lack of positive controls, this systematic review can support the application of aPDT to a limited extent only in terms of reducing the microbial load in deep carious lesions before restorative treatment. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed Central

2010-01-01

Background Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. Results In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. Conclusions CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu. PMID:20946609

The Neotoma Paleoecology Database

NASA Astrophysics Data System (ADS)

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

2015-12-01

The Neotoma Paleoecology Database (www.neotomadb.org) is a multiproxy, open-access, relational database that includes fossil data for the past 5 million years (the late Neogene and Quaternary Periods). Modern distributional data for various organisms are also being made available for calibration and paleoecological analyses. The project is a collaborative effort among individuals from more than 20 institutions worldwide, including domain scientists representing a spectrum of Pliocene-Quaternary fossil data types, as well as experts in information technology. Working groups are active for diatoms, insects, ostracodes, pollen and plant macroscopic remains, testate amoebae, rodent middens, vertebrates, age models, geochemistry and taphonomy. Groups are also active in developing online tools for data analyses and for developing modules for teaching at different levels. A key design concept of NeotomaDB is that stewards for various data types are able to remotely upload and manage data. Cooperatives for different kinds of paleo data, or from different regions, can appoint their own stewards. Over the past year, much progress has been made on development of the steward software-interface that will enable this capability. The steward interface uses web services that provide access to the database. More generally, these web services enable remote programmatic access to the database, which both desktop and web applications can use and which provide real-time access to the most current data. Use of these services can alleviate the need to download the entire database, which can be out-of-date as soon as new data are entered. In general, the Neotoma web services deliver data either from an entire table or from the results of a view. Upon request, new web services can be quickly generated. Future developments will likely expand the spatial and temporal dimensions of the database. NeotomaDB is open to receiving new datasets and stewards from the global Quaternary community. Research is supported by NSF EAR-0622349.

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

PubMed

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

2010-10-07

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

Improving data management and dissemination in web based information systems by semantic enrichment of descriptive data aspects

NASA Astrophysics Data System (ADS)

Gebhardt, Steffen; Wehrmann, Thilo; Klinger, Verena; Schettler, Ingo; Huth, Juliane; Künzer, Claudia; Dech, Stefan

2010-10-01

The German-Vietnamese water-related information system for the Mekong Delta (WISDOM) project supports business processes in Integrated Water Resources Management in Vietnam. Multiple disciplines bring together earth and ground based observation themes, such as environmental monitoring, water management, demographics, economy, information technology, and infrastructural systems. This paper introduces the components of the web-based WISDOM system including data, logic and presentation tier. It focuses on the data models upon which the database management system is built, including techniques for tagging or linking metadata with the stored information. The model also uses ordered groupings of spatial, thematic and temporal reference objects to semantically tag datasets to enable fast data retrieval, such as finding all data in a specific administrative unit belonging to a specific theme. A spatial database extension is employed by the PostgreSQL database. This object-oriented database was chosen over a relational database to tag spatial objects to tabular data, improving the retrieval of census and observational data at regional, provincial, and local areas. While the spatial database hinders processing raster data, a "work-around" was built into WISDOM to permit efficient management of both raster and vector data. The data model also incorporates styling aspects of the spatial datasets through styled layer descriptions (SLD) and web mapping service (WMS) layer specifications, allowing retrieval of rendered maps. Metadata elements of the spatial data are based on the ISO19115 standard. XML structured information of the SLD and metadata are stored in an XML database. The data models and the data management system are robust for managing the large quantity of spatial objects, sensor observations, census and document data. The operational WISDOM information system prototype contains modules for data management, automatic data integration, and web services for data retrieval, analysis, and distribution. The graphical user interfaces facilitate metadata cataloguing, data warehousing, web sensor data analysis and thematic mapping.

The unified database for the fixed target experiment BM@N

NASA Astrophysics Data System (ADS)

Gertsenberger, K. V.

2016-09-01

The article describes the developed database designed as comprehensive data storage of the fixed target experiment BM@N [1] at Joint Institute for Nuclear Research (JINR) in Dubna. The structure and purposes of the BM@N facility will be briefly presented. The scheme of the unified database and its parameters will be described in detail. The use of the BM@N database implemented on the PostgreSQL database management system (DBMS) allows one to provide user access to the actual information of the experiment. Also the interfaces developed for the access to the database will be presented. One was implemented as the set of C++ classes to access the data without SQL statements, the other-Web-interface being available on the Web page of the BM@N experiment.

Katherine Fleming | NREL

Science.gov Websites

Fleming Photo of Katherine Fleming Katherine Fleming Database and Web Applications Engineer and web application development in the Commercial Buildings Research group. Her projects include the , Katherine was pursuing a Ph.D. with a focus on robotics and working as a Web developer and Web accessibility

Content and Workflow Management for Library Websites: Case Studies

ERIC Educational Resources Information Center

Yu, Holly, Ed.

2005-01-01

Using database-driven web pages or web content management (WCM) systems to manage increasingly diverse web content and to streamline workflows is a commonly practiced solution recognized in libraries today. However, limited library web content management models and funding constraints prevent many libraries from purchasing commercially available…

Protecting Database Centric Web Services against SQL/XPath Injection Attacks

NASA Astrophysics Data System (ADS)

Laranjeiro, Nuno; Vieira, Marco; Madeira, Henrique

Web services represent a powerful interface for back-end database systems and are increasingly being used in business critical applications. However, field studies show that a large number of web services are deployed with security flaws (e.g., having SQL Injection vulnerabilities). Although several techniques for the identification of security vulnerabilities have been proposed, developing non-vulnerable web services is still a difficult task. In fact, security-related concerns are hard to apply as they involve adding complexity to already complex code. This paper proposes an approach to secure web services against SQL and XPath Injection attacks, by transparently detecting and aborting service invocations that try to take advantage of potential vulnerabilities. Our mechanism was applied to secure several web services specified by the TPC-App benchmark, showing to be 100% effective in stopping attacks, non-intrusive and very easy to use.

JANIS 4: An Improved Version of the NEA Java-based Nuclear Data Information System

NASA Astrophysics Data System (ADS)

Soppera, N.; Bossant, M.; Dupont, E.

2014-06-01

JANIS is software developed to facilitate the visualization and manipulation of nuclear data, giving access to evaluated data libraries, and to the EXFOR and CINDA databases. It is stand-alone Java software, downloadable from the web and distributed on DVD. Used offline, the system also makes use of an internet connection to access the NEA Data Bank database. It is now also offered as a full web application, only requiring a browser. The features added in the latest version of the software and this new web interface are described.

JANIS 4: An Improved Version of the NEA Java-based Nuclear Data Information System

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

Soppera, N., E-mail: nicolas.soppera@oecd.org; Bossant, M.; Dupont, E.

JANIS is software developed to facilitate the visualization and manipulation of nuclear data, giving access to evaluated data libraries, and to the EXFOR and CINDA databases. It is stand-alone Java software, downloadable from the web and distributed on DVD. Used offline, the system also makes use of an internet connection to access the NEA Data Bank database. It is now also offered as a full web application, only requiring a browser. The features added in the latest version of the software and this new web interface are described.

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

Anderson, Mathew; Bowen, Brian; Coles, Dwight

The Middleware Automated Deployment Utilities consists the these three components: MAD: Utility designed to automate the deployment of java applications to multiple java application servers. The product contains a front end web utility and backend deployment scripts. MAR: Web front end to maintain and update the components inside database. MWR-Encrypt: Web utility to convert a text string to an encrypted string that is used by the Oracle Weblogic application server. The encryption is done using the built in functions if the Oracle Weblogic product and is mainly used to create an encrypted version of a database password.

East-China Geochemistry Database (ECGD):A New Networking Database for North China Craton

NASA Astrophysics Data System (ADS)

Wang, X.; Ma, W.

2010-12-01

North China Craton is one of the best natural laboratories that research some Earth Dynamic questions[1]. Scientists made much progress in research on this area, and got vast geochemistry data, which are essential for answering many fundamental questions about the age, composition, structure, and evolution of the East China area. But the geochemical data have long been accessible only through the scientific literature and theses where they have been widely dispersed, making it difficult for the broad Geosciences community to find, access and efficiently use the full range of available data[2]. How to effectively store, manage, share and reuse the existing geochemical data in the North China Craton area? East-China Geochemistry Database(ECGD) is a networking geochemical scientific database system that has been designed based on WebGIS and relational database for the structured storage and retrieval of geochemical data and geological map information. It is integrated the functions of data retrieval, spatial visualization and online analysis. ECGD focus on three areas: 1.Storage and retrieval of geochemical data and geological map information. Research on the characters of geochemical data, including its composing and connecting of each other, we designed a relational database, which based on geochemical relational data model, to store a variety of geological sample information such as sampling locality, age, sample characteristics, reference, major elements, rare earth elements, trace elements and isotope system et al. And a web-based user-friendly interface is provided for constructing queries. 2.Data view. ECGD is committed to online data visualization by different ways, especially to view data in digital map with dynamic way. Because ECGD was integrated WebGIS technology, the query results can be mapped on digital map, which can be zoomed, translation and dot selection. Besides of view and output query results data by html, txt or xls formats, researchers also can generate classification thematic maps using query results, according different parameters. 3.Data analysis on-line. Here we designed lots of geochemical online analysis tools, including geochemical diagrams, CIPW computing, and so on, which allows researchers to analyze query data without download query results. Operation of all these analysis tools is very easy; users just do it by click mouse one or two time. In summary, ECGD provide a geochemical platform for researchers, whom to know where various data are, to view various data in a synthetic and dynamic way, and analyze interested data online. REFERENCES [1] S. Gao, R.L. Rudnick, and W.L. Xu, “Recycling deep cratonic lithosphere and generation of intraplate magmatism in the North China Craton,” Earth and Planetary Science Letters,270,41-53,2008. [2] K.A. Lehnert, U. Harms, and E. Ito, “Promises, Achievements, and Challenges of Networking Global Geoinformatics Resources - Experiences of GeosciNET and EarthChem,” Geophysical Research Abstracts, Vol.10, EGU2008-A-05242,2008.

Biofuel Database

National Institute of Standards and Technology Data Gateway

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

Automated grading of homework assignments and tests in introductory and intermediate statistics courses using active server pages.

PubMed

Stockburger, D W

1999-05-01

Active server pages permit a software developer to customize the Web experience for users by inserting server-side script and database access into Web pages. This paper describes applications of these techniques and provides a primer on the use of these methods. Applications include a system that generates and grades individualized homework assignments and tests for statistics students. The student accesses the system as a Web page, prints out the assignment, does the assignment, and enters the answers on the Web page. The server, running on NT Server 4.0, grades the assignment, updates the grade book (on a database), and returns the answer key to the student.

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.

Design Considerations for a Web-based Database System of ELISpot Assay in Immunological Research

PubMed Central

Ma, Jingming; Mosmann, Tim; Wu, Hulin

2005-01-01

The enzyme-linked immunospot (ELISpot) assay has been a primary means in immunological researches (such as HIV-specific T cell response). Due to huge amount of data involved in ELISpot assay testing, the database system is needed for efficient data entry, easy retrieval, secure storage, and convenient data process. Besides, the NIH has recently issued a policy to promote the sharing of research data (see http://grants.nih.gov/grants/policy/data_sharing). The Web-based database system will be definitely benefit to data sharing among broad research communities. Here are some considerations for a database system of ELISpot assay (DBSEA). PMID:16779326

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.

PubMed

Kawano, Shin; Watanabe, Tsutomu; Mizuguchi, Sohei; Araki, Norie; Katayama, Toshiaki; Yamaguchi, Atsuko

2014-07-01

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

HepSEQ: International Public Health Repository for Hepatitis B

PubMed Central

Gnaneshan, Saravanamuttu; Ijaz, Samreen; Moran, Joanne; Ramsay, Mary; Green, Jonathan

2007-01-01

HepSEQ is a repository for an extensive library of public health and molecular data relating to hepatitis B virus (HBV) infection collected from international sources. It is hosted by the Centre for Infections, Health Protection Agency (HPA), England, United Kingdom. This repository has been developed as a web-enabled, quality-controlled database to act as a tool for surveillance, HBV case management and for research. The web front-end for the database system can be accessed from . The format of the database system allows for comprehensive molecular, clinical and epidemiological data to be deposited into a functional database, to search and manipulate the stored data and to extract and visualize the information on epidemiological, virological, clinical, nucleotide sequence and mutational aspects of HBV infection through web front-end. Specific tools, built into the database, can be utilized to analyse deposited data and provide information on HBV genotype, identify mutations with known clinical significance (e.g. vaccine escape, precore and antiviral-resistant mutations) and carry out sequence homology searches against other deposited strains. Further mechanisms are also in place to allow specific tailored searches of the database to be undertaken. PMID:17130143

The Physiology Constant Database of Teen-Agers in Beijing

PubMed Central

Wei-Qi, Wei; Guang-Jin, Zhu; Cheng-Li, Xu; Shao-Mei, Han; Bao-Shen, Qi; Li, Chen; Shu-Yu, Zu; Xiao-Mei, Zhou; Wen-Feng, Hu; Zheng-Guo, Zhang

2004-01-01

Physiology constants of adolescents are important to understand growing living systems and are a useful reference in clinical and epidemiological research. Until recently, physiology constants were not available in China and therefore most physiologists, physicians, and nutritionists had to use data from abroad for reference. However, the very difference between the Eastern and Western races casts doubt on the usefulness of overseas data. We have therefore created a database system to provide a repository for the storage of physiology constants of teen-agers in Beijing. The several thousands of pieces of data are now divided into hematological biochemistry, lung function, and cardiac function with all data manually checked before being transferred into the database. The database was accomplished through the development of a web interface, scripts, and a relational database. The physiology data were integrated into the relational database system to provide flexible facilities by using combinations of various terms and parameters. A web browser interface was designed for the users to facilitate their searching. The database is available on the web. The statistical table, scatter diagram, and histogram of the data are available for both anonym and user according to queries, while only the user can achieve detail, including download data and advanced search. PMID:15258669

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

PubMed

Dogrusoz, U; Erson, E Z; Giral, E; Demir, E; Babur, O; Cetintas, A; Colak, R

2006-02-01

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

A Web-Based Multi-Database System Supporting Distributed Collaborative Management and Sharing of Microarray Experiment Information

PubMed Central

Burgarella, Sarah; Cattaneo, Dario; Masseroli, Marco

2006-01-01

We developed MicroGen, a multi-database Web based system for managing all the information characterizing spotted microarray experiments. It supports information gathering and storing according to the Minimum Information About Microarray Experiments (MIAME) standard. It also allows easy sharing of information and data among all multidisciplinary actors involved in spotted microarray experiments. PMID:17238488

Resources | Division of Cancer Prevention

Cancer.gov

Manual of Operations Version 3, 12/13/2012 (PDF, 162KB) Database Sources Consortium for Functional Glycomics databases Design Studies Related to the Development of Distributed, Web-based European Carbohydrate Databases (EUROCarbDB) |

NABIC marker database: A molecular markers information network of agricultural crops.

PubMed

Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

2013-01-01

In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

Coverage and quality: A comparison of Web of Science and Scopus databases for reporting faculty nursing publication metrics.

PubMed

Powell, Kimberly R; Peterson, Shenita R

Web of Science and Scopus are the leading databases of scholarly impact. Recent studies outside the field of nursing report differences in journal coverage and quality. A comparative analysis of nursing publications reported impact. Journal coverage by each database for the field of nursing was compared. Additionally, publications by 2014 nursing faculty were collected in both databases and compared for overall coverage and reported quality, as modeled by Scimajo Journal Rank, peer review status, and MEDLINE inclusion. Individual author impact, modeled by the h-index, was calculated by each database for comparison. Scopus offered significantly higher journal coverage. For 2014 faculty publications, 100% of journals were found in Scopus, Web of Science offered 82%. No significant difference was found in the quality of reported journals. Author h-index was found to be higher in Scopus. When reporting faculty publications and scholarly impact, academic nursing programs may be better represented by Scopus, without compromising journal quality. Programs with strong interdisciplinary work should examine all areas of strength to ensure appropriate coverage. Copyright © 2017 Elsevier Inc. All rights reserved.

Distributed spatial information integration based on web service

NASA Astrophysics Data System (ADS)

Tong, Hengjian; Zhang, Yun; Shao, Zhenfeng

2008-10-01

Spatial information systems and spatial information in different geographic locations usually belong to different organizations. They are distributed and often heterogeneous and independent from each other. This leads to the fact that many isolated spatial information islands are formed, reducing the efficiency of information utilization. In order to address this issue, we present a method for effective spatial information integration based on web service. The method applies asynchronous invocation of web service and dynamic invocation of web service to implement distributed, parallel execution of web map services. All isolated information islands are connected by the dispatcher of web service and its registration database to form a uniform collaborative system. According to the web service registration database, the dispatcher of web services can dynamically invoke each web map service through an asynchronous delegating mechanism. All of the web map services can be executed at the same time. When each web map service is done, an image will be returned to the dispatcher. After all of the web services are done, all images are transparently overlaid together in the dispatcher. Thus, users can browse and analyze the integrated spatial information. Experiments demonstrate that the utilization rate of spatial information resources is significantly raised thought the proposed method of distributed spatial information integration.

Distributed spatial information integration based on web service

NASA Astrophysics Data System (ADS)

Tong, Hengjian; Zhang, Yun; Shao, Zhenfeng

2009-10-01

Spatial information systems and spatial information in different geographic locations usually belong to different organizations. They are distributed and often heterogeneous and independent from each other. This leads to the fact that many isolated spatial information islands are formed, reducing the efficiency of information utilization. In order to address this issue, we present a method for effective spatial information integration based on web service. The method applies asynchronous invocation of web service and dynamic invocation of web service to implement distributed, parallel execution of web map services. All isolated information islands are connected by the dispatcher of web service and its registration database to form a uniform collaborative system. According to the web service registration database, the dispatcher of web services can dynamically invoke each web map service through an asynchronous delegating mechanism. All of the web map services can be executed at the same time. When each web map service is done, an image will be returned to the dispatcher. After all of the web services are done, all images are transparently overlaid together in the dispatcher. Thus, users can browse and analyze the integrated spatial information. Experiments demonstrate that the utilization rate of spatial information resources is significantly raised thought the proposed method of distributed spatial information integration.

Phynx: an open source software solution supporting data management and web-based patient-level data review for drug safety studies in the general practice research database and other health care databases.

PubMed

Egbring, Marco; Kullak-Ublick, Gerd A; Russmann, Stefan

2010-01-01

To develop a software solution that supports management and clinical review of patient data from electronic medical records databases or claims databases for pharmacoepidemiological drug safety studies. We used open source software to build a data management system and an internet application with a Flex client on a Java application server with a MySQL database backend. The application is hosted on Amazon Elastic Compute Cloud. This solution named Phynx supports data management, Web-based display of electronic patient information, and interactive review of patient-level information in the individual clinical context. This system was applied to a dataset from the UK General Practice Research Database (GPRD). Our solution can be setup and customized with limited programming resources, and there is almost no extra cost for software. Access times are short, the displayed information is structured in chronological order and visually attractive, and selected information such as drug exposure can be blinded. External experts can review patient profiles and save evaluations and comments via a common Web browser. Phynx provides a flexible and economical solution for patient-level review of electronic medical information from databases considering the individual clinical context. It can therefore make an important contribution to an efficient validation of outcome assessment in drug safety database studies.

EVpedia: a community web portal for extracellular vesicles research.

PubMed

Kim, Dae-Kyum; Lee, Jaewook; Kim, Sae Rom; Choi, Dong-Sic; Yoon, Yae Jin; Kim, Ji Hyun; Go, Gyeongyun; Nhung, Dinh; Hong, Kahye; Jang, Su Chul; Kim, Si-Hyun; Park, Kyong-Su; Kim, Oh Youn; Park, Hyun Taek; Seo, Ji Hye; Aikawa, Elena; Baj-Krzyworzeka, Monika; van Balkom, Bas W M; Belting, Mattias; Blanc, Lionel; Bond, Vincent; Bongiovanni, Antonella; Borràs, Francesc E; Buée, Luc; Buzás, Edit I; Cheng, Lesley; Clayton, Aled; Cocucci, Emanuele; Dela Cruz, Charles S; Desiderio, Dominic M; Di Vizio, Dolores; Ekström, Karin; Falcon-Perez, Juan M; Gardiner, Chris; Giebel, Bernd; Greening, David W; Gross, Julia Christina; Gupta, Dwijendra; Hendrix, An; Hill, Andrew F; Hill, Michelle M; Nolte-'t Hoen, Esther; Hwang, Do Won; Inal, Jameel; Jagannadham, Medicharla V; Jayachandran, Muthuvel; Jee, Young-Koo; Jørgensen, Malene; Kim, Kwang Pyo; Kim, Yoon-Keun; Kislinger, Thomas; Lässer, Cecilia; Lee, Dong Soo; Lee, Hakmo; van Leeuwen, Johannes; Lener, Thomas; Liu, Ming-Lin; Lötvall, Jan; Marcilla, Antonio; Mathivanan, Suresh; Möller, Andreas; Morhayim, Jess; Mullier, François; Nazarenko, Irina; Nieuwland, Rienk; Nunes, Diana N; Pang, Ken; Park, Jaesung; Patel, Tushar; Pocsfalvi, Gabriella; Del Portillo, Hernando; Putz, Ulrich; Ramirez, Marcel I; Rodrigues, Marcio L; Roh, Tae-Young; Royo, Felix; Sahoo, Susmita; Schiffelers, Raymond; Sharma, Shivani; Siljander, Pia; Simpson, Richard J; Soekmadji, Carolina; Stahl, Philip; Stensballe, Allan; Stępień, Ewa; Tahara, Hidetoshi; Trummer, Arne; Valadi, Hadi; Vella, Laura J; Wai, Sun Nyunt; Witwer, Kenneth; Yáñez-Mó, María; Youn, Hyewon; Zeidler, Reinhard; Gho, Yong Song

2015-03-15

Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research. The web site was implemented in PHP, Java, MySQL and Apache, and is freely available at http://evpedia.info. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Integration of multiple DICOM Web servers into an enterprise-wide Web-based electronic medical record

NASA Astrophysics Data System (ADS)

Stewart, Brent K.; Langer, Steven G.; Martin, Kelly P.

1999-07-01

The purpose of this paper is to integrate multiple DICOM image webservers into the currently existing enterprises- wide web-browsable electronic medical record. Over the last six years the University of Washington has created a clinical data repository combining in a distributed relational database information from multiple departmental databases (MIND). A character cell-based view of this data called the Mini Medical Record (MMR) has been available for four years, MINDscape, unlike the text-based MMR. provides a platform independent, dynamic, web browser view of the MIND database that can be easily linked with medical knowledge resources on the network, like PubMed and the Federated Drug Reference. There are over 10,000 MINDscape user accounts at the University of Washington Academic Medical Centers. The weekday average number of hits to MINDscape is 35,302 and weekday average number of individual users is 1252. DICOM images from multiple webservers are now being viewed through the MINDscape electronic medical record.

Capturing citation activity in three health sciences departments: a comparison study of Scopus and Web of Science.

PubMed

Sarkozy, Alexandra; Slyman, Alison; Wu, Wendy

2015-01-01

Scopus and Web of Science are the two major citation databases that collect and disseminate bibliometric statistics about research articles, journals, institutions, and individual authors. Liaison librarians are now regularly called upon to utilize these databases to assist faculty in finding citation activity on their published works for tenure and promotion, grant applications, and more. But questions about the accuracy, scope, and coverage of these tools deserve closer scrutiny. Discrepancies in citation capture led to a systematic study on how Scopus and Web of Science compared in a real-life situation encountered by liaisons: comparing three different disciplines at a medical school and nursing program. How many articles would each database retrieve for each faculty member using the author-searching tools provided? How many cited references for each faculty member would each tool generate? Results demonstrated troubling differences in publication and citation activity capture between Scopus and Web of Science. Implications for librarians are discussed.

An overview of biomedical literature search on the World Wide Web in the third millennium.

PubMed

Kumar, Prince; Goel, Roshni; Jain, Chandni; Kumar, Ashish; Parashar, Abhishek; Gond, Ajay Ratan

2012-06-01

Complete access to the existing pool of biomedical literature and the ability to "hit" upon the exact information of the relevant specialty are becoming essential elements of academic and clinical expertise. With the rapid expansion of the literature database, it is almost impossible to keep up to date with every innovation. Using the Internet, however, most people can freely access this literature at any time, from almost anywhere. This paper highlights the use of the Internet in obtaining valuable biomedical research information, which is mostly available from journals, databases, textbooks and e-journals in the form of web pages, text materials, images, and so on. The authors present an overview of web-based resources for biomedical researchers, providing information about Internet search engines (e.g., Google), web-based bibliographic databases (e.g., PubMed, IndMed) and how to use them, and other online biomedical resources that can assist clinicians in reaching well-informed clinical decisions.

The Xeno-glycomics database (XDB): a relational database of qualitative and quantitative pig glycome repertoire.

PubMed

Park, Hae-Min; Park, Ju-Hyeong; Kim, Yoon-Woo; Kim, Kyoung-Jin; Jeong, Hee-Jin; Jang, Kyoung-Soon; Kim, Byung-Gee; Kim, Yun-Gon

2013-11-15

In recent years, the improvement of mass spectrometry-based glycomics techniques (i.e. highly sensitive, quantitative and high-throughput analytical tools) has enabled us to obtain a large dataset of glycans. Here we present a database named Xeno-glycomics database (XDB) that contains cell- or tissue-specific pig glycomes analyzed with mass spectrometry-based techniques, including a comprehensive pig glycan information on chemical structures, mass values, types and relative quantities. It was designed as a user-friendly web-based interface that allows users to query the database according to pig tissue/cell types or glycan masses. This database will contribute in providing qualitative and quantitative information on glycomes characterized from various pig cells/organs in xenotransplantation and might eventually provide new targets in the α1,3-galactosyltransferase gene-knock out pigs era. The database can be accessed on the web at http://bioinformatics.snu.ac.kr/xdb.

SWS: accessing SRS sites contents through Web Services.

PubMed

Romano, Paolo; Marra, Domenico

2008-03-26

Web Services and Workflow Management Systems can support creation and deployment of network systems, able to automate data analysis and retrieval processes in biomedical research. Web Services have been implemented at bioinformatics centres and workflow systems have been proposed for biological data analysis. New databanks are often developed by taking into account these technologies, but many existing databases do not allow a programmatic access. Only a fraction of available databanks can thus be queried through programmatic interfaces. SRS is a well know indexing and search engine for biomedical databanks offering public access to many databanks and analysis tools. Unfortunately, these data are not easily and efficiently accessible through Web Services. We have developed 'SRS by WS' (SWS), a tool that makes information available in SRS sites accessible through Web Services. Information on known sites is maintained in a database, srsdb. SWS consists in a suite of WS that can query both srsdb, for information on sites and databases, and SRS sites. SWS returns results in a text-only format and can be accessed through a WSDL compliant client. SWS enables interoperability between workflow systems and SRS implementations, by also managing access to alternative sites, in order to cope with network and maintenance problems, and selecting the most up-to-date among available systems. Development and implementation of Web Services, allowing to make a programmatic access to an exhaustive set of biomedical databases can significantly improve automation of in-silico analysis. SWS supports this activity by making biological databanks that are managed in public SRS sites available through a programmatic interface.

Use of XML and Java for collaborative petroleum reservoir modeling on the Internet

NASA Astrophysics Data System (ADS)

Victorine, John; Watney, W. Lynn; Bhattacharya, Saibal

2005-11-01

The GEMINI (Geo-Engineering Modeling through INternet Informatics) is a public-domain, web-based freeware that is made up of an integrated suite of 14 Java-based software tools to accomplish on-line, real-time geologic and engineering reservoir modeling. GEMINI facilitates distant collaborations for small company and academic clients, negotiating analyses of both single and multiple wells. The system operates on a single server and an enterprise database. External data sets must be uploaded into this database. Feedback from GEMINI users provided the impetus to develop Stand Alone Web Start Applications of GEMINI modules that reside in and operate from the user's PC. In this version, the GEMINI modules run as applets, which may reside in local user PCs, on the server, or Java Web Start. In this enhanced version, XML-based data handling procedures are used to access data from remote and local databases and save results for later access and analyses. The XML data handling process also integrates different stand-alone GEMINI modules enabling the user(s) to access multiple databases. It provides flexibility to the user to customize analytical approach, database location, and level of collaboration. An example integrated field-study using GEMINI modules and Stand Alone Web Start Applications is provided to demonstrate the versatile applicability of this freeware for cost-effective reservoir modeling.

Use of XML and Java for collaborative petroleum reservoir modeling on the Internet

USGS Publications Warehouse

Victorine, J.; Watney, W.L.; Bhattacharya, S.

2005-01-01

The GEMINI (Geo-Engineering Modeling through INternet Informatics) is a public-domain, web-based freeware that is made up of an integrated suite of 14 Java-based software tools to accomplish on-line, real-time geologic and engineering reservoir modeling. GEMINI facilitates distant collaborations for small company and academic clients, negotiating analyses of both single and multiple wells. The system operates on a single server and an enterprise database. External data sets must be uploaded into this database. Feedback from GEMINI users provided the impetus to develop Stand Alone Web Start Applications of GEMINI modules that reside in and operate from the user's PC. In this version, the GEMINI modules run as applets, which may reside in local user PCs, on the server, or Java Web Start. In this enhanced version, XML-based data handling procedures are used to access data from remote and local databases and save results for later access and analyses. The XML data handling process also integrates different stand-alone GEMINI modules enabling the user(s) to access multiple databases. It provides flexibility to the user to customize analytical approach, database location, and level of collaboration. An example integrated field-study using GEMINI modules and Stand Alone Web Start Applications is provided to demonstrate the versatile applicability of this freeware for cost-effective reservoir modeling. ?? 2005 Elsevier Ltd. All rights reserved.

Saada: A Generator of Astronomical Database

NASA Astrophysics Data System (ADS)

Michel, L.

2011-11-01

Saada transforms a set of heterogeneous FITS files or VOtables of various categories (images, tables, spectra, etc.) in a powerful database deployed on the Web. Databases are located on your host and stay independent of any external server. This job doesn’t require writing code. Saada can mix data of various categories in multiple collections. Data collections can be linked each to others making relevant browsing paths and allowing data-mining oriented queries. Saada supports 4 VO services (Spectra, images, sources and TAP) . Data collections can be published immediately after the deployment of the Web interface.

Internet-based information system of digital geological data providing

NASA Astrophysics Data System (ADS)

Yuon, Egor; Soukhanov, Mikhail; Markov, Kirill

2015-04-01

One of the Russian Federal аgency of mineral resources problems is to provide the geological information which was delivered during the field operation for the means of federal budget. This information should be present in the current, conditional form. Before, the leading way of presenting geological information were paper geological maps, slices, borehole diagrams reports etc. Technologies of database construction, including distributed databases, technologies of construction of distributed information-analytical systems and Internet-technologies are intensively developing nowadays. Most of geological organizations create their own information systems without any possibility of integration into other systems of the same orientation. In 2012, specialists of VNIIgeosystem together with specialists of VSEGEI started the large project - creating the system of providing digital geological materials with using modern and perspective internet-technologies. The system is based on the web-server and the set of special programs, which allows users to efficiently get rasterized and vectorised geological materials. These materials are: geological maps of scale 1:1M, geological maps of scale 1:200 000 and 1:2 500 000, the fragments of seamless geological 1:1M maps, structural zoning maps inside the seamless fragments, the legends for State geological maps 1:200 000 and 1:1 000 000, full author's set of maps and also current materials for international projects «Atlas of geological maps for Circumpolar Arctic scale 1:5 000 000» and «Atlas of Geologic maps of central Asia and adjacent areas scale 1:2 500 000». The most interesting and functional block of the system - is the block of providing structured and well-formalized geological vector materials, based on Gosgeolkart database (NGKIS), managed by Oracle and the Internet-access is supported by web-subsystem NGKIS, which is currently based on MGS-Framework platform, developed by VNIIgeosystem. One of the leading elements is the web-service, which realizes the interaction of all parts of the system and controls whole the way of the request from the user to the database and back, adopted to the GeoSciML and EarthResourceML view. The experience of creation the Internet-based information system of digital geological data providing, and also previous works, including the developing of web-service of NGKIS-system, allows to tell, that technological realization of presenting Russian geological-cartographical data with using of international standards is possible. While realizing, it could be some difficulties, associated with geological material depth. Russian informational geological model is more deep and wide, than foreign. This means the main problem of using international standards and formats: Russian geological data presentation is possible only with decreasing the data detalisation. But, such a problem becomes not very important, if the service publishes also Russian vocabularies, not associated with international vocabularies. In this case, the international format could be the interchange format to change data between Russian users. The integration into the international projects reaches developing of the correlation schemes between Russian and foreign classificators and vocabularies.

WebCN: A web-based computation tool for in situ-produced cosmogenic nuclides

NASA Astrophysics Data System (ADS)

Ma, Xiuzeng; Li, Yingkui; Bourgeois, Mike; Caffee, Marc; Elmore, David; Granger, Darryl; Muzikar, Paul; Smith, Preston

2007-06-01

Cosmogenic nuclide techniques are increasingly being utilized in geoscience research. For this it is critical to establish an effective, easily accessible and well defined tool for cosmogenic nuclide computations. We have been developing a web-based tool (WebCN) to calculate surface exposure ages and erosion rates based on the nuclide concentrations measured by the accelerator mass spectrometry. WebCN for 10Be and 26Al has been finished and published at http://www.physics.purdue.edu/primelab/for_users/rockage.html. WebCN for 36Cl is under construction. WebCN is designed as a three-tier client/server model and uses the open source PostgreSQL for the database management and PHP for the interface design and calculations. On the client side, an internet browser and Microsoft Access are used as application interfaces to access the system. Open Database Connectivity is used to link PostgreSQL and Microsoft Access. WebCN accounts for both spatial and temporal distributions of the cosmic ray flux to calculate the production rates of in situ-produced cosmogenic nuclides at the Earth's surface.

Structure, functioning, and cumulative stressors of Mediterranean deep-sea ecosystems

NASA Astrophysics Data System (ADS)

Tecchio, Samuele; Coll, Marta; Sardà, Francisco

2015-06-01

Environmental stressors, such as climate fluctuations, and anthropogenic stressors, such as fishing, are of major concern for the management of deep-sea ecosystems. Deep-water habitats are limited by primary productivity and are mainly dependent on the vertical input of organic matter from the surface. Global change over the latest decades is imparting variations in primary productivity levels across oceans, and thus it has an impact on the amount of organic matter landing on the deep seafloor. In addition, anthropogenic impacts are now reaching the deep ocean. The Mediterranean Sea, the largest enclosed basin on the planet, is not an exception. However, ecosystem-level studies of response to varying food input and anthropogenic stressors on deep-sea ecosystems are still scant. We present here a comparative ecological network analysis of three food webs of the deep Mediterranean Sea, with contrasting trophic structure. After modelling the flows of these food webs with the Ecopath with Ecosim approach, we compared indicators of network structure and functioning. We then developed temporal dynamic simulations varying the organic matter input to evaluate its potential effect. Results show that, following the west-to-east gradient in the Mediterranean Sea of marine snow input, organic matter recycling increases, net production decreases to negative values and trophic organisation is overall reduced. The levels of food-web activity followed the gradient of organic matter availability at the seafloor, confirming that deep-water ecosystems directly depend on marine snow and are therefore influenced by variations of energy input, such as climate-driven changes. In addition, simulations of varying marine snow arrival at the seafloor, combined with the hypothesis of a possible fishery expansion on the lower continental slope in the western basin, evidence that the trawling fishery may pose an impact which could be an order of magnitude stronger than a climate-driven reduction of marine snow.

Why Is My Voice Changing? (For Teens)

MedlinePlus

... enter puberty earlier or later than others. How Deep Will My Voice Get? How deep a guy's voice gets depends on his genes: ... of Use Notice of Nondiscrimination Visit the Nemours Web site. Note: All information on TeensHealth® is for ...

Relational databases: a transparent framework for encouraging biology students to think informatically.

PubMed

Rice, Michael; Gladstone, William; Weir, Michael

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills.

Relational Databases: A Transparent Framework for Encouraging Biology Students To Think Informatically

PubMed Central

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills. PMID:15592597

33 CFR 401.2 - Interpretation.

Code of Federal Regulations, 2014 CFR

2014-07-01

...: (a) Corporation means the Saint Lawrence Seaway Development Corporation; (b) E-business means web applications on the St. Lawrence Seaway Management Corporation Web site which provides direct electronic...) Seaway means the deep waterway between the Port of Montreal and Lake Erie and includes all locks, canals...

A World Wide Web Human Dimensions Framework and Database for Wildlife and Forest Planning

Treesearch

Michael A. Tarrant; Alan D. Bright; H. Ken Cordell

1999-01-01

The paper describes a human dimensions framework(HDF) for application in wildlife and forest planning. The HDF is delivered via the world wide web and retrieves data on-line from the Social, Economic, Environmental, Leisure, and Attitudes (SEELA) database. The proposed HDF is guided by ten fundamental HD principles, and is applied to wildlife and forest planning using...

dbHiMo: a web-based epigenomics platform for histone-modifying enzymes

PubMed Central

Choi, Jaeyoung; Kim, Ki-Tae; Huh, Aram; Kwon, Seomun; Hong, Changyoung; Asiegbu, Fred O.; Jeon, Junhyun; Lee, Yong-Hwan

2015-01-01

Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11 576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies. Database URL: http://hme.riceblast.snu.ac.kr/ PMID:26055100

Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1.

PubMed

Park, Jeongbin; Bae, Sangsu

2018-03-15

Following the type II CRISPR-Cas9 system, type V CRISPR-Cpf1 endonucleases have been found to be applicable for genome editing in various organisms in vivo. However, there are as yet no web-based tools capable of optimally selecting guide RNAs (gRNAs) among all possible genome-wide target sites. Here, we present Cpf1-Database, a genome-wide gRNA library design tool for LbCpf1 and AsCpf1, which have DNA recognition sequences of 5'-TTTN-3' at the 5' ends of target sites. Cpf1-Database provides a sophisticated but simple way to design gRNAs for AsCpf1 nucleases on the genome scale. One can easily access the data using a straightforward web interface, and using the powerful collections feature one can easily design gRNAs for thousands of genes in short time. Free access at http://www.rgenome.net/cpf1-database/. sangsubae@hanyang.ac.kr.

Image query and indexing for digital x rays

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Thoma, George R.

1998-12-01

The web-based medical information retrieval system (WebMIRS) allows interned access to databases containing 17,000 digitized x-ray spine images and associated text data from National Health and Nutrition Examination Surveys (NHANES). WebMIRS allows SQL query of the text, and viewing of the returned text records and images using a standard browser. We are now working (1) to determine utility of data directly derived from the images in our databases, and (2) to investigate the feasibility of computer-assisted or automated indexing of the images to support image retrieval of images of interest to biomedical researchers in the field of osteoarthritis. To build an initial database based on image data, we are manually segmenting a subset of the vertebrae, using techniques from vertebral morphometry. From this, we will derive and add to the database vertebral features. This image-derived data will enhance the user's data access capability by enabling the creation of combined SQL/image-content queries.

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

PubMed

Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

2016-07-08

The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

NAWeb 2000: Web-Based Learning - On Track! International Conference on Web-Based Learning. (6th, New Brunswick, Canada, October 14-17, 2000).

ERIC Educational Resources Information Center

Hall, Richard., Ed.

This proceedings of the Sixth International Conference on Web-Based Learning, NAWeb 2000, includes the following papers: "Is a Paradigm Shift Required To Effectively Teach Web-Based Instruction?"; "Issues in Courseware Reuse for a Web-Based Information System"; "The Digital Curriculum Database: Meeting the Needs of Industry and the Challenge of…

Development of a web geoservices platform for School of Environmental Sciences, Mahatma Gandhi University, Kerala, India

NASA Astrophysics Data System (ADS)

Satheendran, S.; John, C. M.; Fasalul, F. K.; Aanisa, K. M.

2014-11-01

Web geoservices is the obvious graduation of Geographic Information System in a distributed environment through a simple browser. It enables organizations to share domain-specific rich and dynamic spatial information over the web. The present study attempted to design and develop a web enabled GIS application for the School of Environmental Sciences, Mahatma Gandhi University, Kottayam, Kerala, India to publish various geographical databases to the public through its website. The development of this project is based upon the open source tools and techniques. The output portal site is platform independent. The premier webgis frame work `Geomoose' is utilized. Apache server is used as the Web Server and the UMN Map Server is used as the map server for this project. It provides various customised tools to query the geographical database in different ways and search for various facilities in the geographical area like banks, attractive places, hospitals, hotels etc. The portal site was tested with the output geographical database of 2 projects of the School such as 1) the Tourism Information System for the Malabar region of Kerala State consisting of 5 northern districts 2) the geoenvironmental appraisal of the Athirappilly Hydroelectric Project covering the entire Chalakkudy river basin.

An overview of Airborne Data for Assessing Models (ADAM): a web development effort to effectively disseminate airborne data products

NASA Astrophysics Data System (ADS)

Mangosing, D. C.; Chen, G.; Kusterer, J.; Rinsland, P.; Perez, J.; Sorlie, S.; Parker, L.

2011-12-01

One of the objectives of the NASA Langley Research Center's MEaSURES project, "Creating a Unified Airborne Database for Model Assessment", is the development of airborne Earth System Data Records (ESDR) for the regional and global model assessment and validation activities performed by the tropospheric chemistry and climate modeling communities. The ongoing development of ADAM, a web site designed to access a unified, standardized and relational ESDR database, meets this objective. The ESDR database is derived from publically available data sets, from NASA airborne field studies to airborne and in-situ studies sponsored by NOAA, NSF, and numerous international partners. The ADAM web development activities provide an opportunity to highlight a growing synergy between the Airborne Science Data for Atmospheric Composition (ASD-AC) group at NASA Langley and the NASA Langley's Atmospheric Sciences Data Center (ASDC). These teams will collaborate on the ADAM web application by leveraging the state-of-the-art service and message-oriented data distribution architecture developed and implemented by ASDC and using a web-based tool provided by the ASD-AC group whose user interface accommodates the nuanced perspective of science users in the atmospheric chemistry and composition and climate modeling communities.

PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database.

PubMed

Wang, Xia; Shen, Yihang; Wang, Shiwei; Li, Shiliang; Zhang, Weilin; Liu, Xiaofeng; Lai, Luhua; Pei, Jianfeng; Li, Honglin

2017-07-03

The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database. The original version of PharmMapper includes more than 7000 target pharmacophores derived from complex crystal structures with corresponding protein target annotations. In this article, we present a new version of the PharmMapper web server, of which the backend pharmacophore database is six times larger than the earlier one, with a total of 23 236 proteins covering 16 159 druggable pharmacophore models and 51 431 ligandable pharmacophore models. The expanded target data cover 450 indications and 4800 molecular functions compared to 110 indications and 349 molecular functions in our last update. In addition, the new web server is united with the statistically meaningful ranking of the identified drug targets, which is achieved through the use of standard scores. It also features an improved user interface. The proposed web server is freely available at http://lilab.ecust.edu.cn/pharmmapper/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Portable power supply options for positive airway pressure devices.

PubMed

Riaz, Muhammad; Certal, Victor; Camacho, Macario

2015-01-01

Patients with obstructive sleep apnea (OSA) often face the challenge of how to power their positive airway pressure (PAP) devices when alternating current power supplies are not available in remote areas with lack of electricity or frequent power outages. This article elucidates portable power supply options for PAP devices with the aim to increase alternative power source awareness among medical providers. A search of scientific databases (Medline, Scopus, Web of Science, Google Scholar, and the Cochrane Library) was carried out on the topic of alternative portable power supply options for treatment of OSA. Scientific databases listed above yielded only limited results. Most articles were found via Google search. These articles were reviewed for alternative power supply options for OSA patients when alternating current is not available. The power supply options in this article include lead-acid batteries (starter, marine and deep-cycle batteries), lithium ion batteries, solar kits, battery packs, backup power systems, portable generators, and travel-size PAP devices. There are several options to power PAP devices with direct current when alternating current is not available. Knowledgeable primary care physicians especially in rural and remote areas can help OSA patients improve PAP compliance in order to mitigate morbidity and long-term complications of OSA.

RaptorX-Property: a web server for protein structure property prediction.

PubMed

Wang, Sheng; Li, Wei; Liu, Shiwang; Xu, Jinbo

2016-07-08

RaptorX Property (http://raptorx2.uchicago.edu/StructurePropertyPred/predict/) is a web server predicting structure property of a protein sequence without using any templates. It outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in-house deep learning model DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent accessibility (ACC) and disorder regions (DISO). DeepCNF not only models complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent property labels. Our experimental results show that, tested on CASP10, CASP11 and the other benchmarks, this server can obtain ∼84% Q3 accuracy for 3-state SS, ∼72% Q8 accuracy for 8-state SS, ∼66% Q3 accuracy for 3-state solvent accessibility, and ∼0.89 area under the ROC curve (AUC) for disorder prediction. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Empowering radiologic education on the Internet: a new virtual website technology for hosting interactive educational content on the World Wide Web.

PubMed

Frank, M S; Dreyer, K

2001-06-01

We describe a virtual web site hosting technology that enables educators in radiology to emblazon and make available for delivery on the world wide web their own interactive educational content, free from dependencies on in-house resources and policies. This suite of technologies includes a graphically oriented software application, designed for the computer novice, to facilitate the input, storage, and management of domain expertise within a database system. The database stores this expertise as choreographed and interlinked multimedia entities including text, imagery, interactive questions, and audio. Case-based presentations or thematic lectures can be authored locally, previewed locally within a web browser, then uploaded at will as packaged knowledge objects to an educator's (or department's) personal web site housed within a virtual server architecture. This architecture can host an unlimited number of unique educational web sites for individuals or departments in need of such service. Each virtual site's content is stored within that site's protected back-end database connected to Internet Information Server (Microsoft Corp, Redmond WA) using a suite of Active Server Page (ASP) modules that incorporate Microsoft's Active Data Objects (ADO) technology. Each person's or department's electronic teaching material appears as an independent web site with different levels of access--controlled by a username-password strategy--for teachers and students. There is essentially no static hypertext markup language (HTML). Rather, all pages displayed for a given site are rendered dynamically from case-based or thematic content that is fetched from that virtual site's database. The dynamically rendered HTML is displayed within a web browser in a Socratic fashion that can assess the recipient's current fund of knowledge while providing instantaneous user-specific feedback. Each site is emblazoned with the logo and identification of the participating institution. Individuals with teacher-level access can use a web browser to upload new content as well as manage content already stored on their virtual site. Each virtual site stores, collates, and scores participants' responses to the interactive questions posed on line. This virtual web site strategy empowers the educator with an end-to-end solution for creating interactive educational content and hosting that content within the educator's personalized and protected educational site on the world wide web, thus providing a valuable outlet that can magnify the impact of his or her talents and contributions.

Astronomical databases of Nikolaev Observatory

NASA Astrophysics Data System (ADS)

Protsyuk, Y.; Mazhaev, A.

2008-07-01

Several astronomical databases were created at Nikolaev Observatory during the last years. The databases are built by using MySQL search engine and PHP scripts. They are available on NAO web-site http://www.mao.nikolaev.ua.

Resolving the problem of multiple accessions of the same transcript deposited across various public databases.

PubMed

Weirick, Tyler; John, David; Uchida, Shizuka

2017-03-01

Maintaining the consistency of genomic annotations is an increasingly complex task because of the iterative and dynamic nature of assembly and annotation, growing numbers of biological databases and insufficient integration of annotations across databases. As information exchange among databases is poor, a 'novel' sequence from one reference annotation could be annotated in another. Furthermore, relationships to nearby or overlapping annotated transcripts are even more complicated when using different genome assemblies. To better understand these problems, we surveyed current and previous versions of genomic assemblies and annotations across a number of public databases containing long noncoding RNA. We identified numerous discrepancies of transcripts regarding their genomic locations, transcript lengths and identifiers. Further investigation showed that the positional differences between reference annotations of essentially the same transcript could lead to differences in its measured expression at the RNA level. To aid in resolving these problems, we present the algorithm 'Universal Genomic Accession Hash (UGAHash)' and created an open source web tool to encourage the usage of the UGAHash algorithm. The UGAHash web tool (http://ugahash.uni-frankfurt.de) can be accessed freely without registration. The web tool allows researchers to generate Universal Genomic Accessions for genomic features or to explore annotations deposited in the public databases of the past and present versions. We anticipate that the UGAHash web tool will be a valuable tool to check for the existence of transcripts before judging the newly discovered transcripts as novel. © The Author 2016. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Ontology-oriented retrieval of putative microRNAs in Vitis vinifera via GrapeMiRNA: a web database of de novo predicted grape microRNAs.

PubMed

Lazzari, Barbara; Caprera, Andrea; Cestaro, Alessandro; Merelli, Ivan; Del Corvo, Marcello; Fontana, Paolo; Milanesi, Luciano; Velasco, Riccardo; Stella, Alessandra

2009-06-29

Two complete genome sequences are available for Vitis vinifera Pinot noir. Based on the sequence and gene predictions produced by the IASMA, we performed an in silico detection of putative microRNA genes and of their targets, and collected the most reliable microRNA predictions in a web database. The application is available at http://www.itb.cnr.it/ptp/grapemirna/. The program FindMiRNA was used to detect putative microRNA genes in the grape genome. A very high number of predictions was retrieved, calling for validation. Nine parameters were calculated and, based on the grape microRNAs dataset available at miRBase, thresholds were defined and applied to FindMiRNA predictions having targets in gene exons. In the resulting subset, predictions were ranked according to precursor positions and sequence similarity, and to target identity. To further validate FindMiRNA predictions, comparisons to the Arabidopsis genome, to the grape Genoscope genome, and to the grape EST collection were performed. Results were stored in a MySQL database and a web interface was prepared to query the database and retrieve predictions of interest. The GrapeMiRNA database encompasses 5,778 microRNA predictions spanning the whole grape genome. Predictions are integrated with information that can be of use in selection procedures. Tools added in the web interface also allow to inspect predictions according to gene ontology classes and metabolic pathways of targets. The GrapeMiRNA database can be of help in selecting candidate microRNA genes to be validated.

Veterans Administration Databases

Cancer.gov

The Veterans Administration Information Resource Center provides database and informatics experts, customer service, expert advice, information products, and web technology to VA researchers and others.

NPIDB: Nucleic acid-Protein Interaction DataBase.

PubMed

Kirsanov, Dmitry D; Zanegina, Olga N; Aksianov, Evgeniy A; Spirin, Sergei A; Karyagina, Anna S; Alexeevski, Andrei V

2013-01-01

The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.

Students' Evaluation Strategies in a Web Research Task: Are They Sensitive to Relevance and Reliability?

ERIC Educational Resources Information Center

Rodicio, Héctor García

2015-01-01

When searching and using resources on the Web, students have to evaluate Web pages in terms of relevance and reliability. This evaluation can be done in a more or less systematic way, by either considering deep or superficial cues of relevance and reliability. The goal of this study was to examine how systematic students are when evaluating Web…

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

PubMed

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

2015-03-01

In this study, we describe the development and utilization of a relational database designed to manage the clinical and radiological data of patients with brain tumors. The Brain Tumor Database was implemented using MySQL v.5.0, while the graphical user interface was created using PHP and HTML, thus making it easily accessible through a web browser. This web-based approach allows for multiple institutions to potentially access the database. The BT Database can record brain tumor patient information (e.g. clinical features, anatomical attributes, and radiological characteristics) and be used for clinical and research purposes. Analytic tools to automatically generate statistics and different plots are provided. The BT Database is a free and powerful user-friendly tool with a wide range of possible clinical and research applications in neurology and neurosurgery. The BT Database graphical user interface source code and manual are freely available at http://tumorsdatabase.altervista.org. © The Author(s) 2013.

Upper extremity deep venous thrombosis after port insertion: What are the risk factors?

PubMed

Tabatabaie, Omidreza; Kasumova, Gyulnara G; Kent, Tara S; Eskander, Mariam F; Fadayomi, Ayotunde B; Ng, Sing Chau; Critchlow, Jonathan F; Tawa, Nicholas E; Tseng, Jennifer F

2017-08-01

Totally implantable venous access devices (ports) are widely used, especially for cancer chemotherapy. Although their use has been associated with upper extremity deep venous thrombosis, the risk factors of upper extremity deep venous thrombosis in patients with a port are not studied adequately. The Healthcare Cost and Utilization Project's Florida State Ambulatory Surgery and Services Database was queried between 2007 and 2011 for patients who underwent outpatient port insertion, identified by Current Procedural Terminology code. Patients were followed in the State Ambulatory Surgery and Services Database, State Inpatient Database, and State Emergency Department Database for upper extremity deep venous thrombosis occurrence. The cohort was divided into a test cohort and a validation cohort based on the year of port placement. A multivariable logistic regression model was developed to identify risk factors for upper extremity deep venous thrombosis in patients with a port. The model then was tested on the validation cohort. Of the 51,049 patients in the derivation cohort, 926 (1.81%) developed an upper extremity deep venous thrombosis. On multivariate analysis, independently significant predictors of upper extremity deep venous thrombosis included age <65 years (odds ratio = 1.22), Elixhauser score of 1 to 2 compared with zero (odds ratio = 1.17), end-stage renal disease (versus no kidney disease; odds ratio = 2.63), history of any deep venous thrombosis (odds ratio = 1.77), all-cause 30-day revisit (odds ratio = 2.36), African American race (versus white; odds ratio = 1.86), and other nonwhite races (odds ratio = 1.35). Additionally, compared with genitourinary malignancies, patients with gastrointestinal (odds ratio = 1.55), metastatic (odds ratio = 1.76), and lung cancers (odds ratio = 1.68) had greater risks of developing an upper extremity deep venous thrombosis. This study identified major risk factors of upper extremity deep venous thrombosis. Further studies are needed to evaluate the appropriateness of thromboprophylaxis in patients at greater risk of upper extremity deep venous thrombosis. Copyright © 2017 Elsevier Inc. All rights reserved.

Web-based Visualization and Query of semantically segmented multiresolution 3D Models in the Field of Cultural Heritage

NASA Astrophysics Data System (ADS)

Auer, M.; Agugiaro, G.; Billen, N.; Loos, L.; Zipf, A.

2014-05-01

Many important Cultural Heritage sites have been studied over long periods of time by different means of technical equipment, methods and intentions by different researchers. This has led to huge amounts of heterogeneous "traditional" datasets and formats. The rising popularity of 3D models in the field of Cultural Heritage in recent years has brought additional data formats and makes it even more necessary to find solutions to manage, publish and study these data in an integrated way. The MayaArch3D project aims to realize such an integrative approach by establishing a web-based research platform bringing spatial and non-spatial databases together and providing visualization and analysis tools. Especially the 3D components of the platform use hierarchical segmentation concepts to structure the data and to perform queries on semantic entities. This paper presents a database schema to organize not only segmented models but also different Levels-of-Details and other representations of the same entity. It is further implemented in a spatial database which allows the storing of georeferenced 3D data. This enables organization and queries by semantic, geometric and spatial properties. As service for the delivery of the segmented models a standardization candidate of the OpenGeospatialConsortium (OGC), the Web3DService (W3DS) has been extended to cope with the new database schema and deliver a web friendly format for WebGL rendering. Finally a generic user interface is presented which uses the segments as navigation metaphor to browse and query the semantic segmentation levels and retrieve information from an external database of the German Archaeological Institute (DAI).

The Ontological Perspectives of the Semantic Web and the Metadata Harvesting Protocol: Applications of Metadata for Improving Web Search.

ERIC Educational Resources Information Center

Fast, Karl V.; Campbell, D. Grant

2001-01-01

Compares the implied ontological frameworks of the Open Archives Initiative Protocol for Metadata Harvesting and the World Wide Web Consortium's Semantic Web. Discusses current search engine technology, semantic markup, indexing principles of special libraries and online databases, and componentization and the distinction between data and…

Web Proxy Auto Discovery for the WLCG

NASA Astrophysics Data System (ADS)

Dykstra, D.; Blomer, J.; Blumenfeld, B.; De Salvo, A.; Dewhurst, A.; Verguilov, V.

2017-10-01

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily support that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which they direct to the nearest publicly accessible web proxy servers. The responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.

Web Proxy Auto Discovery for the WLCG

DOE PAGES

Dykstra, D.; Blomer, J.; Blumenfeld, B.; ...

2017-11-23

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily supportmore » that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which it directs to the nearest publicly accessible web proxy servers. Furthermore, the responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.« less

Web Proxy Auto Discovery for the WLCG

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

Dykstra, D.; Blomer, J.; Blumenfeld, B.

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily supportmore » that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which it directs to the nearest publicly accessible web proxy servers. Furthermore, the responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.« less

The Footprint Database and Web Services of the Herschel Space Observatory

NASA Astrophysics Data System (ADS)

Dobos, László; Varga-Verebélyi, Erika; Verdugo, Eva; Teyssier, David; Exter, Katrina; Valtchanov, Ivan; Budavári, Tamás; Kiss, Csaba

2016-10-01

Data from the Herschel Space Observatory is freely available to the public but no uniformly processed catalogue of the observations has been published so far. To date, the Herschel Science Archive does not contain the exact sky coverage (footprint) of individual observations and supports search for measurements based on bounding circles only. Drawing on previous experience in implementing footprint databases, we built the Herschel Footprint Database and Web Services for the Herschel Space Observatory to provide efficient search capabilities for typical astronomical queries. The database was designed with the following main goals in mind: (a) provide a unified data model for meta-data of all instruments and observational modes, (b) quickly find observations covering a selected object and its neighbourhood, (c) quickly find every observation in a larger area of the sky, (d) allow for finding solar system objects crossing observation fields. As a first step, we developed a unified data model of observations of all three Herschel instruments for all pointing and instrument modes. Then, using telescope pointing information and observational meta-data, we compiled a database of footprints. As opposed to methods using pixellation of the sphere, we represent sky coverage in an exact geometric form allowing for precise area calculations. For easier handling of Herschel observation footprints with rather complex shapes, two algorithms were implemented to reduce the outline. Furthermore, a new visualisation tool to plot footprints with various spherical projections was developed. Indexing of the footprints using Hierarchical Triangular Mesh makes it possible to quickly find observations based on sky coverage, time and meta-data. The database is accessible via a web site http://herschel.vo.elte.hu and also as a set of REST web service functions, which makes it readily usable from programming environments such as Python or IDL. The web service allows downloading footprint data in various formats including Virtual Observatory standards.

50 CFR 679.21 - Prohibited species bycatch management.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Region Web site (http://alaskafisheries.noaa.gov/). (c) Salmon taken in the BS pollock fisheries... GOA groundfish species or species group. (B) Deep-water species fishery. Fishing with trawl gear... the NMFS Alaska Region Web site (http://alaskafisheries.noaa.gov/): (A) The Chinook salmon PSC...

50 CFR 679.21 - Prohibited species bycatch management.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Region Web site (http://alaskafisheries.noaa.gov/). (c) Salmon taken in the BS pollock fisheries... GOA groundfish species or species group. (B) Deep-water species fishery. Fishing with trawl gear... the NMFS Alaska Region Web site (http://alaskafisheries.noaa.gov/): (A) The Chinook salmon PSC...

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface.

PubMed

Rot, Gregor; Parikh, Anup; Curk, Tomaz; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaz

2009-08-25

Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface

PubMed Central

Rot, Gregor; Parikh, Anup; Curk, Tomaz; Kuspa, Adam; Shaulsky, Gad; Zupan, Blaz

2009-01-01

Background Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. Results We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. Conclusion dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms. PMID:19706156

[Study on Information Extraction of Clinic Expert Information from Hospital Portals].

PubMed

Zhang, Yuanpeng; Dong, Jiancheng; Qian, Danmin; Geng, Xingyun; Wu, Huiqun; Wang, Li

2015-12-01

Clinic expert information provides important references for residents in need of hospital care. Usually, such information is hidden in the deep web and cannot be directly indexed by search engines. To extract clinic expert information from the deep web, the first challenge is to make a judgment on forms. This paper proposes a novel method based on a domain model, which is a tree structure constructed by the attributes of search interfaces. With this model, search interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from the returned web pages indexed by search interfaces. To filter the noise information on a web page, a block importance model is proposed. The experiment results indicated that the domain model yielded a precision 10.83% higher than that of the rule-based method, whereas the block importance model yielded an F₁ measure 10.5% higher than that of the XPath method.

[The Development and Application of the Orthopaedics Implants Failure Database Software Based on WEB].

PubMed

Huang, Jiahua; Zhou, Hai; Zhang, Binbin; Ding, Biao

2015-09-01

This article develops a new failure database software for orthopaedics implants based on WEB. The software is based on B/S mode, ASP dynamic web technology is used as its main development language to achieve data interactivity, Microsoft Access is used to create a database, these mature technologies make the software extend function or upgrade easily. In this article, the design and development idea of the software, the software working process and functions as well as relative technical features are presented. With this software, we can store many different types of the fault events of orthopaedics implants, the failure data can be statistically analyzed, and in the macroscopic view, it can be used to evaluate the reliability of orthopaedics implants and operations, it also can ultimately guide the doctors to improve the clinical treatment level.

Illinois hospital using Web to build database for relationship marketing.

PubMed

Rees, T

2000-01-01

Silver Cross Hospital and Medical Centers, Joliet, Ill., is promoting its Web site as a tool for gathering health information about patients and prospective patients in order to build a relationship marketing database. The database will enable the hospital to identify health care needs of consumers in Joliet, Will County and many southwestern suburbs of Chicago. The Web site is promoted in a multimedia advertising campaign that invites residents to participate in a Healthy Living Quiz that rewards respondents with free health screenings. The effort is part of a growing planning and marketing strategy in the health care industry called customer relationship management (CRM). Not only does a total CRM plan offer health care organizations the chance to discover the potential for meeting consumers' needs; it also helps find any marketplace gaps that may exist.

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation.

PubMed

Klee, Kathrin; Ernst, Rebecca; Spannagl, Manuel; Mayer, Klaus F X

2007-08-30

Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity. To overcome these limitations we extended the Apollo data adapter with a generic, configurable web service client that is able to retrieve annotation data in a GAME-XML-formatted string and pass it on to Apollo's internal input routine. This Apollo web service adapter, Apollo2Go, simplifies the data exchange in distributed projects and aims to render the annotation process more comfortable. The Apollo2Go software is freely available from ftp://ftpmips.gsf.de/plants/apollo_webservice.

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation

PubMed Central

Klee, Kathrin; Ernst, Rebecca; Spannagl, Manuel; Mayer, Klaus FX

2007-01-01

Background Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity. Results To overcome these limitations we extended the Apollo data adapter with a generic, configurable web service client that is able to retrieve annotation data in a GAME-XML-formatted string and pass it on to Apollo's internal input routine. Conclusion This Apollo web service adapter, Apollo2Go, simplifies the data exchange in distributed projects and aims to render the annotation process more comfortable. The Apollo2Go software is freely available from . PMID:17760972

The Human Transcript Database: A Catalogue of Full Length cDNA Inserts

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

Bouckk John; Michael McLeod; Kim Worley

1999-09-10

The BCM Search Launcher provided improved access to web-based sequence analysis services during the granting period and beyond. The Search Launcher web site grouped analysis procedures by function and provided default parameters that provided reasonable search results for most applications. For instance, most queries were automatically masked for repeat sequences prior to sequence database searches to avoid spurious matches. In addition to the web-based access and arrangements that were made using the functions easier, the BCM Search Launcher provided unique value-added applications like the BEAUTY sequence database search tool that combined information about protein domains and sequence database search resultsmore » to give an enhanced, more complete picture of the reliability and relative value of the information reported. This enhanced search tool made evaluating search results more straight-forward and consistent. Some of the favorite features of the web site are the sequence utilities and the batch client functionality that allows processing of multiple samples from the command line interface. One measure of the success of the BCM Search Launcher is the number of sites that have adopted the models first developed on the site. The graphic display on the BLAST search from the NCBI web site is one such outgrowth, as is the display of protein domain search results within BLAST search results, and the design of the Biology Workbench application. The logs of usage and comments from users confirm the great utility of this resource.« less

Hybrid Schema Matching for Deep Web

NASA Astrophysics Data System (ADS)

Chen, Kerui; Zuo, Wanli; He, Fengling; Chen, Yongheng

Schema matching is the process of identifying semantic mappings, or correspondences, between two or more schemas. Schema matching is a first step and critical part of data integration. For schema matching of deep web, most researches only interested in query interface, while rarely pay attention to abundant schema information contained in query result pages. This paper proposed a mixed schema matching technique, which combines attributes that appeared in query structures and query results of different data sources, and mines the matched schemas inside. Experimental results prove the effectiveness of this method for improving the accuracy of schema matching.

Database Reports Over the Internet

NASA Technical Reports Server (NTRS)

Smith, Dean Lance

2002-01-01

Most of the summer was spent developing software that would permit existing test report forms to be printed over the web on a printer that is supported by Adobe Acrobat Reader. The data is stored in a DBMS (Data Base Management System). The client asks for the information from the database using an HTML (Hyper Text Markup Language) form in a web browser. JavaScript is used with the forms to assist the user and verify the integrity of the entered data. Queries to a database are made in SQL (Sequential Query Language), a widely supported standard for making queries to databases. Java servlets, programs written in the Java programming language running under the control of network server software, interrogate the database and complete a PDF form template kept in a file. The completed report is sent to the browser requesting the report. Some errors are sent to the browser in an HTML web page, others are reported to the server. Access to the databases was restricted since the data are being transported to new DBMS software that will run on new hardware. However, the SQL queries were made to Microsoft Access, a DBMS that is available on most PCs (Personal Computers). Access does support the SQL commands that were used, and a database was created with Access that contained typical data for the report forms. Some of the problems and features are discussed below.

Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network.

PubMed

Frey, Lewis J; Sward, Katherine A; Newth, Christopher J L; Khemani, Robinder G; Cryer, Martin E; Thelen, Julie L; Enriquez, Rene; Shaoyu, Su; Pollack, Murray M; Harrison, Rick E; Meert, Kathleen L; Berg, Robert A; Wessel, David L; Shanley, Thomas P; Dalton, Heidi; Carcillo, Joseph; Jenkins, Tammara L; Dean, J Michael

2015-11-01

To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality. Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers. Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56% to 1% and demonstrated that 99% of the data consistently transferred using the data dictionary and 1% needed human curation. Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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.

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

Wojick, D E; Warnick, W L; Carroll, B C

With the United States federal government spending billions annually for research and development, ways to increase the productivity of that research can have a significant return on investment. The process by which science knowledge is spread is called diffusion. It is therefore important to better understand and measure the benefits of this diffusion of knowledge. In particular, it is important to understand whether advances in Internet searching can speed up the diffusion of scientific knowledge and accelerate scientific progress despite the fact that the vast majority of scientific information resources continue to be held in deep web databases that manymore » search engines cannot fully access. To address the complexity of the search issue, the term global discovery is used for the act of searching across heterogeneous environments and distant communities. This article discusses these issues and describes research being conducted by the Office of Scientific and Technical Information (OSTI).« less

Development of spatial density maps based on geoprocessing web services: application to tuberculosis incidence in Barcelona, Spain.

PubMed

Dominkovics, Pau; Granell, Carlos; Pérez-Navarro, Antoni; Casals, Martí; Orcau, Angels; Caylà, Joan A

2011-11-29

Health professionals and authorities strive to cope with heterogeneous data, services, and statistical models to support decision making on public health. Sophisticated analysis and distributed processing capabilities over geocoded epidemiological data are seen as driving factors to speed up control and decision making in these health risk situations. In this context, recent Web technologies and standards-based web services deployed on geospatial information infrastructures have rapidly become an efficient way to access, share, process, and visualize geocoded health-related information. Data used on this study is based on Tuberculosis (TB) cases registered in Barcelona city during 2009. Residential addresses are geocoded and loaded into a spatial database that acts as a backend database. The web-based application architecture and geoprocessing web services are designed according to the Representational State Transfer (REST) principles. These web processing services produce spatial density maps against the backend database. The results are focused on the use of the proposed web-based application to the analysis of TB cases in Barcelona. The application produces spatial density maps to ease the monitoring and decision making process by health professionals. We also include a discussion of how spatial density maps may be useful for health practitioners in such contexts. In this paper, we developed web-based client application and a set of geoprocessing web services to support specific health-spatial requirements. Spatial density maps of TB incidence were generated to help health professionals in analysis and decision-making tasks. The combined use of geographic information tools, map viewers, and geoprocessing services leads to interesting possibilities in handling health data in a spatial manner. In particular, the use of spatial density maps has been effective to identify the most affected areas and its spatial impact. This study is an attempt to demonstrate how web processing services together with web-based mapping capabilities suit the needs of health practitioners in epidemiological analysis scenarios.

Development of spatial density maps based on geoprocessing web services: application to tuberculosis incidence in Barcelona, Spain

PubMed Central

2011-01-01

Background Health professionals and authorities strive to cope with heterogeneous data, services, and statistical models to support decision making on public health. Sophisticated analysis and distributed processing capabilities over geocoded epidemiological data are seen as driving factors to speed up control and decision making in these health risk situations. In this context, recent Web technologies and standards-based web services deployed on geospatial information infrastructures have rapidly become an efficient way to access, share, process, and visualize geocoded health-related information. Methods Data used on this study is based on Tuberculosis (TB) cases registered in Barcelona city during 2009. Residential addresses are geocoded and loaded into a spatial database that acts as a backend database. The web-based application architecture and geoprocessing web services are designed according to the Representational State Transfer (REST) principles. These web processing services produce spatial density maps against the backend database. Results The results are focused on the use of the proposed web-based application to the analysis of TB cases in Barcelona. The application produces spatial density maps to ease the monitoring and decision making process by health professionals. We also include a discussion of how spatial density maps may be useful for health practitioners in such contexts. Conclusions In this paper, we developed web-based client application and a set of geoprocessing web services to support specific health-spatial requirements. Spatial density maps of TB incidence were generated to help health professionals in analysis and decision-making tasks. The combined use of geographic information tools, map viewers, and geoprocessing services leads to interesting possibilities in handling health data in a spatial manner. In particular, the use of spatial density maps has been effective to identify the most affected areas and its spatial impact. This study is an attempt to demonstrate how web processing services together with web-based mapping capabilities suit the needs of health practitioners in epidemiological analysis scenarios. PMID:22126392

Anatomy and histology of apical support: a literature review concerning cardinal and uterosacral ligaments.

PubMed

Ramanah, Rajeev; Berger, Mitchell B; Parratte, Bernard M; DeLancey, John O L

2012-11-01

The objective of this work was to collect and summarize relevant literature on the anatomy, histology, and imaging of apical support of the upper vagina and the uterus provided by the cardinal (CL) and uterosacral (USL) ligaments. A literature search in English, French, and German languages was carried out with the keywords apical support, cardinal ligament, transverse cervical ligament, Mackenrodt ligament, parametrium, paracervix, retinaculum uteri, web, uterosacral ligament, and sacrouterine ligament in the PubMed database. Other relevant journal and textbook articles were sought by retrieving references cited in previous PubMed articles. Fifty references were examined in peer-reviewed journals and textbooks. The USL extends from the S2 to the S4 vertebra region to the dorsal margin of the uterine cervix and/or to the upper third of the posterior vaginal wall. It has a superficial and deep component. Autonomous nerve fibers are a major constituent of the deep USL. CL is defined as a perivascular sheath with a proximal insertion around the origin of the internal iliac artery and a distal insertion on the cervix and/or vagina. It is divided into a cranial (vascular) and a caudal (neural) portions. Histologically, it contains mainly vessels, with no distinct band of connective tissue. Both the deep USL and the caudal CL are closely related to the inferior hypogastric plexus. USL and CL are visceral ligaments, with mesentery-like structures containing vessels, nerves, connective tissue, and adipose tissue.

Anatomy and histology of apical support: a literature review concerning cardinal and uterosacral ligaments

PubMed Central

Ramanah, Rajeev; Berger, Mitchell B.; Parratte, Bernard M.

2014-01-01

The objective of this work was to collect and summarize relevant literature on the anatomy, histology, and imaging of apical support of the upper vagina and the uterus provided by the cardinal (CL) and uterosacral (USL) ligaments. A literature search in English, French, and German languages was carried out with the keywords apical support, cardinal ligament, transverse cervical ligament, Mackenrodt ligament, parametrium, paracervix, retinaculum uteri, web, uterosacral ligament, and sacrouterine ligament in the PubMed database. Other relevant journal and textbook articles were sought by retrieving references cited in previous PubMed articles. Fifty references were examined in peer-reviewed journals and textbooks. The USL extends from the S2 to the S4 vertebra region to the dorsal margin of the uterine cervix and/or to the upper third of the posterior vaginal wall. It has a superficial and deep component. Autonomous nerve fibers are a major constituent of the deep USL. CL is defined as a perivascular sheath with a proximal insertion around the origin of the internal iliac artery and a distal insertion on the cervix and/or vagina. It is divided into a cranial (vascular) and a caudal (neural) portions. Histologically, it contains mainly vessels, with no distinct band of connective tissue. Both the deep USL and the caudal CL are closely related to the inferior hypogastric plexus. USL and CL are visceral ligaments, with mesentery-like structures containing vessels, nerves, connective tissue, and adipose tissue. PMID:22618209

CAM on PubMed

MedlinePlus

... citations from the MEDLINE database and additional life science journals. It also includes links to many full-text articles at journal Web sites and other related Web resources. Sample Searches ...

A web-based platform for virtual screening.

PubMed

Watson, Paul; Verdonk, Marcel; Hartshorn, Michael J

2003-09-01

A fully integrated, web-based, virtual screening platform has been developed to allow rapid virtual screening of large numbers of compounds. ORACLE is used to store information at all stages of the process. The system includes a large database of historical compounds from high throughput screenings (HTS) chemical suppliers, ATLAS, containing over 3.1 million unique compounds with their associated physiochemical properties (ClogP, MW, etc.). The database can be screened using a web-based interface to produce compound subsets for virtual screening or virtual library (VL) enumeration. In order to carry out the latter task within ORACLE a reaction data cartridge has been developed. Virtual libraries can be enumerated rapidly using the web-based interface to the cartridge. The compound subsets can be seamlessly submitted for virtual screening experiments, and the results can be viewed via another web-based interface allowing ad hoc querying of the virtual screening data stored in ORACLE.

Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods.

PubMed

Brandt, C; Nadkarni, P

2001-01-01

The Web is increasingly the medium of choice for multi-user application program delivery. Yet selection of an appropriate programming environment for rapid prototyping, code portability, and maintainability remain issues. We summarize our experience on the conversion of a LISP Web application, Search/SR to a new, functionally identical application, Search/SR-ASP using a relational database and active server pages (ASP) technology. Our results indicate that provision of easy access to database engines and external objects is almost essential for a development environment to be considered viable for rapid and robust application delivery. While LISP itself is a robust language, its use in Web applications may be hard to justify given that current vendor implementations do not provide such functionality. Alternative, currently available scripting environments for Web development appear to have most of LISP's advantages and few of its disadvantages.

JetWeb: A WWW interface and database for Monte Carlo tuning and validation

NASA Astrophysics Data System (ADS)

Butterworth, J. M.; Butterworth, S.

2003-06-01

A World Wide Web interface to a Monte Carlo tuning facility is described. The aim of the package is to allow rapid and reproducible comparisons to be made between detailed measurements at high-energy physics colliders and general physics simulation packages. The package includes a relational database, a Java servlet query and display facility, and clean interfaces to simulation packages and their parameters.

Image

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

Marsh, Amber; Harsch, Tim; Pitt, Julie

2007-08-31

The computer side of the IMAGE project consists of a collection of Perl scripts that perform a variety of tasks; scripts are available to insert, update and delete data from the underlying Oracle database, download data from NCBI's Genbank and other sources, and generate data files for download by interested parties. Web scripts make up the tracking interface, and various tools available on the project web-site (image.llnl.gov) that provide a search interface to the database.

Shifting Sands: Science Researchers on Google Scholar, Web of Science, and PubMed, with Implications for Library Collections Budgets

ERIC Educational Resources Information Center

Hightower, Christy; Caldwell, Christy

2010-01-01

Science researchers at the University of California Santa Cruz were surveyed about their article database use and preferences in order to inform collection budget choices. Web of Science was the single most used database, selected by 41.6%. Statistically there was no difference between PubMed (21.5%) and Google Scholar (18.7%) as the second most…

Modernizing the MagIC Paleomagnetic and Rock Magnetic Database Technology Stack to Encourage Code Reuse and Reproducible Science

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A. A. P.; Jarboe, N.; Jonestrask, L.; Tauxe, L.; Constable, C.

2016-12-01

The Magnetics Information Consortium (https://earthref.org/MagIC/) develops and maintains a database and web application for supporting the paleo-, geo-, and rock magnetic scientific community. Historically, this objective has been met with an Oracle database and a Perl web application at the San Diego Supercomputer Center (SDSC). The Oracle Enterprise Cluster at SDSC, however, was decommissioned in July of 2016 and the cost for MagIC to continue using Oracle became prohibitive. This provided MagIC with a unique opportunity to reexamine the entire technology stack and data model. MagIC has developed an open-source web application using the Meteor (http://meteor.com) framework and a MongoDB database. The simplicity of the open-source full-stack framework that Meteor provides has improved MagIC's development pace and the increased flexibility of the data schema in MongoDB encouraged the reorganization of the MagIC Data Model. As a result of incorporating actively developed open-source projects into the technology stack, MagIC has benefited from their vibrant software development communities. This has translated into a more modern web application that has significantly improved the user experience for the paleo-, geo-, and rock magnetic scientific community.

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.

Web client and ODBC access to legacy database information: a low cost approach.

PubMed Central

Sanders, N. W.; Mann, N. H.; Spengler, D. M.

1997-01-01

A new method has been developed for the Department of Orthopaedics of Vanderbilt University Medical Center to access departmental clinical data. Previously this data was stored only in the medical center's mainframe DB2 database, it is now additionally stored in a departmental SQL database. Access to this data is available via any ODBC compliant front-end or a web client. With a small budget and no full time staff, we were able to give our department on-line access to many years worth of patient data that was previously inaccessible. PMID:9357735

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

PubMed

Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

PubMed Central

Zheng, Wenning; Mutha, Naresh V.R.; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

G6PDdb, an integrated database of glucose-6-phosphate dehydrogenase (G6PD) mutations.

PubMed

Kwok, Colin J; Martin, Andrew C R; Au, Shannon W N; Lam, Veronica M S

2002-03-01

G6PDdb (http://www.rubic.rdg.ac.uk/g6pd/ or http://www.bioinf.org.uk/g6pd/) is a newly created web-accessible locus-specific mutation database for the human Glucose-6-phosphate dehydrogenase (G6PD) gene. The relational database integrates up-to-date mutational and structural data from various databanks (GenBank, Protein Data Bank, etc.) with biochemically characterized variants and their associated phenotypes obtained from published literature and the Favism website. An automated analysis of the mutations likely to have a significant impact on the structure of the protein has been performed using a recently developed procedure. The database may be queried online and the full results of the analysis of the structural impact of mutations are available. The web page provides a form for submitting additional mutation data and is linked to resources such as the Favism website, OMIM, HGMD, HGVBASE, and the PDB. This database provides insights into the molecular aspects and clinical significance of G6PD deficiency for researchers and clinicians and the web page functions as a knowledge base relevant to the understanding of G6PD deficiency and its management. Copyright 2002 Wiley-Liss, Inc.

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

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.

A comprehensive view of the web-resources related to sericulture

PubMed Central

Singh, Deepika; Chetia, Hasnahana; Kabiraj, Debajyoti; Sharma, Swagata; Kumar, Anil; Sharma, Pragya; Deka, Manab; Bora, Utpal

2016-01-01

Recent progress in the field of sequencing and analysis has led to a tremendous spike in data and the development of data science tools. One of the outcomes of this scientific progress is development of numerous databases which are gaining popularity in all disciplines of biology including sericulture. As economically important organism, silkworms are studied extensively for their numerous applications in the field of textiles, biomaterials, biomimetics, etc. Similarly, host plants, pests, pathogens, etc. are also being probed to understand the seri-resources more efficiently. These studies have led to the generation of numerous seri-related databases which are extremely helpful for the scientific community. In this article, we have reviewed all the available online resources on silkworm and its related organisms, including databases as well as informative websites. We have studied their basic features and impact on research through citation count analysis, finally discussing the role of emerging sequencing and analysis technologies in the field of seri-data science. As an outcome of this review, a web portal named SeriPort, has been created which will act as an index for the various sericulture-related databases and web resources available in cyberspace. Database URL: http://www.seriport.in/ PMID:27307138

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.

Introducing glycomics data into the Semantic Web

PubMed Central

2013-01-01

Background Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. Results In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as “proofs-of-concept” to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement. Conclusions We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains. PMID:24280648

Introducing glycomics data into the Semantic Web.

PubMed

Aoki-Kinoshita, Kiyoko F; Bolleman, Jerven; Campbell, Matthew P; Kawano, Shin; Kim, Jin-Dong; Lütteke, Thomas; Matsubara, Masaaki; Okuda, Shujiro; Ranzinger, Rene; Sawaki, Hiromichi; Shikanai, Toshihide; Shinmachi, Daisuke; Suzuki, Yoshinori; Toukach, Philip; Yamada, Issaku; Packer, Nicolle H; Narimatsu, Hisashi

2013-11-26

Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as "switches" that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as "proofs-of-concept" to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement. We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains.

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre.

PubMed

Sommer, Stephanie A; Van Woudenberg, Lauren; Lenz, Petra H; Cepeda, Georgina; Goetze, Erica

2017-11-01

Although metazoan animals in the mesopelagic zone play critical roles in deep pelagic food webs and in the attenuation of carbon in midwaters, the diversity of these assemblages is not fully known. A metabarcoding survey of mesozooplankton diversity across the epipelagic, mesopelagic and upper bathypelagic zones (0-1500 m) in the North Pacific Subtropical Gyre revealed far higher estimates of species richness than expected given prior morphology-based studies in the region (4,024 OTUs, 10-fold increase), despite conservative bioinformatic processing. Operational taxonomic unit (OTU) richness of the full assemblage peaked at lower epipelagic-upper mesopelagic depths (100-300 m), with slight shoaling of maximal richness at night due to diel vertical migration, in contrast to expectations of a deep mesopelagic diversity maximum as reported for several plankton groups in early systematic and zoogeographic studies. Four distinct depth-stratified species assemblages were identified, with faunal transitions occurring at 100 m, 300 m and 500 m. Highest diversity occurred in the smallest zooplankton size fractions (0.2-0.5 mm), which had significantly lower % OTUs classified due to poor representation in reference databases, suggesting a deep reservoir of poorly understood diversity in the smallest metazoan animals. A diverse meroplankton assemblage also was detected (350 OTUs), including larvae of both shallow and deep living benthic species. Our results provide some of the first insights into the hidden diversity present in zooplankton assemblages in midwaters, and a molecular reappraisal of vertical gradients in species richness, depth distributions and community composition for the full zooplankton assemblage across the epipelagic, mesopelagic and upper bathypelagic zones. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Nuclear Science References (NSR)

Science.gov Websites

be included. For more information, see the help page. The NSR database schema and Web applications have undergone some recent changes. This is a revised version of the NSR Web Interface. NSR Quick Manager: Boris Pritychenko, NNDC, Brookhaven National Laboratory Web Programming: Boris Pritychenko, NNDC

Getting To Know the "Invisible Web."

ERIC Educational Resources Information Center

Smith, C. Brian

2001-01-01

Discusses the portions of the World Wide Web that cannot be accessed via directories or search engines, explains why they can't be accessed, and offers suggestions for reference librarians to find these sites. Lists helpful resources and gives examples of invisible Web sites which are often databases. (LRW)

Integration of the NRL Digital Library.

ERIC Educational Resources Information Center

King, James

2001-01-01

The Naval Research Laboratory (NRL) Library has identified six primary areas that need improvement: infrastructure, InfoWeb, TORPEDO Ultra, journal data management, classified data, and linking software. It is rebuilding InfoWeb and TORPEDO Ultra as database-driven Web applications, upgrading the STILAS library catalog, and creating other support…

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

PubMed

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

2014-03-01

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

A web-based approach for electrocardiogram monitoring in the home.

PubMed

Magrabi, F; Lovell, N H; Celler, B G

1999-05-01

A Web-based electrocardiogram (ECG) monitoring service in which a longitudinal clinical record is used for management of patients, is described. The Web application is used to collect clinical data from the patient's home. A database on the server acts as a central repository where this clinical information is stored. A Web browser provides access to the patient's records and ECG data. We discuss the technologies used to automate the retrieval and storage of clinical data from a patient database, and the recording and reviewing of clinical measurement data. On the client's Web browser, ActiveX controls embedded in the Web pages provide a link between the various components including the Web server, Web page, the specialised client side ECG review and acquisition software, and the local file system. The ActiveX controls also implement FTP functions to retrieve and submit clinical data to and from the server. An intelligent software agent on the server is activated whenever new ECG data is sent from the home. The agent compares historical data with newly acquired data. Using this method, an optimum patient care strategy can be evaluated, a summarised report along with reminders and suggestions for action is sent to the doctor and patient by email.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

PubMed Central

Lizio, Marina; Harshbarger, Jayson; Abugessaisa, Imad; Noguchi, Shuei; Kondo, Atsushi; Severin, Jessica; Mungall, Chris; Arenillas, David; Mathelier, Anthony; Medvedeva, Yulia A.; Lennartsson, Andreas; Drabløs, Finn; Ramilowski, Jordan A.; Rackham, Owen; Gough, Julian; Andersson, Robin; Sandelin, Albin; Ienasescu, Hans; Ono, Hiromasa; Bono, Hidemasa; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R.R.; Kasukawa, Takeya; Kawaji, Hideya

2017-01-01

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives. PMID:27794045

50 CFR 679.21 - Prohibited species bycatch management.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Region Web site (http://alaskafisheries.noaa.gov/). (c) Salmon taken in the BS pollock fisheries... GOA groundfish species or species group. (B) Deep-water species fishery. Fishing with trawl gear... combine management of available trawl halibut PSC limits in the second season deep-water and shallow-water...

Deep Lake Explorer: Bringing citizen scientists to the underwater world of the Great Lakes

EPA Science Inventory

Deep Lake Explorer is a web application hosted on the Zooniverse platform that allows the public to interpret underwater video collected in the Great Lakes. Crowdsourcing image interpretation using the Zooniverse platform has proven successful for many projects, but few projects ...

THE NASA AMES POLYCYCLIC AROMATIC HYDROCARBON INFRARED SPECTROSCOPIC DATABASE: THE COMPUTED SPECTRA

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

Bauschlicher, C. W.; Ricca, A.; Boersma, C.

The astronomical emission features, formerly known as the unidentified infrared bands, are now commonly ascribed to polycyclic aromatic hydrocarbons (PAHs). The laboratory experiments and computational modeling done at the NASA Ames Research Center to create a collection of PAH IR spectra relevant to test and refine the PAH hypothesis have been assembled into a spectroscopic database. This database now contains over 800 PAH spectra spanning 2-2000 {mu}m (5000-5 cm{sup -1}). These data are now available on the World Wide Web at www.astrochem.org/pahdb. This paper presents an overview of the computational spectra in the database and the tools developed to analyzemore » and interpret astronomical spectra using the database. A description of the online and offline user tools available on the Web site is also presented.« less

Correspondence: World Wide Web access to the British Universities Human Embryo Database

PubMed Central

AITON, JAMES F.; MCDONOUGH, ARIANA; MCLACHLAN, JOHN C.; SMART, STEVEN D.; WHITEN, SUSAN C.

1997-01-01

The British Universities Human Embryo Database has been created by merging information from the Walmsley Collection of Human Embryos at the School of Biological and Medical Sciences, University of St Andrews and from the Boyd Collection of Human Embryos at the Department of Anatomy, University of Cambridge. The database has been made available electronically on the Internet and World Wide Web browsers can be used to implement interactive access to the information stored in the British Universities Human Embryo Database. The database can, therefore, be accessed and searched from remote sites and specific embryos can be identified in terms of their location, age, developmental stage, plane of section, staining technique, and other parameters. It is intended to add information from other similar collections in the UK as it becomes available. PMID:9034891

LigSearch: a knowledge-based web server to identify likely ligands for a protein target

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

Beer, Tjaart A. P. de; Laskowski, Roman A.; Duban, Mark-Eugene

LigSearch is a web server for identifying ligands likely to bind to a given protein. Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

Querying XML Data with SPARQL

NASA Astrophysics Data System (ADS)

Bikakis, Nikos; Gioldasis, Nektarios; Tsinaraki, Chrisa; Christodoulakis, Stavros

SPARQL is today the standard access language for Semantic Web data. In the recent years XML databases have also acquired industrial importance due to the widespread applicability of XML in the Web. In this paper we present a framework that bridges the heterogeneity gap and creates an interoperable environment where SPARQL queries are used to access XML databases. Our approach assumes that fairly generic mappings between ontology constructs and XML Schema constructs have been automatically derived or manually specified. The mappings are used to automatically translate SPARQL queries to semantically equivalent XQuery queries which are used to access the XML databases. We present the algorithms and the implementation of SPARQL2XQuery framework, which is used for answering SPARQL queries over XML databases.

ESTuber db: an online database for Tuber borchii EST sequences.

PubMed

Lazzari, Barbara; Caprera, Andrea; Cosentino, Cristian; Stella, Alessandra; Milanesi, Luciano; Viotti, Angelo

2007-03-08

The ESTuber database (http://www.itb.cnr.it/estuber) includes 3,271 Tuber borchii expressed sequence tags (EST). The dataset consists of 2,389 sequences from an in-house prepared cDNA library from truffle vegetative hyphae, and 882 sequences downloaded from GenBank and representing four libraries from white truffle mycelia and ascocarps at different developmental stages. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts. Data were collected in a MySQL database, which can be queried via a php-based web interface. Sequences included in the ESTuber db were clustered and annotated against three databases: the GenBank nr database, the UniProtKB database and a third in-house prepared database of fungi genomic sequences. An algorithm was implemented to infer statistical classification among Gene Ontology categories from the ontology occurrences deduced from the annotation procedure against the UniProtKB database. Ontologies were also deduced from the annotation of more than 130,000 EST sequences from five filamentous fungi, for intra-species comparison purposes. Further analyses were performed on the ESTuber db dataset, including tandem repeats search and comparison of the putative protein dataset inferred from the EST sequences to the PROSITE database for protein patterns identification. All the analyses were performed both on the complete sequence dataset and on the contig consensus sequences generated by the EST assembly procedure. The resulting web site is a resource of data and links related to truffle expressed genes. The Sequence Report and Contig Report pages are the web interface core structures which, together with the Text search utility and the Blast utility, allow easy access to the data stored in the database.

A systematic review of ultrasound-accelerated catheter-directed thrombolysis in the treatment of deep vein thrombosis.

PubMed

Shi, Yadong; Shi, Wanyin; Chen, Liang; Gu, Jianping

2018-04-01

To review the clinical evidence for ultrasound-accelerated catheter-directed thrombolysis (UACDT) using the EKOS system in the treatment of deep vein thrombosis (DVT) in terms of case selection, procedural outcomes, clinical outcomes and safety outcomes. A systematic literature search strategy was used to identify the use of the EKOS system in the treatment of DVT using the following electronic databases: MEDLINE, EMBASE, the Cochrane databases and the Web of Science. The references in the relevant literature were also screened. Our literature search identified a total of 16 unique clinical studies. Twelve of the sixteen studies were retrospective case series studies. To date, only one randomised controlled trial (RCT) is available. Overall, UACDT using the EKOS system was performed 548 times in 512 patients. Among all cases, 77-100% achieved substantial lysis (> 50%) based on the different definitions of the individual studies. This treatment modality appears to be safe, as there were no reported procedure-related pulmonary embolisms (PE) and only one procedure-related death was reported. Bleeding events were reported in 14 of the 16 studies, and 3.9% (20/512) of the cases of bleeding were considered major. During the follow-up, post-thrombotic syndrome was observed in 17.1% (20/117) of cases. UACDT using the EKOS system is an effective, safe and promising treatment modality for DVT, but the existing clinical evidence is inadequate to make UACDT using the EKOS system the first-line choice for DVT. Additional prospective large-sample RCTs with long-term follow-ups are warranted to define the role of UACDT using the EKOS system in the treatment of DVT.

Meta-analysis of the efficacy and safety of combined surgery in the management of eyes with coexisting cataract and open angle glaucoma.

PubMed

Jiang, Nan; Zhao, Gui-Qiu; Lin, Jing; Hu, Li-Ting; Che, Cheng-Ye; Wang, Qian; Xu, Qiang; Li, Cui; Zhang, Jie

2018-01-01

To conduct a systematic review and quantitative Meta-analysis of the efficacy and safety of combined surgery for the eyes with coexisting cataract and open angle glaucoma. We performed a systematic search of the related literature in the Cochrane Library, PubMed, EMBASE, Web of Science databases, CNKI, CBM and Wan Fang databases, with no limitations on language or publication date. The primary efficacy estimate was identified by weighted mean difference of the percentage of intraocular pressure reduction (IOPR%) from baseline to end-point, the percentage of number of glaucoma medications reduction from pre- to post-operation, and the secondary efficacy evaluations were performed by odds ratio (OR) and 95% confidence interval (CI) for complete and qualified success rate. Besides, ORs were applied to assess the tolerability of adverse incidents. Meta-analyses of fixed or random effect models were performed using RevMan software 5.2 to gather the consequences. Heterogeneity was evaluated by Chi 2 test and the I 2 measure. Ten studies enrolling 3108 patients were included. The combined consequences indicated that both glaucoma and combined cataract and glaucoma surgery significantly decreased IOP. For deep sclerectomy vs deep sclerectomy plus phacoemulsification and canaloplasty vs phaco-canaloplasty, the differences in IOPR% were not all statistically significant while trabeculotomy was detected to gain a quantitatively greater IOPR% compared with trabeculotomy plus phacoemulsification. Furthermore, there was no statistical significance in the complete and qualified success rate, and the rates of adverse incidents for trabeculotomy vs trabeculotomy plus phacoemulsification. Compared with trabeculotomy plus phacoemulsification, trabeculectomy alone is more effective in lowering IOP and the number of glaucoma medications, while the two surgeries can not demonstrate statistical differences in the complete success rate, qualified success rate, or incidence of adverse incidents.

Hot Topics on the Web: Strategies for Research.

ERIC Educational Resources Information Center

Diaz, Karen R.; O'Hanlon, Nancy

2001-01-01

Presents strategies for researching topics on the Web that are controversial or current in nature. Discusses topic selection and overviews, including the use of online encyclopedias; search engines; finding laws and pending legislation; advocacy groups; proprietary databases; Web site evaluation; and the continuing usefulness of print materials.…

Market Research: The World Wide Web Meets the Online Services.

ERIC Educational Resources Information Center

Bing, Michelle

1996-01-01

The World Wide Web can provide direct market research data inexpensively or can target the appropriate professional online database and narrow the search. This article discusses the Web presence of research and investment firms, financial pages, trade associations, and electronic publications containing market research data. It lists Uniform…

The Implications of Well-Formedness on Web-Based Educational Resources.

ERIC Educational Resources Information Center

Mohler, James L.

Within all institutions, Web developers are beginning to utilize technologies that make sites more than static information resources. Databases such as XML (Extensible Markup Language) and XSL (Extensible Stylesheet Language) are key technologies that promise to extend the Web beyond the "information storehouse" paradigm and provide…

50 CFR 679.21 - Prohibited species bycatch management.

Code of Federal Regulations, 2012 CFR

2012-10-01

... to 907-586-7465. Forms are available on the NMFS Alaska Region Web site (http://alaskafisheries.noaa... the retained aggregate amount of other GOA groundfish species or species group. (B) Deep-water species... the NMFS Alaska Region Web site (http://alaskafisheries.noaa.gov/): (A) The Chinook salmon PSC...

Asynchronous Discourse in a Web-Assisted Mathematics Education Course

ERIC Educational Resources Information Center

Li, Zhongxiao

2009-01-01

Fall term of 2006, a web-assisted undergraduate mathematics course was taught at the University of Idaho: Math 235 Mathematics for Elementary Teachers I. The course goals were: To foster a deep understanding of critical mathematical content; and to promote the development of mathematical communication and collaboration concepts, skills, and…

Search Interface Design Using Faceted Indexing for Web Resources.

ERIC Educational Resources Information Center

Devadason, Francis; Intaraksa, Neelawat; Patamawongjariya, Pornprapa; Desai, Kavita

2001-01-01

Describes an experimental system designed to organize and provide access to Web documents using a faceted pre-coordinate indexing system based on the Deep Structure Indexing System (DSIS) derived from POPSI (Postulate based Permuted Subject Indexing) of Bhattacharyya, and the facet analysis and chain indexing system of Ranganathan. (AEF)

Next-Gen Search Engines

ERIC Educational Resources Information Center

Gupta, Amardeep

2005-01-01

Current search engines--even the constantly surprising Google--seem unable to leap the next big barrier in search: the trillions of bytes of dynamically generated data created by individual web sites around the world, or what some researchers call the "deep web." The challenge now is not information overload, but information overlook.…

Web-based Electronic Sharing and RE-allocation of Assets

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

Leverett, Dave; Miller, Robert A.; Berlin, Gary J.

2002-09-09

The Electronic Asses Sharing Program is a web-based application that provides the capability for complex-wide sharing and reallocation of assets that are excess, under utilized, or un-utilized. through a web-based fron-end and supporting has database with a search engine, users can search for assets that they need, search for assets needed by others, enter assets they need, and enter assets they have available for reallocation. In addition, entire listings of available assets and needed assets can be viewed. The application is written in Java, the hash database and search engine are in Object-oriented Java Database Management (OJDBM). The application willmore » be hosted on an SRS-managed server outside the Firewall and access will be controlled via a protected realm. An example of the application can be viewed at the followinig (temporary) URL: http://idgdev.srs.gov/servlet/srs.weshare.WeShare« less

Design and implementation of website information disclosure assessment system.

PubMed

Cho, Ying-Chiang; Pan, Jen-Yi

2015-01-01

Internet application technologies, such as cloud computing and cloud storage, have increasingly changed people's lives. Websites contain vast amounts of personal privacy information. In order to protect this information, network security technologies, such as database protection and data encryption, attract many researchers. The most serious problems concerning web vulnerability are e-mail address and network database leakages. These leakages have many causes. For example, malicious users can steal database contents, taking advantage of mistakes made by programmers and administrators. In order to mitigate this type of abuse, a website information disclosure assessment system is proposed in this study. This system utilizes a series of technologies, such as web crawler algorithms, SQL injection attack detection, and web vulnerability mining, to assess a website's information disclosure. Thirty websites, randomly sampled from the top 50 world colleges, were used to collect leakage information. This testing showed the importance of increasing the security and privacy of website information for academic websites.

Automatic Generation of Data Types for Classification of Deep Web Sources

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

Ngu, A H; Buttler, D J; Critchlow, T J

2005-02-14

A Service Class Description (SCD) is an effective meta-data based approach for discovering Deep Web sources whose data exhibit some regular patterns. However, it is tedious and error prone to create an SCD description manually. Moreover, a manually created SCD is not adaptive to the frequent changes of Web sources. It requires its creator to identify all the possible input and output types of a service a priori. In many domains, it is impossible to exhaustively list all the possible input and output data types of a source in advance. In this paper, we describe machine learning approaches for automaticmore » generation of the data types of an SCD. We propose two different approaches for learning data types of a class of Web sources. The Brute-Force Learner is able to generate data types that can achieve high recall, but with low precision. The Clustering-based Learner generates data types that have a high precision rate, but with a lower recall rate. We demonstrate the feasibility of these two learning-based solutions for automatic generation of data types for citation Web sources and presented a quantitative evaluation of these two solutions.« less

ToTem: a tool for variant calling pipeline optimization.

PubMed

Tom, Nikola; Tom, Ondrej; Malcikova, Jitka; Pavlova, Sarka; Kubesova, Blanka; Rausch, Tobias; Kolarik, Miroslav; Benes, Vladimir; Bystry, Vojtech; Pospisilova, Sarka

2018-06-26

High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall. Here we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user's priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data. ToTem is a tool for automated pipeline optimization which is freely available as a web application at  https://totem.software .

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.

Drinking Water Treatability Database (Database)

EPA Science Inventory

The drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, rec...

Evaluation of the Content and Accessibility of Web Sites for Accredited Orthopaedic Trauma Surgery Fellowships.

PubMed

Shaath, M Kareem; Yeranosian, Michael G; Ippolito, Joseph A; Adams, Mark R; Sirkin, Michael S; Reilly, Mark C

2018-05-02

Orthopaedic trauma fellowship applicants use online-based resources when researching information on potential U.S. fellowship programs. The 2 primary sources for identifying programs are the Orthopaedic Trauma Association (OTA) database and the San Francisco Match (SF Match) database. Previous studies in other orthopaedic subspecialty areas have demonstrated considerable discrepancies among fellowship programs. The purpose of this study was to analyze content and availability of information on orthopaedic trauma surgery fellowship web sites. The online databases of the OTA and SF Match were reviewed to determine the availability of embedded program links or external links for the included programs. Thereafter, a Google search was performed for each program individually by typing the program's name, followed by the term "orthopaedic trauma fellowship." All identified fellowship web sites were analyzed for accessibility and content. Web sites were evaluated for comprehensiveness in mentioning key components of the orthopaedic trauma surgery curriculum. By consensus, we refined the final list of variables utilizing the methodology of previous studies on the topic. We identified 54 OTA-accredited fellowship programs, offering 87 positions. The majority (94%) of programs had web sites accessible through a Google search. Of the 51 web sites found, all (100%) described their program. Most commonly, hospital affiliation (88%), operative experiences (76%), and rotation overview (65%) were listed, and, least commonly, interview dates (6%), selection criteria (16%), on-call requirements (20%), and fellow evaluation criteria (20%) were listed. Programs with ≥2 fellows provided more information with regard to education content (p = 0.0001) and recruitment content (p = 0.013). Programs with Accreditation Council for Graduate Medical Education (ACGME) accreditation status also provided greater information with regard to education content (odds ratio, 4.0; p = 0.0001). Otherwise, no differences were seen by region, residency affiliation, medical school affiliation, or hospital affiliation. The SF Match and OTA databases provide few direct links to fellowship web sites. Individual program web sites do not effectively and completely convey information about the programs. The Internet is an underused resource for fellow recruitment. The lack of information on these sites allows for future opportunity to optimize this resource.

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data

PubMed Central

2016-01-01

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app. PMID:27302480

An XML-based Generic Tool for Information Retrieval in Solar Databases

NASA Astrophysics Data System (ADS)

Scholl, Isabelle F.; Legay, Eric; Linsolas, Romain

This paper presents the current architecture of the `Solar Web Project' now in its development phase. This tool will provide scientists interested in solar data with a single web-based interface for browsing distributed and heterogeneous catalogs of solar observations. The main goal is to have a generic application that can be easily extended to new sets of data or to new missions with a low level of maintenance. It is developed with Java and XML is used as a powerful configuration language. The server, independent of any database scheme, can communicate with a client (the user interface) and several local or remote archive access systems (such as existing web pages, ftp sites or SQL databases). Archive access systems are externally described in XML files. The user interface is also dynamically generated from an XML file containing the window building rules and a simplified database description. This project is developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France). Successful tests have been conducted with other solar archive access systems.

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.

PubMed

Riffle, Michael; Jaschob, Daniel; Zelter, Alex; Davis, Trisha N

2016-08-05

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app .

ShapeShop: Towards Understanding Deep Learning Representations via Interactive Experimentation.

PubMed

Hohman, Fred; Hodas, Nathan; Chau, Duen Horng

2017-05-01

Deep learning is the driving force behind many recent technologies; however, deep neural networks are often viewed as "black-boxes" due to their internal complexity that is hard to understand. Little research focuses on helping people explore and understand the relationship between a user's data and the learned representations in deep learning models. We present our ongoing work, ShapeShop, an interactive system for visualizing and understanding what semantics a neural network model has learned. Built using standard web technologies, ShapeShop allows users to experiment with and compare deep learning models to help explore the robustness of image classifiers.

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.

X-ray Photoelectron Spectroscopy Database (Version 4.1)

National Institute of Standards and Technology Data Gateway

SRD 20 X-ray Photoelectron Spectroscopy Database (Version 4.1) (Web, free access)   The NIST XPS Database gives access to energies of many photoelectron and Auger-electron spectral lines. The database contains over 22,000 line positions, chemical shifts, doublet splittings, and energy separations of photoelectron and Auger-electron lines.

Mashups over the Deep Web

NASA Astrophysics Data System (ADS)

Hornung, Thomas; Simon, Kai; Lausen, Georg

Combining information from different Web sources often results in a tedious and repetitive process, e.g. even simple information requests might require to iterate over a result list of one Web query and use each single result as input for a subsequent query. One approach for this chained queries are data-centric mashups, which allow to visually model the data flow as a graph, where the nodes represent the data source and the edges the data flow.

Sagace: A web-based search engine for biomedical databases in Japan

PubMed Central

2012-01-01

Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data) and biological resource banks (such as mouse models of disease and cell lines). With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/. PMID:23110816

The EMBL nucleotide sequence database

PubMed Central

Stoesser, Guenter; Baker, Wendy; van den Broek, Alexandra; Camon, Evelyn; Garcia-Pastor, Maria; Kanz, Carola; Kulikova, Tamara; Lombard, Vincent; Lopez, Rodrigo; Parkinson, Helen; Redaschi, Nicole; Sterk, Peter; Stoehr, Peter; Tuli, Mary Ann

2001-01-01

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. PMID:11125039

Transvaginal ultrasound versus magnetic resonance imaging for preoperative assessment of myometrial infiltration in patients with endometrial cancer: a systematic review and meta-analysis.

PubMed

Alcázar, Juan Luis; Gastón, Begoña; Navarro, Beatriz; Salas, Rocío; Aranda, Juana; Guerriero, Stefano

2017-11-01

To compare the diagnostic accuracy of transvaginal ultrasound (TVS) and magnetic resonance imaging (MRI) for detecting myometrial infiltration (MI) in endometrial carcinoma. An extensive search of papers comparing TVS and MRI in assessing MI in endometrial cancer was performed in MEDLINE (PubMed), Web of Science, and Cochrane Database from January 1989 to January 2017. Quality was assessed using Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool. Our extended search identified 747 citations but after exclusions we finally included in the meta-analysis 8 articles. The risk of bias for most studies was low for most 4 domains assessed in QUADAS-2. Overall, pooled estimated sensitivity and specificity for diagnosing deep MI were 75% (95% confidence interval [CI]=67%-82%) and 82% (95% CI=75%-93%) for TVS, and 83% (95% CI=76%-89%) and 82% (95% CI=72%-89%) for MRI, respectively. No statistical differences were found when comparing both methods (p=0.314). Heterogeneity was low for sensitivity and high for specificity for TVS and MRI. MRI showed a better sensitivity than TVS for detecting deep MI in women with endometrial cancer. However, the difference observed was not statistically significant. Copyright © 2017. Asian Society of Gynecologic Oncology, Korean Society of Gynecologic Oncology

Accuracy of magnetic resonance in deeply infiltrating endometriosis: a systematic review and meta-analysis.

PubMed

Medeiros, Lídia Rossi; Rosa, Maria Inês; Silva, Bruno Rosa; Reis, Maria Eduarda; Simon, Carla Sasso; Dondossola, Eduardo Ronconi; da Cunha Filho, João Sabino

2015-03-01

To estimate the accuracy of pelvic magnetic resonance imaging (MRI) in the diagnosis of deeply infiltrating endometriosis (DIE). A comprehensive search of the Medline, Pubmed, Lilacs, Scopus, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Biomed Central, and ISI Web of Science databases was conducted from January 1990 to December 2013. The medical subject headings (MeSHs) and text words "deep endometriosis", "deeply infiltrating endometriosis", "DIE", "magnetic resonance", and "MRI" were searched. Studies that compared the parameters of pelvic MRIs with those of paraffin-embedded sections for the diagnosis of DIE were included. Twenty studies were analyzed, which included 1,819 women. Pooled sensitivity and specificity were calculated across eight subgroups: for all sites, these were 0.83 and 0.90, respectively; for the bladder, 0.64 and 0.98, respectively; for the intestine, 0.84 and 0.97, respectively; for the pouch of Douglas, 0.89 and 0.94, respectively; for the rectosigmoid, 0.83 and 0.88, respectively; for the rectovaginal, 0.77 and 0.95, respectively; for the uterosacral ligaments, 0.85 and 0.80, respectively; and for the vagina and the posterior vaginal fornix, 0.82 and 0.82, respectively. In summary, pelvic MRI is a useful preoperative test for predicting the diagnosis of multiple sites of deep infiltrating endometriosis.

Bayesian mixture analysis for metagenomic community profiling.

PubMed

Morfopoulou, Sofia; Plagnol, Vincent

2015-09-15

Deep sequencing of clinical samples is now an established tool for the detection of infectious pathogens, with direct medical applications. The large amount of data generated produces an opportunity to detect species even at very low levels, provided that computational tools can effectively profile the relevant metagenomic communities. Data interpretation is complicated by the fact that short sequencing reads can match multiple organisms and by the lack of completeness of existing databases, in particular for viral pathogens. Here we present metaMix, a Bayesian mixture model framework for resolving complex metagenomic mixtures. We show that the use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species most likely to contribute to the mixture. We demonstrate the greater accuracy of metaMix compared with relevant methods, particularly for profiling complex communities consisting of several related species. We designed metaMix specifically for the analysis of deep transcriptome sequencing datasets, with a focus on viral pathogen detection; however, the principles are generally applicable to all types of metagenomic mixtures. metaMix is implemented as a user friendly R package, freely available on CRAN: http://cran.r-project.org/web/packages/metaMix sofia.morfopoulou.10@ucl.ac.uk Supplementary data are available at Bionformatics online. © The Author 2015. Published by Oxford University Press.

Transvaginal ultrasound versus magnetic resonance imaging for preoperative assessment of myometrial infiltration in patients with endometrial cancer: a systematic review and meta-analysis

PubMed Central

2017-01-01

Objective To compare the diagnostic accuracy of transvaginal ultrasound (TVS) and magnetic resonance imaging (MRI) for detecting myometrial infiltration (MI) in endometrial carcinoma. Methods An extensive search of papers comparing TVS and MRI in assessing MI in endometrial cancer was performed in MEDLINE (PubMed), Web of Science, and Cochrane Database from January 1989 to January 2017. Quality was assessed using Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool. Results Our extended search identified 747 citations but after exclusions we finally included in the meta-analysis 8 articles. The risk of bias for most studies was low for most 4 domains assessed in QUADAS-2. Overall, pooled estimated sensitivity and specificity for diagnosing deep MI were 75% (95% confidence interval [CI]=67%–82%) and 82% (95% CI=75%–93%) for TVS, and 83% (95% CI=76%–89%) and 82% (95% CI=72%–89%) for MRI, respectively. No statistical differences were found when comparing both methods (p=0.314). Heterogeneity was low for sensitivity and high for specificity for TVS and MRI. Conclusion MRI showed a better sensitivity than TVS for detecting deep MI in women with endometrial cancer. However, the difference observed was not statistically significant. PMID:29027404

Organizational Alignment Through Information Technology: A Web-Based Approach to Change

NASA Technical Reports Server (NTRS)

Heinrichs, W.; Smith, J.

1999-01-01

This paper reports on the effectiveness of web-based internet tools and databases to facilitate integration of technical organizations with interfaces that minimize modification of each technical organization.

Similar cerebral protective effectiveness of antegrade and retrograde cerebral perfusion combined with deep hypothermia circulatory arrest in aortic arch surgery: a meta-analysis and systematic review of 5060 patients.

PubMed

Hu, Zhipeng; Wang, Zhiwei; Ren, Zongli; Wu, Hongbing; Zhang, Min; Zhang, Hao; Hu, Xiaoping

2014-08-01

Our objective was to determine if antegrade cerebral perfusion (ACP) and retrograde cerebral perfusion (RCP) combined with deep hypothermia circulatory arrest in aortic arch surgery results in different mortality and neurologic outcomes. The Cochrane Library, Medline, EMBASE, CINAHL, Web of Science, and the Chinese Biomedical Database were searched for studies reporting on postoperative strokes, permanent neurologic dysfunction, temporary neurologic dysfunction, and all causes mortality within 30 days postoperation in aortic arch surgery. Meta-analysis for effect size, t test, and I(2) for detecting heterogeneity and sensitivity analysis for assessing the relative influence of each study was performed. Fifteen included studies encompassed a total of 5060 patients of whom 2855 were treated with deep hypothermic circulatory arrest plus ACP and 1897 were treated with deep hypothermic circulatory arrest plus RCP. Pooled analysis showed no significant statistical difference (P > .01) of 30-day mortality, permanent neurologic dysfunction, and transient neurologic dysfunction in the 2 groups. Before sensitivity analysis, postoperative stroke incidence in the ACP group was higher than in the RCP group (7.2% vs 4.7%; P < .01). After a study that included a different percentage of patients with a history of central neurologic events in the 2 groups was ruled out, postoperative stroke incidence in the 2 groups also showed no significant statistical difference (P > .01). ACP and RCP provide similar cerebral protective effectiveness combined with deep hypothermia circulatory arrest and could be selected according to the actual condition in aortic arch surgery. A high-quality randomized controlled trial is urgently needed to confirm this conclusion, especially for stroke morbidity following ACP or RCP. Copyright © 2014 The American Association for Thoracic Surgery. Published by Mosby, Inc. All rights reserved.

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

CHIP Demonstrator: Semantics-Driven Recommendations and Museum Tour Generation

NASA Astrophysics Data System (ADS)

Aroyo, Lora; Stash, Natalia; Wang, Yiwen; Gorgels, Peter; Rutledge, Lloyd

The main objective of the CHIP project is to demonstrate how Semantic Web technologies can be deployed to provide personalized access to digital museum collections. We illustrate our approach with the digital database ARIA of the Rijksmuseum Amsterdam. For the semantic enrichment of the Rijksmuseum ARIA database we collaborated with the CATCH STITCH project to produce mappings to Iconclass, and with the MultimediaN E-culture project to produce the RDF/OWL of the ARIA and Adlib databases. The main focus of CHIP is on exploring the potential of applying adaptation techniques to provide personalized experience for the museum visitors both on the Web site and in the museum.

The JANA calibrations and conditions database API

NASA Astrophysics Data System (ADS)

Lawrence, David

2010-04-01

Calibrations and conditions databases can be accessed from within the JANA Event Processing framework through the API defined in its JCalibration base class. The API is designed to support everything from databases, to web services to flat files for the backend. A Web Service backend using the gSOAP toolkit has been implemented which is particularly interesting since it addresses many modern cybersecurity issues including support for SSL. The API allows constants to be retrieved through a single line of C++ code with most of the context, including the transport mechanism, being implied by the run currently being analyzed and the environment relieving developers from implementing such details.

CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.

PubMed

Hallin, Peter F; Ussery, David W

2004-12-12

Currently, new bacterial genomes are being published on a monthly basis. With the growing amount of genome sequence data, there is a demand for a flexible and easy-to-maintain structure for storing sequence data and results from bioinformatic analysis. More than 150 sequenced bacterial genomes are now available, and comparisons of properties for taxonomically similar organisms are not readily available to many biologists. In addition to the most basic information, such as AT content, chromosome length, tRNA count and rRNA count, a large number of more complex calculations are needed to perform detailed comparative genomics. DNA structural calculations like curvature and stacking energy, DNA compositions like base skews, oligo skews and repeats at the local and global level are just a few of the analysis that are presented on the CBS Genome Atlas Web page. Complex analysis, changing methods and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently, these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues. A web based user interface which is dynamically linked to the Genome Atlas Database can be accessed via www.cbs.dtu.dk/services/GenomeAtlas/. This paper has a supplemental information page which links to the examples presented: www.cbs.dtu.dk/services/GenomeAtlas/suppl/bioinfdatabase.

Advancements in web-database applications for rabies surveillance.

PubMed

Rees, Erin E; Gendron, Bruno; Lelièvre, Frédérick; Coté, Nathalie; Bélanger, Denise

2011-08-02

Protection of public health from rabies is informed by the analysis of surveillance data from human and animal populations. In Canada, public health, agricultural and wildlife agencies at the provincial and federal level are responsible for rabies disease control, and this has led to multiple agency-specific data repositories. Aggregation of agency-specific data into one database application would enable more comprehensive data analyses and effective communication among participating agencies. In Québec, RageDB was developed to house surveillance data for the raccoon rabies variant, representing the next generation in web-based database applications that provide a key resource for the protection of public health. RageDB incorporates data from, and grants access to, all agencies responsible for the surveillance of raccoon rabies in Québec. Technological advancements of RageDB to rabies surveillance databases include (1) automatic integration of multi-agency data and diagnostic results on a daily basis; (2) a web-based data editing interface that enables authorized users to add, edit and extract data; and (3) an interactive dashboard to help visualize data simply and efficiently, in table, chart, and cartographic formats. Furthermore, RageDB stores data from citizens who voluntarily report sightings of rabies suspect animals. We also discuss how sightings data can indicate public perception to the risk of racoon rabies and thus aid in directing the allocation of disease control resources for protecting public health. RageDB provides an example in the evolution of spatio-temporal database applications for the storage, analysis and communication of disease surveillance data. The database was fast and inexpensive to develop by using open-source technologies, simple and efficient design strategies, and shared web hosting. The database increases communication among agencies collaborating to protect human health from raccoon rabies. Furthermore, health agencies have real-time access to a wide assortment of data documenting new developments in the raccoon rabies epidemic and this enables a more timely and appropriate response.

Advancements in web-database applications for rabies surveillance

PubMed Central

2011-01-01

Background Protection of public health from rabies is informed by the analysis of surveillance data from human and animal populations. In Canada, public health, agricultural and wildlife agencies at the provincial and federal level are responsible for rabies disease control, and this has led to multiple agency-specific data repositories. Aggregation of agency-specific data into one database application would enable more comprehensive data analyses and effective communication among participating agencies. In Québec, RageDB was developed to house surveillance data for the raccoon rabies variant, representing the next generation in web-based database applications that provide a key resource for the protection of public health. Results RageDB incorporates data from, and grants access to, all agencies responsible for the surveillance of raccoon rabies in Québec. Technological advancements of RageDB to rabies surveillance databases include 1) automatic integration of multi-agency data and diagnostic results on a daily basis; 2) a web-based data editing interface that enables authorized users to add, edit and extract data; and 3) an interactive dashboard to help visualize data simply and efficiently, in table, chart, and cartographic formats. Furthermore, RageDB stores data from citizens who voluntarily report sightings of rabies suspect animals. We also discuss how sightings data can indicate public perception to the risk of racoon rabies and thus aid in directing the allocation of disease control resources for protecting public health. Conclusions RageDB provides an example in the evolution of spatio-temporal database applications for the storage, analysis and communication of disease surveillance data. The database was fast and inexpensive to develop by using open-source technologies, simple and efficient design strategies, and shared web hosting. The database increases communication among agencies collaborating to protect human health from raccoon rabies. Furthermore, health agencies have real-time access to a wide assortment of data documenting new developments in the raccoon rabies epidemic and this enables a more timely and appropriate response. PMID:21810215

WheatGenome.info: A Resource for Wheat Genomics Resource.

PubMed

Lai, Kaitao

2016-01-01

An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ .

UnCover on the Web: search hints and applications in library environments.

PubMed

Galpern, N F; Albert, K M

1997-01-01

Among the huge maze of resources available on the Internet, UnCoverWeb stands out as a valuable tool for medical libraries. This up-to-date, free-access, multidisciplinary database of periodical references is searched through an easy-to-learn graphical user interface that is a welcome improvement over the telnet version. This article reviews the basic and advanced search techniques for UnCoverWeb, as well as providing information on the document delivery functions and table of contents alerting service called Reveal. UnCover's currency is evaluated and compared with other current awareness resources. System deficiencies are discussed, with the conclusion that although UnCoverWeb lacks the sophisticated features of many commercial database search services, it is nonetheless a useful addition to the repertoire of information sources available in a library.

Public outreach and communications of the Alaska Volcano Observatory during the 2005-2006 eruption of Augustine Volcano: Chapter 27 in The 2006 eruption of Augustine Volcano, Alaska

USGS Publications Warehouse

Adleman, Jennifer N.; Cameron, Cheryl E.; Snedigar, Seth F.; Neal, Christina A.; Wallace, Kristi L.; Power, John A.; Coombs, Michelle L.; Freymueller, Jeffrey T.

2010-01-01

The AVO Web site, with its accompanying database, is the backbone of AVO's external and internal communications. This was the first Cook Inlet volcanic eruption with a public expectation of real-time access to data, updates, and hazards information over the Internet. In March 2005, AVO improved the Web site from individual static pages to a dynamic, database-driven site. This new system provided quick and straightforward access to the latest information for (1) staff within the observatory, (2) emergency managers from State and local governments and organizations, (3) the media, and (4) the public. From mid-December 2005 through April 2006, the AVO Web site served more than 45 million Web pages and about 5.5 terabytes of data.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

PubMed

Lizio, Marina; Harshbarger, Jayson; Abugessaisa, Imad; Noguchi, Shuei; Kondo, Atsushi; Severin, Jessica; Mungall, Chris; Arenillas, David; Mathelier, Anthony; Medvedeva, Yulia A; Lennartsson, Andreas; Drabløs, Finn; Ramilowski, Jordan A; Rackham, Owen; Gough, Julian; Andersson, Robin; Sandelin, Albin; Ienasescu, Hans; Ono, Hiromasa; Bono, Hidemasa; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Kasukawa, Takeya; Kawaji, Hideya

2017-01-04

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

TIGER 2010 Boundaries

EPA Pesticide Factsheets

This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This web service includes the State and County boundaries from the TIGER shapefiles compiled into a single national coverage for each layer. The TIGER/Line Files are shapefiles and related database files (.dbf) that are an extract of selected geographic and cartographic information from the U.S. Census Bureau's Master Address File / Topologically Integrated Geographic Encoding and Referencing (MAF/TIGER) Database (MTDB).

A Geospatial Database that Supports Derivation of Climatological Features of Severe Weather

NASA Astrophysics Data System (ADS)

Phillips, M.; Ansari, S.; Del Greco, S.

2007-12-01

The Severe Weather Data Inventory (SWDI) at NOAA's National Climatic Data Center (NCDC) provides user access to archives of several datasets critical to the detection and evaluation of severe weather. These datasets include archives of: · NEXRAD Level-III point features describing general storm structure, hail, mesocyclone and tornado signatures · National Weather Service Storm Events Database · National Weather Service Local Storm Reports collected from storm spotters · National Weather Service Warnings · Lightning strikes from Vaisala's National Lightning Detection Network (NLDN) SWDI archives all of these datasets in a spatial database that allows for convenient searching and subsetting. These data are accessible via the NCDC web site, Web Feature Services (WFS) or automated web services. The results of interactive web page queries may be saved in a variety of formats, including plain text, XML, Google Earth's KMZ, standards-based NetCDF and Shapefile. NCDC's Storm Risk Assessment Project (SRAP) uses data from the SWDI database to derive gridded climatology products that show the spatial distributions of the frequency of various events. SRAP also can relate SWDI events to other spatial data such as roads, population, watersheds, and other geographic, sociological, or economic data to derive products that are useful in municipal planning, emergency management, the insurance industry, and other areas where there is a need to quantify and qualify how severe weather patterns affect people and property.

GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii).

PubMed

Xu, Zhenzhen; Liu, Jing; Ni, Wanchao; Peng, Zhen; Guo, Yue; Ye, Wuwei; Huang, Fang; Zhang, Xianggui; Xu, Peng; Guo, Qi; Shen, Xinlian; Du, Jianchang

2017-01-01

Although several diploid and tetroploid Gossypium species genomes have been sequenced, the well annotated web-based transposable elements (TEs) database is lacking. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the cotton genome, a comprehensive, specific, and user-friendly web-based database, Gossypium raimondii transposable elements database (GrTEdb), was constructed. A total of 14 332 TEs were structurally annotated and clearly categorized in G. raimondii genome, and these elements have been classified into seven distinct superfamilies based on the order of protein-coding domains, structures and/or sequence similarity, including 2929 Copia-like elements, 10 368 Gypsy-like elements, 299 L1 , 12 Mutators , 435 PIF-Harbingers , 275 CACTAs and 14 Helitrons . Meanwhile, the web-based sequence browsing, searching, downloading and blast tool were implemented to help users easily and effectively to annotate the TEs or TE fragments in genomic sequences from G. raimondii and other closely related Gossypium species. GrTEdb provides resources and information related with TEs in G. raimondii , and will facilitate gene and genome analyses within or across Gossypium species, evaluating the impact of TEs on their host genomes, and investigating the potential interaction between TEs and protein-coding genes in Gossypium species. http://www.grtedb.org/. © The Author(s) 2017. Published by Oxford University Press.

Longitudinal analysis of meta-analysis literatures in the database of ISI Web of Science.

PubMed

Zhu, Changtai; Jiang, Ting; Cao, Hao; Sun, Wenguang; Chen, Zhong; Liu, Jinming

2015-01-01

The meta-analysis is regarded as an important evidence for making scientific decision. The database of ISI Web of Science collected a great number of high quality literatures including meta-analysis literatures. However, it is significant to understand the general characteristics of meta-analysis literatures to outline the perspective of meta-analysis. In this present study, we summarized and clarified some features on these literatures in the database of ISI Web of Science. We retrieved the meta-analysis literatures in the database of ISI Web of Science including SCI-E, SSCI, A&HCI, CPCI-S, CPCI-SSH, CCR-E, and IC. The annual growth rate, literature category, language, funding, index citation, agencies and countries/territories of the meta-analysis literatures were analyzed, respectively. A total of 95,719 records, which account for 0.38% (99% CI: 0.38%-0.39%) of all literatures, were found in the database. From 1997 to 2012, the annual growth rate of meta-analysis literatures was 18.18%. The literatures involved in many categories, languages, fundings, citations, publication agencies, and countries/territories. Interestingly, the index citation frequencies of the meta-analysis were significantly higher than that of other type literatures such as multi-centre study, randomize controlled trial, cohort study, case control study, and cases report (P<0.0001). The increasing numbers, intensively global influence and high citations revealed that the meta-analysis has been becoming more and more prominent in recent years. In future, in order to promote the validity of meta-analysis, the CONSORT and PRISMA standard should be continuously popularized in the field of evidence-based medicine.

Secure, web-accessible call rosters for academic radiology departments.

PubMed

Nguyen, A V; Tellis, W M; Avrin, D E

2000-05-01

Traditionally, radiology department call rosters have been posted via paper and bulletin boards. Frequently, changes to these lists are made by multiple people independently, but often not synchronized, resulting in confusion among the house staff and technical staff as to who is on call and when. In addition, multiple and disparate copies exist in different sections of the department, and changes made would not be propagated to all the schedules. To eliminate such difficulties, a paperless call scheduling application was developed. Our call scheduling program allowed Java-enabled web access to a database by designated personnel from each radiology section who have privileges to make the necessary changes. Once a person made a change, everyone accessing the database would see the modification. This eliminates the chaos resulting from people swapping shifts at the last minute and not having the time to record or broadcast the change. Furthermore, all changes to the database were logged. Users are given a log-in name and password and can only edit their section; however, all personnel have access to all sections' schedules. Our applet was written in Java 2 using the latest technology in database access. We access our Interbase database through the DataExpress and DB Swing (Borland, Scotts Valley, CA) components. The result is secure access to the call rosters via the web. There are many advantages to the web-enabled access, mainly the ability for people to make changes and have the changes recorded and propagated in a single virtual location and available to all who need to know.

PhamDB: a web-based application for building Phamerator databases.

PubMed

Lamine, James G; DeJong, Randall J; Nelesen, Serita M

2016-07-01

PhamDB is a web application which creates databases of bacteriophage genes, grouped by gene similarity. It is backwards compatible with the existing Phamerator desktop software while providing an improved database creation workflow. Key features include a graphical user interface, validation of uploaded GenBank files, and abilities to import phages from existing databases, modify existing databases and queue multiple jobs. Source code and installation instructions for Linux, Windows and Mac OSX are freely available at https://github.com/jglamine/phage PhamDB is also distributed as a docker image which can be managed via Kitematic. This docker image contains the application and all third party software dependencies as a pre-configured system, and is freely available via the installation instructions provided. snelesen@calvin.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Federated or cached searches: providing expected performance from multiple invasive species databases

USGS Publications Warehouse

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-01-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search “deep” web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

Ocean Drilling Program: Publication Services: Online Manuscript Submission

Science.gov Websites

products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP/TAMU Science Operator Home ODP's main web site Publications Policy Author Instructions Scientific Results Manuscript use the submission and review forms available on the IODP-USIO publications web site. ODP | Search

Mining Hidden Gems Beneath the Surface: A Look At the Invisible Web.

ERIC Educational Resources Information Center

Carlson, Randal D.; Repman, Judi

2002-01-01

Describes resources for researchers called the Invisible Web that are hidden from the usual search engines and other tools and contrasts them with those resources available on the surface Web. Identifies specialized search tools, databases, and strategies that can be used to locate credible in-depth information. (Author/LRW)

Web Design Matters

ERIC Educational Resources Information Center

Mathews, Brian

2009-01-01

The web site is a library's most important feature. Patrons use the web site for numerous functions, such as renewing materials, placing holds, requesting information, and accessing databases. The homepage is the place they turn to look up the hours, branch locations, policies, and events. Whether users are at work, at home, in a building, or on…

Classification of ECG beats using deep belief network and active learning.

PubMed

G, Sayantan; T, Kien P; V, Kadambari K

2018-04-12

A new semi-supervised approach based on deep learning and active learning for classification of electrocardiogram signals (ECG) is proposed. The objective of the proposed work is to model a scientific method for classification of cardiac irregularities using electrocardiogram beats. The model follows the Association for the Advancement of medical instrumentation (AAMI) standards and consists of three phases. In phase I, feature representation of ECG is learnt using Gaussian-Bernoulli deep belief network followed by a linear support vector machine (SVM) training in the consecutive phase. It yields three deep models which are based on AAMI-defined classes, namely N, V, S, and F. In the last phase, a query generator is introduced to interact with the expert to label few beats to improve accuracy and sensitivity. The proposed approach depicts significant improvement in accuracy with minimal queries posed to the expert and fast online training as tested on the MIT-BIH Arrhythmia Database and the MIT-BIH Supra-ventricular Arrhythmia Database (SVDB). With 100 queries labeled by the expert in phase III, the method achieves an accuracy of 99.5% in "S" versus all classifications (SVEB) and 99.4% accuracy in "V " versus all classifications (VEB) on MIT-BIH Arrhythmia Database. In a similar manner, it is attributed that an accuracy of 97.5% for SVEB and 98.6% for VEB on SVDB database is achieved respectively. Graphical Abstract Reply- Deep belief network augmented by active learning for efficient prediction of arrhythmia.

Construction of a Virginia short-span bridge with the Strongwell 36-inch double-web I-beam.

DOT National Transportation Integrated Search

2005-01-01

The Route 601 Bridge in Sugar Grove, VA, spans 39 ft over Dickey Creek. The bridge is the first to use the Strongwell 36-in-deep fiber-reinforced polymer (FRP) double-web beam (DWB) in a vehicular bridge superstructure. Construction of the new bridge...

77 FR 71590 - Lock+TM

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-03

..., 50-foot-deep frame module fitted with a trash rack and containing 10 low-head bulb turbines each... electronically via the Internet. See 18 CFR 385.2001(a)(1)(iii) and the instructions on the Commission's Web site... Commission's Web site at http://www.ferc.gov/docs-filing/elibrary.asp . Enter the docket number (P-13500-002...

A federated information management system for the Deep Space Network. M.S. Thesis - Univ. of Southern California

NASA Technical Reports Server (NTRS)

Dobinson, E.

1982-01-01

General requirements for an information management system for the deep space network (DSN) are examined. A concise review of available database management system technology is presented. It is recommended that a federation of logically decentralized databases be implemented for the Network Information Management System of the DSN. Overall characteristics of the federation are specified, as well as reasons for adopting this approach.

NOAA Propagation Database Value in Tsunami Forecast Guidance

NASA Astrophysics Data System (ADS)

Eble, M. C.; Wright, L. M.

2016-02-01

The National Oceanic and Atmospheric Administration (NOAA) Center for Tsunami Research (NCTR) has developed a tsunami forecasting capability that combines a graphical user interface with data ingestion and numerical models to produce estimates of tsunami wave arrival times, amplitudes, current or water flow rates, and flooding at specific coastal communities. The capability integrates several key components: deep-ocean observations of tsunamis in real-time, a basin-wide pre-computed propagation database of water level and flow velocities based on potential pre-defined seismic unit sources, an inversion or fitting algorithm to refine the tsunami source based on the observations during an event, and tsunami forecast models. As tsunami waves propagate across the ocean, observations from the deep ocean are automatically ingested into the application in real-time to better define the source of the tsunami itself. Since passage of tsunami waves over a deep ocean reporting site is not immediate, we explore the value of the NOAA propagation database in providing placeholder forecasts in advance of deep ocean observations. The propagation database consists of water elevations and flow velocities pre-computed for 50 x 100 [km] unit sources in a continuous series along all known ocean subduction zones. The 2011 Japan Tohoku tsunami is presented as the case study

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

PubMed Central

Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-01

Abstract The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. PMID:29040670

A Web-based Tool for SDSS and 2MASS Database Searches

NASA Astrophysics Data System (ADS)

Hendrickson, M. A.; Uomoto, A.; Golimowski, D. A.

We have developed a web site using HTML, Php, Python, and MySQL that extracts, processes, and displays data from the Sloan Digital Sky Survey (SDSS) and the Two-Micron All-Sky Survey (2MASS). The goal is to locate brown dwarf candidates in the SDSS database by looking at color cuts; however, this site could also be useful for targeted searches of other databases as well. MySQL databases are created from broad searches of SDSS and 2MASS data. Broad queries on the SDSS and 2MASS database servers are run weekly so that observers have the most up-to-date information from which to select candidates for observation. Observers can look at detailed information about specific objects including finding charts, images, and available spectra. In addition, updates from previous observations can be added by any collaborators; this format makes observational collaboration simple. Observers can also restrict the database search, just before or during an observing run, to select objects of special interest.

Database resources of the National Center for Biotechnology Information: 2002 update

PubMed Central

Wheeler, David L.; Church, Deanna M.; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Tatusova, Tatiana A.; Wagner, Lukas; Rapp, Barbara A.

2002-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, Human¡VMouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. PMID:11752242

The VLab repository of thermodynamics and thermoelastic properties of minerals

NASA Astrophysics Data System (ADS)

Da Silveira, P. R.; Sarkar, K.; Wentzcovitch, R. M.; Shukla, G.; Lindemann, W.; Wu, Z.

2015-12-01

Thermodynamics and thermoelastic properties of minerals at planetary interior conditions are essential as input for geodynamics simulations and for interpretation of seismic tomography models. Precise experimental determination of these properties at such extreme conditions is very challenging. Therefore, ab initio calculations play an essential role in this context, but at the cost of great computational effort and memory use. Setting up a widely accessible and versatile mineral physics database can relax unnecessary repetition of such computationally intensive calculations. Access to such data facilitates transactional interaction across fields and can advance more quickly insights about deep Earth processes. Hosted by the Minnesota Supercomputing Institute, the Virtual Laboratory for Earth and Planetary Materials (VLab) was designed to develop and promote the theory of planetary materials using distributed, high-throughput quantum calculations. VLab hosts an interactive database of thermodynamics and thermoelastic properties or minerals computed by ab initio. Such properties can be obtained according to user's preference. The database is accompanied by interactive visualization tools, allowing users to repeat and build upon previously published results. Using VLab2015, we have evaluated thermoelastic properties, such as elastic coefficients (Cij), Voigt, Reuss, and Voigt-Reuss-Hill aggregate averages for bulk (K) and shear modulus (G), shear wave velocity (VS), longitudinal wave velocity (Vp), and bulk sound velocity (V0) for several important minerals. Developed web services are general and can be used for crystals of any symmetry. Results can be tabulated, plotted, or downloaded from the VLab website according to user's preference.

[Establishment of a comprehensive database for laryngeal cancer related genes and the miRNAs].

PubMed

Li, Mengjiao; E, Qimin; Liu, Jialin; Huang, Tingting; Liang, Chuanyu

2015-09-01

By collecting and analyzing the laryngeal cancer related genes and the miRNAs, to build a comprehensive laryngeal cancer-related gene database, which differs from the current biological information database with complex and clumsy structure and focuses on the theme of gene and miRNA, and it could make the research and teaching more convenient and efficient. Based on the B/S architecture, using Apache as a Web server, MySQL as coding language of database design and PHP as coding language of web design, a comprehensive database for laryngeal cancer-related genes was established, providing with the gene tables, protein tables, miRNA tables and clinical information tables of the patients with laryngeal cancer. The established database containsed 207 laryngeal cancer related genes, 243 proteins, 26 miRNAs, and their particular information such as mutations, methylations, diversified expressions, and the empirical references of laryngeal cancer relevant molecules. The database could be accessed and operated via the Internet, by which browsing and retrieval of the information were performed. The database were maintained and updated regularly. The database for laryngeal cancer related genes is resource-integrated and user-friendly, providing a genetic information query tool for the study of laryngeal cancer.

The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

PubMed

Galperin, Michael Y; Rigden, Daniel J; Fernández-Suárez, Xosé M

2015-01-01

The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Progressive and self-limiting neurodegenerative disorders in Africa: a new prominent field of research led by South Africa but without strong health policy.

PubMed

Poreau, Brice

2016-01-01

Neurodegenerative disorders are involved in mortality and morbidity of every country. A high prevalence is estimated in Africa. Neurodegenerative disorders are defined by a progressive or self-limiting alteration of neurons implied in specific functional and anatomical functions. It encompasses a various range of clinical disorders from self-limiting to progressive. Focus on public health policies and scientific research is needed to understand the mechanisms to reduce this high prevalence. We use bibliometrics and mapping tools to explore the area studies and countries involved in scientific research on neurodegenerative disorders in Africa. We used two databases: Web of Science and Pubmed. We analyzed the journals, most cited articles, authors, publication years, organizations, funding agencies, countries and keywords in Web of Science Core collection database and publication years and Medical Subject Headings in Pubmed database. We mapped the data using VOSviewer. We accessed 44 articles published between 1975 and 2014 in Web of Science Core collection Database and 669 from Pubmed database. The majority of which were after 2006. The main countries involved in research on neurodegenerative disorders in Africa the USA, the United Kingdom, France and South Africa representing the main network collaboration. Clinical neurology and Genetics hereditary are the main Web of Science categories whereas Neurosciences and Biochemistry and Molecular Biology are the main Web of Science categories for the general search "neurodegenerative disorders" not restrained to Africa. This is confirmed by Medical Subject Headings analysis from Pubmed with one more area study: Treatment. Neurodegenerative disorders research is leaded by South Africa with a network involving the USA, the UK, as well as African countries such Zambia. The chief field that emerged was on patient and hereditary as well as treatment. Public health policies were lacking fields in research whereas prevalence is estimated to be important in every country. New 17 sustainable development goals of the United Nations could help in this way.

Fermilab Security Site Access Request Database

Science.gov Websites

Fermilab Security Site Access Request Database Use of the online version of the Fermilab Security Site Access Request Database requires that you login into the ESH&Q Web Site. Note: Only Fermilab generated from the ESH&Q Section's Oracle database on May 27, 2018 05:48 AM. If you have a question

75 FR 78234 - Lock+TM

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-15

... project (Project No. 13780-000) would consist of: (1) An 85-foot-long, 100-foot-wide, 14-foot-deep excavated power canal; (2) a 95-foot-long, 100-foot-wide, 10-foot-deep excavated tailrace; (3) a 100-foot...)(iii) and the instructions on the Commission's Web site http://www.ferc.gov/docs-filing/efiling.asp...

76 FR 28224 - Science Advisory Board Staff Office; Notification of a Public Teleconference of the Science...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-16

... Advisory Board can be found at the EPA SAB Web site at http://www.epa.gov/sab . SUPPLEMENTARY INFORMATION..., and human health effects. The Deep Water Horizon spill identified the need for additional research on alternative spill response technologies; environmental impacts of chemical dispersants under deep sea...

Web based tools for data manipulation, visualisation and validation with interactive georeferenced graphs

NASA Astrophysics Data System (ADS)

Ivankovic, D.; Dadic, V.

2009-04-01

Some of oceanographic parameters have to be manually inserted into database; some (for example data from CTD probe) are inserted from various files. All this parameters requires visualization, validation and manipulation from research vessel or scientific institution, and also public presentation. For these purposes is developed web based system, containing dynamic sql procedures and java applets. Technology background is Oracle 10g relational database, and Oracle application server. Web interfaces are developed using PL/SQL stored database procedures (mod PL/SQL). Additional parts for data visualization include use of Java applets and JavaScript. Mapping tool is Google maps API (javascript) and as alternative java applet. Graph is realized as dynamically generated web page containing java applet. Mapping tool and graph are georeferenced. That means that click on some part of graph, automatically initiate zoom or marker onto location where parameter was measured. This feature is very useful for data validation. Code for data manipulation and visualization are partially realized with dynamic SQL and that allow as to separate data definition and code for data manipulation. Adding new parameter in system requires only data definition and description without programming interface for this kind of data.

Lecturers’ Understanding on Indexing Databases of SINTA, DOAJ, Google Scholar, SCOPUS, and Web of Science: A Study of Indonesians

NASA Astrophysics Data System (ADS)

Saleh Ahmar, Ansari; Kurniasih, Nuning; Irawan, Dasapta Erwin; Utami Sutiksno, Dian; Napitupulu, Darmawan; Ikhsan Setiawan, Muhammad; Simarmata, Janner; Hidayat, Rahmat; Busro; Abdullah, Dahlan; Rahim, Robbi; Abraham, Juneman

2018-01-01

The Ministry of Research, Technology and Higher Education of Indonesia has introduced several national and international indexers of scientific works. This policy becomes a guideline for lecturers and researchers in choosing the reputable publications. This study aimed to describe the understanding level of Indonesian lecturers related to indexing databases, i.e. SINTA, DOAJ, Scopus, Web of Science, and Google Scholar. This research used descriptive design and survey method. The populations in this study were Indonesian lecturers and researchers. The primary data were obtained from a questionnaire filled by 316 lecturers and researchers from 33 Provinces in Indonesia recruited with convenience sampling technique on October-November 2017. The data analysis was performed using frequency distribution tables, cross tabulation and descriptive analysis. The results of this study showed that the understanding of Indonesian lecturers and researchers regarding publications in indexing databases SINTA, DOAJ, Scopus, Web of Science and Google Scholar is that, on average, 66,5% have known about SINTA, DOAJ, Scopus, Web of Science and Google Scholar. However, based on empirical frequency 76% of them have never published with journals or proceedings indexed in Scopus.

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins.

PubMed

van Heel, Auke J; de Jong, Anne; Song, Chunxu; Viel, Jakob H; Kok, Jan; Kuipers, Oscar P

2018-05-21

Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters of interest are discovered using the core-peptide database and/or through HMM motifs that are present in associated context genes. The databases used for mining have been updated and extended with literature references and links to UniProt and NCBI. Additionally, we have included automated promoter and terminator prediction and the option to upload RNA expression data, which can be displayed along with the identified clusters. Further improvements include the annotation of the context genes, which is now based on a fast blast against the prokaryote part of the UniRef90 database, and the improved web-BLAST feature that dynamically loads structural data such as internal cross-linking from UniProt. Overall BAGEL4 provides the user with more information through a user-friendly web-interface which simplifies data evaluation. BAGEL4 is freely accessible at http://bagel4.molgenrug.nl.

48 CFR 404.1103 - Procedures.

Code of Federal Regulations, 2010 CFR

2010-10-01

... employees shall not enter information into the Central Contractor Registration (CCR) database on behalf of... be advised to submit a written application to CCR for registration into the CCR database. USDA... registered in the CCR database shall be done via the CCR Internet Web site http://www.ccr.gov. This...

48 CFR 404.1103 - Procedures.

Code of Federal Regulations, 2014 CFR

2014-10-01

... employees shall not enter information into the Central Contractor Registration (CCR) database on behalf of... be advised to submit a written application to CCR for registration into the CCR database. USDA... registered in the CCR database shall be done via the CCR Internet Web site http://www.ccr.gov. This...

48 CFR 404.1103 - Procedures.

Code of Federal Regulations, 2012 CFR

2012-10-01

... employees shall not enter information into the Central Contractor Registration (CCR) database on behalf of... be advised to submit a written application to CCR for registration into the CCR database. USDA... registered in the CCR database shall be done via the CCR Internet Web site http://www.ccr.gov. This...

48 CFR 404.1103 - Procedures.

Code of Federal Regulations, 2013 CFR

2013-10-01

... employees shall not enter information into the Central Contractor Registration (CCR) database on behalf of... be advised to submit a written application to CCR for registration into the CCR database. USDA... registered in the CCR database shall be done via the CCR Internet Web site http://www.ccr.gov. This...

48 CFR 404.1103 - Procedures.

Code of Federal Regulations, 2011 CFR

2011-10-01

... employees shall not enter information into the Central Contractor Registration (CCR) database on behalf of... be advised to submit a written application to CCR for registration into the CCR database. USDA... registered in the CCR database shall be done via the CCR Internet Web site http://www.ccr.gov. This...

Atomic Spectra Database (ASD)

National Institute of Standards and Technology Data Gateway

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

Six Online Periodical Databases: A Librarian's View.

ERIC Educational Resources Information Center

Willems, Harry

1999-01-01

Compares the following World Wide Web-based periodical databases, focusing on their usefulness in K-12 school libraries: EBSCO, Electric Library, Facts on File, SIRS, Wilson, and UMI. Search interfaces, display options, help screens, printing, home access, copyright restrictions, database administration, and making a decision are discussed. A…

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

NASA Astrophysics Data System (ADS)

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

2013-11-01

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

TIGER 2010 Boundaries

EPA Pesticide Factsheets

This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This web service includes the State, County, and Census Block Groups boundaries from the TIGER shapefiles compiled into a single national coverage for each layer. The TIGER/Line Files are shapefiles and related database files (.dbf) that are an extract of selected geographic and cartographic information from the U.S. Census Bureau's Master Address File / Topologically Integrated Geographic Encoding and Referencing (MAF/TIGER) Database (MTDB).

Version VI of the ESTree db: an improved tool for peach transcriptome analysis

PubMed Central

Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Merelli, Ivan; Barale, Francesca; Milanesi, Luciano; Stella, Alessandra; Pozzi, Carlo

2008-01-01

Background The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach libraries. Nine peach genotypes and four peach tissues are represented, from four fruit developmental stages. The aim of this work was to implement the already existing ESTree db by adding new sequences and analysis programs. Particular care was given to the implementation of the web interface, that allows querying each of the database features. Results A Perl modular pipeline is the backbone of sequence analysis in the ESTree db project. Outputs obtained during the pipeline steps are automatically arrayed into the fields of a MySQL database. Apart from standard clustering and annotation analyses, version VI of the ESTree db encompasses new tools for tandem repeat identification, annotation against genomic Rosaceae sequences, and positioning on the database of oligomer sequences that were used in a peach microarray study. Furthermore, known protein patterns and motifs were identified by comparison to PROSITE. Based on data retrieved from sequence annotation against the UniProtKB database, a script was prepared to track positions of homologous hits on the GO tree and build statistics on the ontologies distribution in GO functional categories. EST mapping data were also integrated in the database. The PHP-based web interface was upgraded and extended. The aim of the authors was to enable querying the database according to all the biological aspects that can be investigated from the analysis of data available in the ESTree db. This is achieved by allowing multiple searches on logical subsets of sequences that represent different biological situations or features. Conclusions The version VI of ESTree db offers a broad overview on peach gene expression. Sequence analyses results contained in the database, extensively linked to external related resources, represent a large amount of information that can be queried via the tools offered in the web interface. Flexibility and modularity of the ESTree analysis pipeline and of the web interface allowed the authors to set up similar structures for different datasets, with limited manual intervention. PMID:18387211

Large-Scale Image Analytics Using Deep Learning

NASA Astrophysics Data System (ADS)

Ganguly, S.; Nemani, R. R.; Basu, S.; Mukhopadhyay, S.; Michaelis, A.; Votava, P.

2014-12-01

High resolution land cover classification maps are needed to increase the accuracy of current Land ecosystem and climate model outputs. Limited studies are in place that demonstrates the state-of-the-art in deriving very high resolution (VHR) land cover products. In addition, most methods heavily rely on commercial softwares that are difficult to scale given the region of study (e.g. continents to globe). Complexities in present approaches relate to (a) scalability of the algorithm, (b) large image data processing (compute and memory intensive), (c) computational cost, (d) massively parallel architecture, and (e) machine learning automation. In addition, VHR satellite datasets are of the order of terabytes and features extracted from these datasets are of the order of petabytes. In our present study, we have acquired the National Agricultural Imaging Program (NAIP) dataset for the Continental United States at a spatial resolution of 1-m. This data comes as image tiles (a total of quarter million image scenes with ~60 million pixels) and has a total size of ~100 terabytes for a single acquisition. Features extracted from the entire dataset would amount to ~8-10 petabytes. In our proposed approach, we have implemented a novel semi-automated machine learning algorithm rooted on the principles of "deep learning" to delineate the percentage of tree cover. In order to perform image analytics in such a granular system, it is mandatory to devise an intelligent archiving and query system for image retrieval, file structuring, metadata processing and filtering of all available image scenes. Using the Open NASA Earth Exchange (NEX) initiative, which is a partnership with Amazon Web Services (AWS), we have developed an end-to-end architecture for designing the database and the deep belief network (following the distbelief computing model) to solve a grand challenge of scaling this process across quarter million NAIP tiles that cover the entire Continental United States. The AWS core components that we use to solve this problem are DynamoDB along with S3 for database query and storage, ElastiCache shared memory architecture for image segmentation, Elastic Map Reduce (EMR) for image feature extraction, and the memory optimized Elastic Cloud Compute (EC2) for the learning algorithm.

Learning Deep Representations for Ground to Aerial Geolocalization (Open Access)

DTIC Science & Technology

2015-10-15

proposed approach, Where-CNN, is inspired by deep learning success in face verification and achieves significant improvements over tra- ditional hand...crafted features and existing deep features learned from other large-scale databases. We show the ef- fectiveness of Where-CNN in finding matches

ShapeShop: Towards Understanding Deep Learning Representations via Interactive Experimentation

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

Hohman, Frederick M.; Hodas, Nathan O.; Chau, Duen Horng

Deep learning is the driving force behind many recent technologies; however, deep neural networks are often viewed as “black-boxes” due to their internal complexity that is hard to understand. Little research focuses on helping people explore and understand the relationship between a user’s data and the learned representations in deep learning models. We present our ongoing work, ShapeShop, an interactive system for visualizing and understanding what semantics a neural network model has learned. Built using standard web technologies, ShapeShop allows users to experiment with and compare deep learning models to help explore the robustness of image classifiers.

Internet Librarian '98: Proceedings of the Internet Librarian Conference (2nd, Monterey, California, November 1-5, 1998).

ERIC Educational Resources Information Center

Nixon, Carol, Comp.; Dengler, M. Heide, Comp.; McHenry, Mare L., Comp.

This proceedings contains 56 papers, presentation summaries, and/or slide presentations pertaining to the Internet, World Wide Web, intranets, and library systems. Topics include: Web databases in medium sized libraries; Dow Jones Intranet Toolkit; the future of online; Web searching and Internet basics; digital archiving; evolution of the online…

An Overview of the use of Bromelain-Based Enzymatic Debridement (Nexobrid®) in Deep Partial & Full Thickness Burns: Appraising the Evidence.

PubMed

Loo, Yew L; Goh, Benjamin K L; Jeffery, S

2018-03-22

Recent introduction of rapid bromelain-based enzymatic debridement has been increasingly popular in its use in non-surgical debridement in deep partial and full thickness burns. We designed this study to evaluate the evidence suggested by current studies on the perceived benefits of using Nexobrid® as compared to traditional surgical standard of care (SOC) in burns wound debridement. A comprehensive search on electronic databases Pubmed, Embase and Web of Science was done to identify studies published between 1986 to 2017 involving the use of Nexobrid in deep partial and full thickness burns. Studies were evaluated for proposed benefits and categorised under supporting evidence, contradicting evidence and anecdotal opinions. 7 well designed prospective studies met the inclusion comprising of 4 randomised controlled trials. 6 proposed benefits associated with the use of Nexobrid were extracted including reduced time to complete debridement, need for surgery, area of burns excised, need for autograft, time to wound closure and improved scar quality. Most proposed benefits have strong supporting evidences with minimal anecdotal opinions from controlled trials except the proposed improvement in scar quality and reduced time to wound healing that had at least 3 refuting evidence and 1 anecdotal evidence. Incidence of pain was also evaluated and were mainly anecdotal lacking formal objective assessment or cohort study. Despite the lack of literatures available, the benefits of Nexobrid is evident in published randomised and single arm studies. Large number of studies are needed to aid further evaluating the proposed benefits of Nexobrid.

Inaccurate Citations in Biomedical Journalism: Effect on the Impact Factor of the American Journal of Roentgenology.

PubMed

Karabulut, Nevzat

2017-03-01

The aim of this study is to investigate the frequency of incorrect citations and its effects on the impact factor of a specific biomedical journal: the American Journal of Roentgenology. The Cited Reference Search function of Thomson Reuters' Web of Science database (formerly the Institute for Scientific Information's Web of Knowledge database) was used to identify erroneous citations. This was done by entering the journal name into the Cited Work field and entering "2011-2012" into the Cited Year(s) field. The errors in any part of the inaccurately cited references (e.g., author names, title, year, volume, issue, and page numbers) were recorded, and the types of errors (i.e., absent, deficient, or mistyped) were analyzed. Erroneous citations were corrected using the Suggest a Correction function of the Web of Science database. The effect of inaccurate citations on the impact factor of the AJR was calculated. Overall, 183 of 1055 citable articles published in 2011-2012 were inaccurately cited 423 times (mean [± SD], 2.31 ± 4.67 times; range, 1-44 times). Of these 183 articles, 110 (60.1%) were web-only articles and 44 (24.0%) were print articles. The most commonly identified errors were page number errors (44.8%) and misspelling of an author's name (20.2%). Incorrect citations adversely affected the impact factor of the AJR by 0.065 in 2012 and by 0.123 in 2013. Inaccurate citations are not infrequent in biomedical journals, yet they can be detected and corrected using the Web of Science database. Although the accuracy of references is primarily the responsibility of authors, the journal editorial office should also define a periodic inaccurate citation check task and correct erroneous citations to reclaim unnecessarily lost credit.

Implants in disabled patients: A review and update

PubMed Central

Romero-Pérez, María J.; Mang-de la Rosa, María R.; López-Jimenez, Julián; Fernández-Feijoo, Javier

2014-01-01

The range of indications for dental implants has broadened enormously owing to their predictability and the improvement of patient satisfaction in terms of stability, comfort, aesthetics and functionality. The aim of this article is to review those indications in patients with mental or physical disabilities as the difficulty to cope with oral hygiene often leads to teeth extraction, adding edentulousness to the impairments already present. Following that goal, available literature in Pubmed database, Scopus, Web of Knowledge and The Cochrane Library database about dental implants placement in these patients has been reviewed, assessing the variables of each study: number of patients, sex, average age, oral hygiene, parafunctional habits, impairment, bone quality, protocol of implant surgery, necessity of deep intravenous sedation or general anesthesia, follow-up period and number of failures. The comparison with studies involving other patient populations without mental or physical impediments did not show statistically significant differences in terms of the failure rate recorded. Although there is not much literature available, the results of this review seem to suggest that osseointegrated oral implants could be a therapeutic option in patients who suffer from any physical or psychological impairment. The success of an oral rehabilitation depends mainly on an adequate selection of the patients. Key words:Implants, disabled, sedation. PMID:24608221

Handprinted Forms and Characters

National Institute of Standards and Technology Data Gateway

NIST Handprinted Forms and Characters (Web, free access)   NIST Special Database 19 contains NIST's entire corpus of training materials for handprinted document and character recognition. It supersedes NIST Special Databases 3 and 7.

Ocean Drilling Program: Mirror Sites

Science.gov Websites

Publication services and products Drilling services and tools Online Janus database Search the ODP/TAMU web information, see www.iodp-usio.org. ODP | Search | Database | Drilling | Publications | Science | Cruise Info

Massage Therapy for Health Purposes

MedlinePlus

... Web site: www.nih.gov/health/clinicaltrials/ Cochrane Database of Systematic Reviews The Cochrane Database of Systematic ... Licensed Complementary and Alternative Healthcare Professions. Seattle, WA: Academic Consortium for Complementary and Alternative Health Care; 2009. ...

76 FR 44048 - Agency Information Collection Activities: Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-22

... Collection: The GSS is a census of all eligible academic institutions and all departments in science and... Policy Analysis and Research (WebCASPAR) database system. The URL for WebCASPAR is http://caspar.nsf.gov...

FRASS: the web-server for RNA structural comparison

PubMed Central

2010-01-01

Background The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules. Results The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank. We observed that FRASS scores correlate well with the ARTS and LaJolla similarity scores. Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method. Conclusions The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases. PMID:20553602

DIMA 3.0: Domain Interaction Map.

PubMed

Luo, Qibin; Pagel, Philipp; Vilne, Baiba; Frishman, Dmitrij

2011-01-01

Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

CottonDB: A resource for cotton genome research

USDA-ARS?s Scientific Manuscript database

CottonDB (http://cottondb.org/) is a database and web resource for cotton genomic and genetic research. Created in 1995, CottonDB was among the first plant genome databases established by the USDA-ARS. Accessed through a website interface, the database aims to be a convenient, inclusive medium of ...

CottonGen: a genomics, genetics and breeding database for cotton research

USDA-ARS?s Scientific Manuscript database

CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, vis...

Characteristics of Resources Represented in the OCLC CORC Database.

ERIC Educational Resources Information Center

Connell, Tschera Harkness; Prabha, Chandra

2002-01-01

Examines the characteristics of Web resources in Online Computer Library Center's (OCLC) Cooperative Online Resource Catalog (CORC) in terms of subject matter, source of content, publication patterns, and units of information chosen for representation in the database. Suggests that the ability to successfully use a database depends on…

HIV Structural Database

National Institute of Standards and Technology Data Gateway

SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

Linking Multiple Databases: Term Project Using "Sentences" DBMS.

ERIC Educational Resources Information Center

King, Ronald S.; Rainwater, Stephen B.

This paper describes a methodology for use in teaching an introductory Database Management System (DBMS) course. Students master basic database concepts through the use of a multiple component project implemented in both relational and associative data models. The associative data model is a new approach for designing multi-user, Web-enabled…

A Machine Reading System for Assembling Synthetic Paleontological Databases

PubMed Central

Peters, Shanan E.; Zhang, Ce; Livny, Miron; Ré, Christopher

2014-01-01

Many aspects of macroevolutionary theory and our understanding of biotic responses to global environmental change derive from literature-based compilations of paleontological data. Existing manually assembled databases are, however, incomplete and difficult to assess and enhance with new data types. Here, we develop and validate the quality of a machine reading system, PaleoDeepDive, that automatically locates and extracts data from heterogeneous text, tables, and figures in publications. PaleoDeepDive performs comparably to humans in several complex data extraction and inference tasks and generates congruent synthetic results that describe the geological history of taxonomic diversity and genus-level rates of origination and extinction. Unlike traditional databases, PaleoDeepDive produces a probabilistic database that systematically improves as information is added. We show that the system can readily accommodate sophisticated data types, such as morphological data in biological illustrations and associated textual descriptions. Our machine reading approach to scientific data integration and synthesis brings within reach many questions that are currently underdetermined and does so in ways that may stimulate entirely new modes of inquiry. PMID:25436610

76 FR 14415 - General and Plastic Surgery Devices Panel of the Medical Devices Advisory Committee; Notice of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-16

.... Therefore, you should always check the Agency's Web site and call the appropriate advisory committee hot... currently approved for mid- to deep- dermal implantation for the correction of moderate to severe facial... material on its Web site prior to the meeting, the background material will be made publicly available at...

75 FR 10248 - GB Energy Park, LLC; Notice of Preliminary Permit Application Accepted for Filing and Soliciting...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-05

...-deep, 3-mile-long canal carrying flows diverted from Cottonwood Creek by an existing diversion... on the Commission's Web site ( http://www.ferc.gov/docs-filing/ferconline.asp ) under the ``eFiling...Library'' link of Commission's Web site at http://www.ferc.gov/docs-filing/elibrary.asp . Enter the docket...

78 FR 72060 - Chimney Rock National Monument Management Plan; San Juan National Forest; Colorado

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-02

..., as well as objects of deep cultural and educational value. The plan will also provide for continued... Ranger District office in Pagosa Springs, Colorado, and on the San Juan National Forest Web site at www..., direct mailings, emails, and will be posted on the San Juan National Forest Web site. It is important...

78 FR 27405 - Anesthetic and Analgesic Drug Products Advisory Committee; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-10

... check the Agency's Web site at http://www.fda.gov/AdvisoryCommittees/default.htm and scroll down to the... proposed indications of routine reversal of moderate and deep neuromuscular blockade (NMB) induced by... meeting. If FDA is unable to post the background material on its Web site prior to the meeting, the...

78 FR 16684 - General and Plastic Surgery Devices Panel of the Medical Devices Advisory Committee; Notice of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-18

... provide timely notice. Therefore, you should always check the Agency's Web site at http://www.fda.gov...]derm Voluma XC is indicated for deep (dermal/subcutaneous and/or submuscular/ supraperiosteal... the background material on its Web site prior to the meeting, the background material will be made...

76 FR 13396 - Notice of Availability of the Draft Environmental Impact Statement for the Mountaineer Commercial...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-11

... deep saline geologic formations for permanent geologic storage. DATES: DOE invites the public to...; or by fax (304) 285-4403. The Draft EIS is available on DOE's NEPA Web page at: http://nepa.energy.gov/DOE_NEPA_documents.htm ; and on the National Energy Technology Laboratory's Web page at: http...

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions

PubMed Central

Karr, Jonathan R.; Phillips, Nolan C.; Covert, Markus W.

2014-01-01

Mechanistic ‘whole-cell’ models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations. We developed WholeCellSimDB, a database for organizing whole-cell simulations. WholeCellSimDB was designed to enable researchers to search simulation metadata to identify simulations for further analysis, and quickly slice and aggregate simulation results data. In addition, WholeCellSimDB enables users to share simulations with the broader research community. The database uses a hybrid relational/hierarchical data format architecture to efficiently store and retrieve both simulation setup metadata and results data. WholeCellSimDB provides a graphical Web-based interface to search, browse, plot and export simulations; a JavaScript Object Notation (JSON) Web service to retrieve data for Web-based visualizations; a command-line interface to deposit simulations; and a Python API to retrieve data for advanced analysis. Overall, we believe WholeCellSimDB will help researchers use whole-cell models to advance basic biological science and bioengineering. Database URL: http://www.wholecellsimdb.org Source code repository URL: http://github.com/CovertLab/WholeCellSimDB PMID:25231498

Overview of Nuclear Physics Data: Databases, Web Applications and Teaching Tools

NASA Astrophysics Data System (ADS)

McCutchan, Elizabeth

2017-01-01

The mission of the United States Nuclear Data Program (USNDP) is to provide current, accurate, and authoritative data for use in pure and applied areas of nuclear science and engineering. This is accomplished by compiling, evaluating, and disseminating extensive datasets. Our main products include the Evaluated Nuclear Structure File (ENSDF) containing information on nuclear structure and decay properties and the Evaluated Nuclear Data File (ENDF) containing information on neutron-induced reactions. The National Nuclear Data Center (NNDC), through the website www.nndc.bnl.gov, provides web-based retrieval systems for these and many other databases. In addition, the NNDC hosts several on-line physics tools, useful for calculating various quantities relating to basic nuclear physics. In this talk, I will first introduce the quantities which are evaluated and recommended in our databases. I will then outline the searching capabilities which allow one to quickly and efficiently retrieve data. Finally, I will demonstrate how the database searches and web applications can provide effective teaching tools concerning the structure of nuclei and how they interact. Work supported by the Office of Nuclear Physics, Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-98CH10886.

The Tropical Biominer Project: mining old sources for new drugs.

PubMed

Artiguenave, François; Lins, André; Maciel, Wesley Dias; Junior, Antonio Celso Caldeira; Nacif-Coelho, Carla; de Souza Linhares, Maria Margarida Ribeiro; de Oliveira, Guilherme Correa; Barbosa, Luis Humberto Rezende; Lopes, Júlio César Dias; Junior, Claudionor Nunes Coelho

2005-01-01

The Tropical Biominer Project is a recent initiative from the Federal University of Minas Gerais (UFMG) and the Oswaldo Cruz foundation, with the participation of the Biominas Foundation (Belo Horizonte, Minas Gerais, Brazil) and the start-up Homologix. The main objective of the project is to build a new resource for the chemogenomics research, on chemical compounds, with a strong emphasis on natural molecules. Adopted technologies include the search of information from structured, semi-structured, and non-structured documents (the last two from the web) and datamining tools in order to gather information from different sources. The database is the support for developing applications to find new potential treatments for parasitic infections by using virtual screening tools. We present here the midpoint of the project: the conception and implementation of the Tropical Biominer Database. This is a Federated Database designed to store data from different resources. Connected to the database, a web crawler is able to gather information from distinct, patented web sites and store them after automatic classification using datamining tools. Finally, we demonstrate the interest of the approach, by formulating new hypotheses on specific targets of a natural compound, violacein, using inferences from a Virtual Screening procedure.

WheatGenome.info: an integrated database and portal for wheat genome information.

PubMed

Lai, Kaitao; Berkman, Paul J; Lorenc, Michal Tadeusz; Duran, Chris; Smits, Lars; Manoli, Sahana; Stiller, Jiri; Edwards, David

2012-02-01

Bread wheat (Triticum aestivum) is one of the most important crop plants, globally providing staple food for a large proportion of the human population. However, improvement of this crop has been limited due to its large and complex genome. Advances in genomics are supporting wheat crop improvement. We provide a variety of web-based systems hosting wheat genome and genomic data to support wheat research and crop improvement. WheatGenome.info is an integrated database resource which includes multiple web-based applications. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second-generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This system includes links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/.

Design and development of a web-based application for diabetes patient data management.

PubMed

Deo, S S; Deobagkar, D N; Deobagkar, Deepti D

2005-01-01

A web-based database management system developed for collecting, managing and analysing information of diabetes patients is described here. It is a searchable, client-server, relational database application, developed on the Windows platform using Oracle, Active Server Pages (ASP), Visual Basic Script (VB Script) and Java Script. The software is menu-driven and allows authorized healthcare providers to access, enter, update and analyse patient information. Graphical representation of data can be generated by the system using bar charts and pie charts. An interactive web interface allows users to query the database and generate reports. Alpha- and beta-testing of the system was carried out and the system at present holds records of 500 diabetes patients and is found useful in diagnosis and treatment. In addition to providing patient data on a continuous basis in a simple format, the system is used in population and comparative analysis. It has proved to be of significant advantage to the healthcare provider as compared to the paper-based system.

dbHiMo: a web-based epigenomics platform for histone-modifying enzymes.

PubMed

Choi, Jaeyoung; Kim, Ki-Tae; Huh, Aram; Kwon, Seomun; Hong, Changyoung; Asiegbu, Fred O; Jeon, Junhyun; Lee, Yong-Hwan

2015-01-01

Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11,576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies. © The Author(s) 2015. Published by Oxford University Press.

Design and Implementation of Website Information Disclosure Assessment System

PubMed Central

Cho, Ying-Chiang; Pan, Jen-Yi

2015-01-01

Internet application technologies, such as cloud computing and cloud storage, have increasingly changed people’s lives. Websites contain vast amounts of personal privacy information. In order to protect this information, network security technologies, such as database protection and data encryption, attract many researchers. The most serious problems concerning web vulnerability are e-mail address and network database leakages. These leakages have many causes. For example, malicious users can steal database contents, taking advantage of mistakes made by programmers and administrators. In order to mitigate this type of abuse, a website information disclosure assessment system is proposed in this study. This system utilizes a series of technologies, such as web crawler algorithms, SQL injection attack detection, and web vulnerability mining, to assess a website’s information disclosure. Thirty websites, randomly sampled from the top 50 world colleges, were used to collect leakage information. This testing showed the importance of increasing the security and privacy of website information for academic websites. PMID:25768434

A Visual Analytics Paradigm Enabling Trillion-Edge Graph Exploration

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

Wong, Pak C.; Haglin, David J.; Gillen, David S.

We present a visual analytics paradigm and a system prototype for exploring web-scale graphs. A web-scale graph is described as a graph with ~one trillion edges and ~50 billion vertices. While there is an aggressive R&D effort in processing and exploring web-scale graphs among internet vendors such as Facebook and Google, visualizing a graph of that scale still remains an underexplored R&D area. The paper describes a nontraditional peek-and-filter strategy that facilitates the exploration of a graph database of unprecedented size for visualization and analytics. We demonstrate that our system prototype can 1) preprocess a graph with ~25 billion edgesmore » in less than two hours and 2) support database query and visualization on the processed graph database afterward. Based on our computational performance results, we argue that we most likely will achieve the one trillion edge mark (a computational performance improvement of 40 times) for graph visual analytics in the near future.« less