Geologic map of the eastern part of the Challis National Forest and vicinity, Idaho

USGS Publications Warehouse

Wilson, A.B.; Skipp, B.A.

1994-01-01

The paper version of the Geologic Map of the eastern part of the Challis National Forest and vicinity, Idaho was compiled by Anna Wilson and Betty Skipp in 1994. The geology was compiled on a 1:250,000 scale topographic base map. TechniGraphic System, Inc. of Fort Collins Colorado digitized this map under contract for N.Shock. G.Green edited and prepared the digital version for publication as a GIS database. The digital geologic map database can be queried in many ways to produce a variety of geologic maps.

Managing data from multiple disciplines, scales, and sites to support synthesis and modeling

USGS Publications Warehouse

Olson, R. J.; Briggs, J. M.; Porter, J.H.; Mah, Grant R.; Stafford, S.G.

1999-01-01

The synthesis and modeling of ecological processes at multiple spatial and temporal scales involves bringing together and sharing data from numerous sources. This article describes a data and information system model that facilitates assembling, managing, and sharing diverse data from multiple disciplines, scales, and sites to support integrated ecological studies. Cross-site scientific-domain working groups coordinate the development of data associated with their particular scientific working group, including decisions about data requirements, data to be compiled, data formats, derived data products, and schedules across the sites. The Web-based data and information system consists of nodes for each working group plus a central node that provides data access, project information, data query, and other functionality. The approach incorporates scientists and computer experts in the working groups and provides incentives for individuals to submit documented data to the data and information system.

An Attempt to Compare EMCS with TOXLINE.

ERIC Educational Resources Information Center

Lorent, Jean-Pierre; Schirner, Hedi

1978-01-01

Sixteen queries, performed on the two systems, resulted in 247 unique relevant references from EMCS and 559 from TOXLINE. The overlap varied considerably, from 6 to 50 percent. It is remarkable that TOXLINE, with nine subfiles specially compiled for toxicology, can be supplemented by EMCS, which in the present study delivered 31 percent of all the…

Shuttle-Data-Tape XML Translator

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

JSDTImport is a computer program for translating native Shuttle Data Tape (SDT) files from American Standard Code for Information Interchange (ASCII) format into databases in other formats. JSDTImport solves the problem of organizing the SDT content, affording flexibility to enable users to choose how to store the information in a database to better support client and server applications. JSDTImport can be dynamically configured by use of a simple Extensible Markup Language (XML) file. JSDTImport uses this XML file to define how each record and field will be parsed, its layout and definition, and how the resulting database will be structured. JSDTImport also includes a client application programming interface (API) layer that provides abstraction for the data-querying process. The API enables a user to specify the search criteria to apply in gathering all the data relevant to a query. The API can be used to organize the SDT content and translate into a native XML database. The XML format is structured into efficient sections, enabling excellent query performance by use of the XPath query language. Optionally, the content can be translated into a Structured Query Language (SQL) database for fast, reliable SQL queries on standard database server computers.

Knowledge Query Language (KQL)

DTIC Science & Technology

2016-02-01

unlimited. This page intentionally left blank. iii EXECUTIVE SUMMARY Currently, queries for data ...retrieval from non-Structured Query Language (NoSQL) data stores are tightly coupled to the specific implementation of the data store implementation, making...of the storage content and format for querying NoSQL or relational data stores. This approach uses address expressions (or A-Expressions) embedded in

The HITRAN2016 Molecular Spectroscopic Database

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

Gordon, I. E.; Rothman, L. S.; Hill, C.

This article describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is composed of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additionalmore » absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 300 additional molecules important in different areas of atmospheric science have been added to the database. The compilation can be accessed through www.hitran.org. Most of the HITRAN data have now been cast into an underlying relational database structure that offers many advantages over the long-standing sequential text-based structure. The new structure empowers the user in many ways. It enables the incorporation of an extended set of fundamental parameters per transition, sophisticated line-shape formalisms, easy user-defined output formats, and very convenient searching, filtering, and plotting of data. Finally, a powerful application programming interface making use of structured query language (SQL) features for higher-level applications of HITRAN is also provided.« less

The HITRAN2016 Molecular Spectroscopic Database

DOE PAGES

Gordon, I. E.; Rothman, L. S.; Hill, C.; ...

2017-07-05

This article describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is composed of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additionalmore » absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 300 additional molecules important in different areas of atmospheric science have been added to the database. The compilation can be accessed through www.hitran.org. Most of the HITRAN data have now been cast into an underlying relational database structure that offers many advantages over the long-standing sequential text-based structure. The new structure empowers the user in many ways. It enables the incorporation of an extended set of fundamental parameters per transition, sophisticated line-shape formalisms, easy user-defined output formats, and very convenient searching, filtering, and plotting of data. Finally, a powerful application programming interface making use of structured query language (SQL) features for higher-level applications of HITRAN is also provided.« less

Managing Rock and Paleomagnetic Data Flow with the MagIC Database: from Measurement and Analysis to Comprehensive Archive and Visualization

NASA Astrophysics Data System (ADS)

Koppers, A. A.; Minnett, R. C.; Tauxe, L.; Constable, C.; Donadini, F.

2008-12-01

The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by rock and paleomagnetic data. The goal of MagIC is to archive all measurements and derived properties for studies of paleomagnetic directions (inclination, declination) and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). Organizing data for presentation in peer-reviewed publications or for ingestion into databases is a time-consuming task, and to facilitate these activities, three tightly integrated tools have been developed: MagIC-PY, the MagIC Console Software, and the MagIC Online Database. A suite of Python scripts is available to help users port their data into the MagIC data format. They allow the user to add important metadata, perform basic interpretations, and average results at the specimen, sample and site levels. These scripts have been validated for use as Open Source software under the UNIX, Linux, PC and Macintosh© operating systems. We have also developed the MagIC Console Software program to assist in collating rock and paleomagnetic data for upload to the MagIC database. The program runs in Microsoft Excel© on both Macintosh© computers and PCs. It performs routine consistency checks on data entries, and assists users in preparing data for uploading into the online MagIC database. The MagIC website is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual FlashMap interface to browse and select locations. Users can also browse the database by data type (inclination, intensity, VGP, hysteresis, susceptibility) or by data compilation to view all contributions associated with previous databases, such as PINT, GMPDB or TAFI or other user-defined compilations. Query results are displayed in a digestible tabular format allowing the user to descend from locations to sites, samples, specimens and measurements. At each stage, the result set can be saved and, when supported by the data, can be visualized by plotting global location maps, equal area, XY, age, and depth plots, or typical Zijderveld, hysteresis, magnetization and remanence diagrams.

Ontology-based geospatial data query and integration

USGS Publications Warehouse

Zhao, T.; Zhang, C.; Wei, M.; Peng, Z.-R.

2008-01-01

Geospatial data sharing is an increasingly important subject as large amount of data is produced by a variety of sources, stored in incompatible formats, and accessible through different GIS applications. Past efforts to enable sharing have produced standardized data format such as GML and data access protocols such as Web Feature Service (WFS). While these standards help enabling client applications to gain access to heterogeneous data stored in different formats from diverse sources, the usability of the access is limited due to the lack of data semantics encoded in the WFS feature types. Past research has used ontology languages to describe the semantics of geospatial data but ontology-based queries cannot be applied directly to legacy data stored in databases or shapefiles, or to feature data in WFS services. This paper presents a method to enable ontology query on spatial data available from WFS services and on data stored in databases. We do not create ontology instances explicitly and thus avoid the problems of data replication. Instead, user queries are rewritten to WFS getFeature requests and SQL queries to database. The method also has the benefits of being able to utilize existing tools of databases, WFS, and GML while enabling query based on ontology semantics. ?? 2008 Springer-Verlag Berlin Heidelberg.

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.

12 CFR 338.8 - Compilation of loan data in register format.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Compilation of loan data in register format... OF GENERAL POLICY FAIR HOUSING Recordkeeping § 338.8 Compilation of loan data in register format. Banks and other lenders required to file a Home Mortgage Disclosure Act loan application register (LAR...

12 CFR 338.8 - Compilation of loan data in register format.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 12 Banks and Banking 5 2012-01-01 2012-01-01 false Compilation of loan data in register format... OF GENERAL POLICY FAIR HOUSING Recordkeeping § 338.8 Compilation of loan data in register format. Banks and other lenders required to file a Home Mortgage Disclosure Act loan application register (LAR...

12 CFR 338.8 - Compilation of loan data in register format.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 12 Banks and Banking 4 2011-01-01 2011-01-01 false Compilation of loan data in register format... OF GENERAL POLICY FAIR HOUSING Recordkeeping § 338.8 Compilation of loan data in register format. Banks and other lenders required to file a Home Mortgage Disclosure Act loan application register (LAR...

An intuitive graphical webserver for multiple-choice protein sequence search.

PubMed

Banky, Daniel; Szalkai, Balazs; Grolmusz, Vince

2014-04-10

Every day tens of thousands of sequence searches and sequence alignment queries are submitted to webservers. The capitalized word "BLAST" becomes a verb, describing the act of performing sequence search and alignment. However, if one needs to search for sequences that contain, for example, two hydrophobic and three polar residues at five given positions, the query formation on the most frequently used webservers will be difficult. Some servers support the formation of queries with regular expressions, but most of the users are unfamiliar with their syntax. Here we present an intuitive, easily applicable webserver, the Protein Sequence Analysis server, that allows the formation of multiple choice queries by simply drawing the residues to their positions; if more than one residue are drawn to the same position, then they will be nicely stacked on the user interface, indicating the multiple choice at the given position. This computer-game-like interface is natural and intuitive, and the coloring of the residues makes possible to form queries requiring not just certain amino acids in the given positions, but also small nonpolar, negatively charged, hydrophobic, positively charged, or polar ones. The webserver is available at http://psa.pitgroup.org. Copyright © 2014 Elsevier B.V. All rights reserved.

Colorado Late Cenozoic Fault and Fold Database and Internet Map Server: User-friendly technology for complex information

USGS Publications Warehouse

Morgan, K.S.; Pattyn, G.J.; Morgan, M.L.

2005-01-01

Internet mapping applications for geologic data allow simultaneous data delivery and collection, enabling quick data modification while efficiently supplying the end user with information. Utilizing Web-based technologies, the Colorado Geological Survey's Colorado Late Cenozoic Fault and Fold Database was transformed from a monothematic, nonspatial Microsoft Access database into a complex information set incorporating multiple data sources. The resulting user-friendly format supports easy analysis and browsing. The core of the application is the Microsoft Access database, which contains information compiled from available literature about faults and folds that are known or suspected to have moved during the late Cenozoic. The database contains nonspatial fields such as structure type, age, and rate of movement. Geographic locations of the fault and fold traces were compiled from previous studies at 1:250,000 scale to form a spatial database containing information such as length and strike. Integration of the two databases allowed both spatial and nonspatial information to be presented on the Internet as a single dataset (http://geosurvey.state.co.us/pubs/ceno/). The user-friendly interface enables users to view and query the data in an integrated manner, thus providing multiple ways to locate desired information. Retaining the digital data format also allows continuous data updating and quick delivery of newly acquired information. This dataset is a valuable resource to anyone interested in earthquake hazards and the activity of faults and folds in Colorado. Additional geologic hazard layers and imagery may aid in decision support and hazard evaluation. The up-to-date and customizable maps are invaluable tools for researchers or the public.

A web-based data-querying tool based on ontology-driven methodology and flowchart-based model.

PubMed

Ping, Xiao-Ou; Chung, Yufang; Tseng, Yi-Ju; Liang, Ja-Der; Yang, Pei-Ming; Huang, Guan-Tarn; Lai, Feipei

2013-10-08

Because of the increased adoption rate of electronic medical record (EMR) systems, more health care records have been increasingly accumulating in clinical data repositories. Therefore, querying the data stored in these repositories is crucial for retrieving the knowledge from such large volumes of clinical data. The aim of this study is to develop a Web-based approach for enriching the capabilities of the data-querying system along the three following considerations: (1) the interface design used for query formulation, (2) the representation of query results, and (3) the models used for formulating query criteria. The Guideline Interchange Format version 3.5 (GLIF3.5), an ontology-driven clinical guideline representation language, was used for formulating the query tasks based on the GLIF3.5 flowchart in the Protégé environment. The flowchart-based data-querying model (FBDQM) query execution engine was developed and implemented for executing queries and presenting the results through a visual and graphical interface. To examine a broad variety of patient data, the clinical data generator was implemented to automatically generate the clinical data in the repository, and the generated data, thereby, were employed to evaluate the system. The accuracy and time performance of the system for three medical query tasks relevant to liver cancer were evaluated based on the clinical data generator in the experiments with varying numbers of patients. In this study, a prototype system was developed to test the feasibility of applying a methodology for building a query execution engine using FBDQMs by formulating query tasks using the existing GLIF. The FBDQM-based query execution engine was used to successfully retrieve the clinical data based on the query tasks formatted using the GLIF3.5 in the experiments with varying numbers of patients. The accuracy of the three queries (ie, "degree of liver damage," "degree of liver damage when applying a mutually exclusive setting," and "treatments for liver cancer") was 100% for all four experiments (10 patients, 100 patients, 1000 patients, and 10,000 patients). Among the three measured query phases, (1) structured query language operations, (2) criteria verification, and (3) other, the first two had the longest execution time. The ontology-driven FBDQM-based approach enriched the capabilities of the data-querying system. The adoption of the GLIF3.5 increased the potential for interoperability, shareability, and reusability of the query tasks.

A parallel data management system for large-scale NASA datasets

NASA Technical Reports Server (NTRS)

Srivastava, Jaideep

1993-01-01

The past decade has experienced a phenomenal growth in the amount of data and resultant information generated by NASA's operations and research projects. A key application is the reprocessing problem which has been identified to require data management capabilities beyond those available today (PRAT93). The Intelligent Information Fusion (IIF) system (ROEL91) is an ongoing NASA project which has similar requirements. Deriving our understanding of NASA's future data management needs based on the above, this paper describes an approach to using parallel computer systems (processor and I/O architectures) to develop an efficient parallel database management system to address the needs. Specifically, we propose to investigate issues in low-level record organizations and management, complex query processing, and query compilation and scheduling.

Optimizability of OGC Standards Implementations - a Case Study

NASA Astrophysics Data System (ADS)

Misev, D.; Baumann, P.

2012-04-01

Why do we shop at Amazon? Because they have a unique offering that is nowhere else available? Certainly not. Rather, Amazon offers (i) simple, yet effective search; (ii) very simple payment; (iii) extremely rapid delivery. This is how scientific services will be distinguished in future: not for their data holding (there will be manifold choice), but for their service quality. We are facing the transition from data stewardship to service stewardship. One of the OGC standards which particularly enables flexible retrieval is the Web Coverage Processing Service (WCPS). It defines a high-level query language on large, multi-dimensional raster data, such as 1D timeseries, 2D EO imagery, 3D x/y/t image time series and x/y/z geophysical data, 4D x/y/z/t climate and ocean data. We have implemented WCPS based on an Array Database Management System, rasdaman, which is available in open source. In this demonstration, we study WCPS queries on 2D, 3D, and 4D data sets. Particular emphasis is placed on the computational load queries generate in such on-demand processing and filtering. We look at different techniques and their impact on performance, such as adaptive storage partitioning, query rewriting, and just-in-time compilation. Results show that there is significant potential for effective server-side optimization once a query language is sufficiently high-level and declarative.

The Magnetics Information Consortium (MagIC) Online Database: Uploading, Searching and Visualizing Paleomagnetic and Rock Magnetic Data

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A.; Tauxe, L.; Constable, C.; Pisarevsky, S. A.; Jackson, M.; Solheid, P.; Banerjee, S.; Johnson, C.

2006-12-01

The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by both rock and paleomagnetic data. The goal of MagIC is to archive all measurements and the derived properties for studies of paleomagnetic directions (inclination, declination) and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). MagIC is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual map interface to browse and select locations. The query result set is displayed in a digestible tabular format allowing the user to descend through hierarchical levels such as from locations to sites, samples, specimens, and measurements. At each stage, the result set can be saved and, if supported by the data, can be visualized by plotting global location maps, equal area plots, or typical Zijderveld, hysteresis, and various magnetization and remanence diagrams. User contributions to the MagIC database are critical to achieving a useful research tool. We have developed a standard data and metadata template (Version 2.1) that can be used to format and upload all data at the time of publication in Earth Science journals. Software tools are provided to facilitate population of these templates within Microsoft Excel. These tools allow for the import/export of text files and provide advanced functionality to manage and edit the data, and to perform various internal checks to maintain data integrity and prepare for uploading. The MagIC Contribution Wizard at http://earthref.org/MAGIC/upload.htm executes the upload and takes only a few minutes to process several thousand data records. The standardized MagIC template files are stored in the digital archives of EarthRef.org where they remain available for download by the public (in both text and Excel format). Finally, the contents of these template files are automatically parsed into the online relational database, making the data available for online searches in the paleomagnetic and rock magnetic search nodes. The MagIC database contains all data transferred from the IAGA paleomagnetic poles database (GPMDB), the lava flow paleosecular variation database (PSVRL), lake sediment database (SECVR) and the PINT database. Additionally, a substantial number of data compiled under the Time Averaged Field Investigations project is now included plus a significant fraction of the data collected at SIO and the IRM. Ongoing additions of legacy data include over 40 papers from studies on the Hawaiian Islands and Mexico, data compilations from archeomagnetic studies and updates to the lake sediment dataset.

Putting Space Physics Data Facility (SPDF) Services to Good Use

NASA Astrophysics Data System (ADS)

Candey, R. M.; Bilitza, D.; Chimiak, R.; Cooper, J. F.; Garcia, L. N.; Harris, B.; Johnson, R. C.; King, J. H.; Kovalick, T.; Leckner, H.; Liu, M.; McGuire, R. E.; Papitashvili, N. E.; Roberts, A.

2009-12-01

The Space Physics Data Facility (SPDF) project provides heliophysics science-enabling information services and is the most widely used single access point to heliophysics science data and orbits from NASA's solar-heliospheric satellite missions. Our emphasis has been on active service of the best digital data products and key ancillary information with graphics, listings and production of subsetted or merged files (mass downloads or parameter-specific selections). Our services today include the: (1) Heliophysics Resource Gateway (HRG) data finding service (also known as the Virtual Space Physics Observatory or VSPO); (2) Data services including the Coordinated Data Analysis Web (CDAWeb), OMNIweb compilation of interplanetary parameters (mapped to the Earth's bow shock) and related indices, and their large underlying collection of datasets; (3) Orbit information and display services including the Satellite Situation Center (SSCweb) and the 4D Orbit Viewer interactive Java client; and the (4) Common Data Format (CDF) software library and file format and science file format translation suite. (5) Upcoming is the Heliospheric Event List Manager (HELM) to coordinate lists of interesting events and provide a mechanism for tying together the above services and others. We describe several research projects that heavily used SPDF's services and resulted in publications. Although not actually all used at once, the following research scenario shows how SPDF and VxO services can be combined for studying solar events that produce energetic particles and effects at Earth: use the HRG/VPSO to locate data of interest, perhaps query OMNIWeb for times when energetic particle solar activity is high and query the SSCWeb orbit location service for when Cluster, Geotail, Polar/IMAGE are in position to measure the cusp, magnetotail and the Earth's aurora, respectively. Also query SSCweb for times when Polar and magnetometer ground stations are on the same field lines. Using these times, use CDAWeb to browse data from these spacecraft, and add Wind and ACE field and plasma data to identify interplanetary shocks arriving at Earth. Use HRG to find and retrieve SOHO LASCO CME data at SDAC. Use the SSCWeb 4D Orbit Viewer to display the relative spacecraft positions and geophysical boundaries and to follow the magnetic footpoints of the satellites. Confirm auroral substorm activity by a quick browse of IMAGE FUV and TIMED GUVI data as movies showing the expanding and intensifying auroral oval. Finally, pull these data directly into your own analysis tool (such as ViSBARD or some model in IDL) via our web services or simple FTP transfer to complete the analysis.

Digitizing Consumption Across the Operational Spectrum

DTIC Science & Technology

2014-09-01

Figure 14.  Java -implemented Dictionary and Query: Result ............................................22  Figure 15.  Global Database Architecture...format. Figure 14 is an illustration of the query submitted in Java and the result which would be shown using the data shown in Figure 13. Figure...13. NoSQL (key, value) Dictionary Example 22 Figure 14. Java -implemented Dictionary and Query: Result While a

Using digital surveillance to examine the impact of public figure pancreatic cancer announcements on media and search query outcomes.

PubMed

Noar, Seth M; Ribisl, Kurt M; Althouse, Benjamin M; Willoughby, Jessica Fitts; Ayers, John W

2013-12-01

Announcements of cancer diagnoses from public figures may stimulate cancer information seeking and media coverage about cancer. This study used digital surveillance to quantify the effects of pancreatic cancer public figure announcements on online cancer information seeking and cancer media coverage. We compiled a list of public figures (N = 25) who had been diagnosed with or had died from pancreatic cancer between 2006 and 2011. We specified interrupted time series models using data from Google Trends to examine search query shifts for pancreatic cancer and other cancers. Weekly media coverage archived on Google News were also analyzed. Most public figures' pancreatic cancer announcements corresponded with no appreciable change in pancreatic cancer search queries or media coverage. In contrast, Patrick Swayze's diagnosis was associated with a 285% (95% confidence interval [CI]: 212 to 360) increase in pancreatic cancer search queries, though it was only weakly associated with increases in pancreatic cancer media coverage. Steve Jobs's death was associated with a 197% (95% CI: 131 to 266) increase in pancreatic cancer queries and a 3517% (95% CI: 2882 to 4492) increase in pancreatic cancer media coverage. In general, a doubling in pancreatic cancer-specific media coverage corresponded with a 325% increase in pancreatic cancer queries. Digital surveillance is an important tool for future cancer control research and practice. The current application of these methods suggested that pancreatic cancer announcements (diagnosis or death) by particular public figures stimulated media coverage of and online information seeking for pancreatic cancer.

A Web-Based Data-Querying Tool Based on Ontology-Driven Methodology and Flowchart-Based Model

PubMed Central

Ping, Xiao-Ou; Chung, Yufang; Liang, Ja-Der; Yang, Pei-Ming; Huang, Guan-Tarn; Lai, Feipei

2013-01-01

Background Because of the increased adoption rate of electronic medical record (EMR) systems, more health care records have been increasingly accumulating in clinical data repositories. Therefore, querying the data stored in these repositories is crucial for retrieving the knowledge from such large volumes of clinical data. Objective The aim of this study is to develop a Web-based approach for enriching the capabilities of the data-querying system along the three following considerations: (1) the interface design used for query formulation, (2) the representation of query results, and (3) the models used for formulating query criteria. Methods The Guideline Interchange Format version 3.5 (GLIF3.5), an ontology-driven clinical guideline representation language, was used for formulating the query tasks based on the GLIF3.5 flowchart in the Protégé environment. The flowchart-based data-querying model (FBDQM) query execution engine was developed and implemented for executing queries and presenting the results through a visual and graphical interface. To examine a broad variety of patient data, the clinical data generator was implemented to automatically generate the clinical data in the repository, and the generated data, thereby, were employed to evaluate the system. The accuracy and time performance of the system for three medical query tasks relevant to liver cancer were evaluated based on the clinical data generator in the experiments with varying numbers of patients. Results In this study, a prototype system was developed to test the feasibility of applying a methodology for building a query execution engine using FBDQMs by formulating query tasks using the existing GLIF. The FBDQM-based query execution engine was used to successfully retrieve the clinical data based on the query tasks formatted using the GLIF3.5 in the experiments with varying numbers of patients. The accuracy of the three queries (ie, “degree of liver damage,” “degree of liver damage when applying a mutually exclusive setting,” and “treatments for liver cancer”) was 100% for all four experiments (10 patients, 100 patients, 1000 patients, and 10,000 patients). Among the three measured query phases, (1) structured query language operations, (2) criteria verification, and (3) other, the first two had the longest execution time. Conclusions The ontology-driven FBDQM-based approach enriched the capabilities of the data-querying system. The adoption of the GLIF3.5 increased the potential for interoperability, shareability, and reusability of the query tasks. PMID:25600078

Spatial and symbolic queries for 3D image data

NASA Astrophysics Data System (ADS)

Benson, Daniel C.; Zick, Gregory L.

1992-04-01

We present a query system for an object-oriented biomedical imaging database containing 3-D anatomical structures and their corresponding 2-D images. The graphical interface facilitates the formation of spatial queries, nonspatial or symbolic queries, and combined spatial/symbolic queries. A query editor is used for the creation and manipulation of 3-D query objects as volumes, surfaces, lines, and points. Symbolic predicates are formulated through a combination of text fields and multiple choice selections. Query results, which may include images, image contents, composite objects, graphics, and alphanumeric data, are displayed in multiple views. Objects returned by the query may be selected directly within the views for further inspection or modification, or for use as query objects in subsequent queries. Our image database query system provides visual feedback and manipulation of spatial query objects, multiple views of volume data, and the ability to combine spatial and symbolic queries. The system allows for incremental enhancement of existing objects and the addition of new objects and spatial relationships. The query system is designed for databases containing symbolic and spatial data. This paper discuses its application to data acquired in biomedical 3- D image reconstruction, but it is applicable to other areas such as CAD/CAM, geographical information systems, and computer vision.

Cyclone: java-based querying and computing with Pathway/Genome databases.

PubMed

Le Fèvre, François; Smidtas, Serge; Schächter, Vincent

2007-05-15

Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL). In addition, Cyclone interfaces easily with Java software including the Eclipse IDE for HQL edition, the Jung API for graph algorithms or Cytoscape for graph visualization. Cyclone is freely available under an open source license at: http://sourceforge.net/projects/nemo-cyclone. For download and installation instructions, tutorials, use cases and examples, see http://nemo-cyclone.sourceforge.net.

Big Data Analytics with Datalog Queries on Spark.

PubMed

Shkapsky, Alexander; Yang, Mohan; Interlandi, Matteo; Chiu, Hsuan; Condie, Tyson; Zaniolo, Carlo

2016-01-01

There is great interest in exploiting the opportunity provided by cloud computing platforms for large-scale analytics. Among these platforms, Apache Spark is growing in popularity for machine learning and graph analytics. Developing efficient complex analytics in Spark requires deep understanding of both the algorithm at hand and the Spark API or subsystem APIs (e.g., Spark SQL, GraphX). Our BigDatalog system addresses the problem by providing concise declarative specification of complex queries amenable to efficient evaluation. Towards this goal, we propose compilation and optimization techniques that tackle the important problem of efficiently supporting recursion in Spark. We perform an experimental comparison with other state-of-the-art large-scale Datalog systems and verify the efficacy of our techniques and effectiveness of Spark in supporting Datalog-based analytics.

Big Data Analytics with Datalog Queries on Spark

PubMed Central

Shkapsky, Alexander; Yang, Mohan; Interlandi, Matteo; Chiu, Hsuan; Condie, Tyson; Zaniolo, Carlo

2017-01-01

There is great interest in exploiting the opportunity provided by cloud computing platforms for large-scale analytics. Among these platforms, Apache Spark is growing in popularity for machine learning and graph analytics. Developing efficient complex analytics in Spark requires deep understanding of both the algorithm at hand and the Spark API or subsystem APIs (e.g., Spark SQL, GraphX). Our BigDatalog system addresses the problem by providing concise declarative specification of complex queries amenable to efficient evaluation. Towards this goal, we propose compilation and optimization techniques that tackle the important problem of efficiently supporting recursion in Spark. We perform an experimental comparison with other state-of-the-art large-scale Datalog systems and verify the efficacy of our techniques and effectiveness of Spark in supporting Datalog-based analytics. PMID:28626296

Map showing geologic terranes of the Hailey 1 degree x 2 degrees quadrangle and the western part of the Idaho Falls 1 degree x 2 degrees quadrangle, south-central Idaho

USGS Publications Warehouse

Worl, R.G.; Johnson, K.M.

1995-01-01

The paper version of Map Showing Geologic Terranes of the Hailey 1x2 Quadrangle and the western part of the Idaho Falls 1x2 Quadrangle, south-central Idaho was compiled by Ron Worl and Kate Johnson in 1995. The plate was compiled on a 1:250,000 scale topographic base map. TechniGraphic System, Inc. of Fort Collins Colorado digitized this map under contract for N.Shock. G.Green edited and prepared the digital version for publication as a geographic information system database. The digital geologic map database can be queried in many ways to produce a variety of geologic maps.

Designing integrated computational biology pipelines visually.

PubMed

Jamil, Hasan M

2013-01-01

The long-term cost of developing and maintaining a computational pipeline that depends upon data integration and sophisticated workflow logic is too high to even contemplate "what if" or ad hoc type queries. In this paper, we introduce a novel application building interface for computational biology research, called VizBuilder, by leveraging a recent query language called BioFlow for life sciences databases. Using VizBuilder, it is now possible to develop ad hoc complex computational biology applications at throw away costs. The underlying query language supports data integration and workflow construction almost transparently and fully automatically, using a best effort approach. Users express their application by drawing it with VizBuilder icons and connecting them in a meaningful way. Completed applications are compiled and translated as BioFlow queries for execution by the data management system LifeDB, for which VizBuilder serves as a front end. We discuss VizBuilder features and functionalities in the context of a real life application after we briefly introduce BioFlow. The architecture and design principles of VizBuilder are also discussed. Finally, we outline future extensions of VizBuilder. To our knowledge, VizBuilder is a unique system that allows visually designing computational biology pipelines involving distributed and heterogeneous resources in an ad hoc manner.

Software Helps Retrieve Information Relevant to the User

NASA Technical Reports Server (NTRS)

Mathe, Natalie; Chen, James

2003-01-01

The Adaptive Indexing and Retrieval Agent (ARNIE) is a code library, designed to be used by an application program, that assists human users in retrieving desired information in a hypertext setting. Using ARNIE, the program implements a computational model for interactively learning what information each human user considers relevant in context. The model, called a "relevance network," incrementally adapts retrieved information to users individual profiles on the basis of feedback from the users regarding specific queries. The model also generalizes such knowledge for subsequent derivation of relevant references for similar queries and profiles, thereby, assisting users in filtering information by relevance. ARNIE thus enables users to categorize and share information of interest in various contexts. ARNIE encodes the relevance and structure of information in a neural network dynamically configured with a genetic algorithm. ARNIE maintains an internal database, wherein it saves associations, and from which it returns associated items in response to a query. A C++ compiler for a platform on which ARNIE will be utilized is necessary for creating the ARNIE library but is not necessary for the execution of the software.

NoSQL: collection document and cloud by using a dynamic web query form

NASA Astrophysics Data System (ADS)

Abdalla, Hemn B.; Lin, Jinzhao; Li, Guoquan

2015-07-01

Mongo-DB (from "humongous") is an open-source document database and the leading NoSQL database. A NoSQL (Not Only SQL, next generation databases, being non-relational, deal, open-source and horizontally scalable) presenting a mechanism for storage and retrieval of documents. Previously, we stored and retrieved the data using the SQL queries. Here, we use the MonogoDB that means we are not utilizing the MySQL and SQL queries. Directly importing the documents into our Drives, retrieving the documents on that drive by not applying the SQL queries, using the IO BufferReader and Writer, BufferReader for importing our type of document files to my folder (Drive). For retrieving the document files, the usage is BufferWriter from the particular folder (or) Drive. In this sense, providing the security for those storing files for what purpose means if we store the documents in our local folder means all or views that file and modified that file. So preventing that file, we are furnishing the security. The original document files will be changed to another format like in this paper; Binary format is used. Our documents will be converting to the binary format after that direct storing in one of our folder, that time the storage space will provide the private key for accessing that file. Wherever any user tries to discover the Document files means that file data are in the binary format, the document's file owner simply views that original format using that personal key from receive the secret key from the cloud.

Implementation of relational data base management systems on micro-computers

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

Huang, C.L.

1982-01-01

This dissertation describes an implementation of a Relational Data Base Management System on a microcomputer. A specific floppy disk based hardward called TERAK is being used, and high level query interface which is similar to a subset of the SEQUEL language is provided. The system contains sub-systems such as I/O, file management, virtual memory management, query system, B-tree management, scanner, command interpreter, expression compiler, garbage collection, linked list manipulation, disk space management, etc. The software has been implemented to fulfill the following goals: (1) it is highly modularized. (2) The system is physically segmented into 16 logically independent, overlayable segments,more » in a way such that a minimal amount of memory is needed at execution time. (3) Virtual memory system is simulated that provides the system with seemingly unlimited memory space. (4) A language translator is applied to recognize user requests in the query language. The code generation of this translator generates compact code for the execution of UPDATE, DELETE, and QUERY commands. (5) A complete set of basic functions needed for on-line data base manipulations is provided through the use of a friendly query interface. (6) To eliminate the dependency on the environment (both software and hardware) as much as possible, so that it would be easy to transplant the system to other computers. (7) To simulate each relation as a sequential file. It is intended to be a highly efficient, single user system suited to be used by small or medium sized organizations for, say, administrative purposes. Experiments show that quite satisfying results have indeed been achieved.« less

Digital geologic map of part of the Thompson Falls 1:100,000 quadrangle, Idaho

USGS Publications Warehouse

Lewis, Reed S.; Derkey, Pamela D.

1999-01-01

The geology of the Thompson Falls 1:100,000 quadrangle, Idaho was compiled by Reed S. Lewis in 1997 onto a 1:100,000-scale greenline mylar of the topographic base map for input into a geographic information system (GIS). The resulting digital geologic map GIS can be queried in many ways to produce a variety of geologic maps. Digital base map data files (topography, roads, towns, rivers and lakes, etc.) are not included: they may be obtained from a variety of commercial and government sources. This database is not meant to be used or displayed at any scale larger than 1:100,000 (e.g., 1:62,500 or 1:24,000). The map area is located in north Idaho. This open-file report describes the geologic map units, the methods used to convert the geologic map data into a digital format, the Arc/Info GIS file structures and relationships, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet.

iSMART: Ontology-based Semantic Query of CDA Documents

PubMed Central

Liu, Shengping; Ni, Yuan; Mei, Jing; Li, Hanyu; Xie, Guotong; Hu, Gang; Liu, Haifeng; Hou, Xueqiao; Pan, Yue

2009-01-01

The Health Level 7 Clinical Document Architecture (CDA) is widely accepted as the format for electronic clinical document. With the rich ontological references in CDA documents, the ontology-based semantic query could be performed to retrieve CDA documents. In this paper, we present iSMART (interactive Semantic MedicAl Record reTrieval), a prototype system designed for ontology-based semantic query of CDA documents. The clinical information in CDA documents will be extracted into RDF triples by a declarative XML to RDF transformer. An ontology reasoner is developed to infer additional information by combining the background knowledge from SNOMED CT ontology. Then an RDF query engine is leveraged to enable the semantic queries. This system has been evaluated using the real clinical documents collected from a large hospital in southern China. PMID:20351883

Does query expansion limit our learning? A comparison of social-based expansion to content-based expansion for medical queries on the internet.

PubMed

Pentoney, Christopher; Harwell, Jeff; Leroy, Gondy

2014-01-01

Searching for medical information online is a common activity. While it has been shown that forming good queries is difficult, Google's query suggestion tool, a type of query expansion, aims to facilitate query formation. However, it is unknown how this expansion, which is based on what others searched for, affects the information gathering of the online community. To measure the impact of social-based query expansion, this study compared it with content-based expansion, i.e., what is really in the text. We used 138,906 medical queries from the AOL User Session Collection and expanded them using Google's Autocomplete method (social-based) and the content of the Google Web Corpus (content-based). We evaluated the specificity and ambiguity of the expansion terms for trigram queries. We also looked at the impact on the actual results using domain diversity and expansion edit distance. Results showed that the social-based method provided more precise expansion terms as well as terms that were less ambiguous. Expanded queries do not differ significantly in diversity when expanded using the social-based method (6.72 different domains returned in the first ten results, on average) vs. content-based method (6.73 different domains, on average).

Molecular implementation of simple logic programs.

PubMed

Ran, Tom; Kaplan, Shai; Shapiro, Ehud

2009-10-01

Autonomous programmable computing devices made of biomolecules could interact with a biological environment and be used in future biological and medical applications. Biomolecular implementations of finite automata and logic gates have already been developed. Here, we report an autonomous programmable molecular system based on the manipulation of DNA strands that is capable of performing simple logical deductions. Using molecular representations of facts such as Man(Socrates) and rules such as Mortal(X) <-- Man(X) (Every Man is Mortal), the system can answer molecular queries such as Mortal(Socrates)? (Is Socrates Mortal?) and Mortal(X)? (Who is Mortal?). This biomolecular computing system compares favourably with previous approaches in terms of expressive power, performance and precision. A compiler translates facts, rules and queries into their molecular representations and subsequently operates a robotic system that assembles the logical deductions and delivers the result. This prototype is the first simple programming language with a molecular-scale implementation.

Catalogue of HI PArameters (CHIPA)

NASA Astrophysics Data System (ADS)

Saponara, J.; Benaglia, P.; Koribalski, B.; Andruchow, I.

2015-08-01

The catalogue of HI parameters of galaxies HI (CHIPA) is the natural continuation of the compilation by M.C. Martin in 1998. CHIPA provides the most important parameters of nearby galaxies derived from observations of the neutral Hydrogen line. The catalogue contains information of 1400 galaxies across the sky and different morphological types. Parameters like the optical diameter of the galaxy, the blue magnitude, the distance, morphological type, HI extension are listed among others. Maps of the HI distribution, velocity and velocity dispersion can also be display for some cases. The main objective of this catalogue is to facilitate the bibliographic queries, through searching in a database accessible from the internet that will be available in 2015 (the website is under construction). The database was built using the open source `` mysql (SQL, Structured Query Language, management system relational database) '', while the website was built with ''HTML (Hypertext Markup Language)'' and ''PHP (Hypertext Preprocessor)''.

Geologic map of outcrop areas of sedimentary units in the eastern part of the Hailey 1 degree x 2 degrees quadrangle and part of the southern part of the Challis 1 degree x 2 degrees quadrangle, south-central Idaho

USGS Publications Warehouse

Link, P.K.; Mahoney, J.B.; Bruner, D.J.; Batatian, L.D.; Wilson, Eric; Williams, F.J.C.

1995-01-01

The paper version of the Geologic map of outcrop areas of sedimentary units in the eastern part of the Hailey 1x2 Quadrangle and part of the southern part of the Challis 1x2 Quadrangle, south-central Idaho was compiled by Paul Link and others in 1995. The plate was compiled on a 1:100,000 scale topographic base map. TechniGraphic System, Inc. of Fort Collins Colorado digitized this map under contract for N.Shock. G.Green edited and prepared the digital version for publication as a GIS database. The digital geologic map database can be queried in many ways to produce a variety of geologic maps.

Modeling and interoperability of heterogeneous genomic big data for integrative processing and querying.

PubMed

Masseroli, Marco; Kaitoua, Abdulrahman; Pinoli, Pietro; Ceri, Stefano

2016-12-01

While a huge amount of (epi)genomic data of multiple types is becoming available by using Next Generation Sequencing (NGS) technologies, the most important emerging problem is the so-called tertiary analysis, concerned with sense making, e.g., discovering how different (epi)genomic regions and their products interact and cooperate with each other. We propose a paradigm shift in tertiary analysis, based on the use of the Genomic Data Model (GDM), a simple data model which links genomic feature data to their associated experimental, biological and clinical metadata. GDM encompasses all the data formats which have been produced for feature extraction from (epi)genomic datasets. We specifically describe the mapping to GDM of SAM (Sequence Alignment/Map), VCF (Variant Call Format), NARROWPEAK (for called peaks produced by NGS ChIP-seq or DNase-seq methods), and BED (Browser Extensible Data) formats, but GDM supports as well all the formats describing experimental datasets (e.g., including copy number variations, DNA somatic mutations, or gene expressions) and annotations (e.g., regarding transcription start sites, genes, enhancers or CpG islands). We downloaded and integrated samples of all the above-mentioned data types and formats from multiple sources. The GDM is able to homogeneously describe semantically heterogeneous data and makes the ground for providing data interoperability, e.g., achieved through the GenoMetric Query Language (GMQL), a high-level, declarative query language for genomic big data. The combined use of the data model and the query language allows comprehensive processing of multiple heterogeneous data, and supports the development of domain-specific data-driven computations and bio-molecular knowledge discovery. Copyright © 2016 Elsevier Inc. All rights reserved.

Design of FastQuery: How to Generalize Indexing and Querying System for Scientific Data

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

Wu, Jerry; Wu, Kesheng

2011-04-18

Modern scientific datasets present numerous data management and analysis challenges. State-of-the-art index and query technologies such as FastBit are critical for facilitating interactive exploration of large datasets. These technologies rely on adding auxiliary information to existing datasets to accelerate query processing. To use these indices, we need to match the relational data model used by the indexing systems with the array data model used by most scientific data, and to provide an efficient input and output layer for reading and writing the indices. In this work, we present a flexible design that can be easily applied to most scientific datamore » formats. We demonstrate this flexibility by applying it to two of the most commonly used scientific data formats, HDF5 and NetCDF. We present two case studies using simulation data from the particle accelerator and climate simulation communities. To demonstrate the effectiveness of the new design, we also present a detailed performance study using both synthetic and real scientific workloads.« less

Digital atlas of the upper Washita River basin, southwestern Oklahoma

USGS Publications Warehouse

Becker, Carol J.; Masoner, Jason R.; Scott, Jonathon C.

2008-01-01

Numerous types of environmental data have been collected in the upper Washita River basin in southwestern Oklahoma. However, to date these data have not been compiled into a format that can be comprehensively queried for the purpose of evaluating the effects of various conservation practices implemented to reduce agricultural runoff and erosion in parts of the upper Washita River basin. This U.S. Geological Survey publication, 'Digital atlas of the upper Washita River basin, southwestern Oklahoma' was created to assist with environmental analysis. This atlas contains 30 spatial data sets that can be used in environmental assessment and decision making for the upper Washita River basin. This digital atlas includes U.S. Geological Survey sampling sites and associated water-quality, biological, water-level, and streamflow data collected from 1903 to 2005. The data were retrieved from the U.S. Geological Survey National Water Information System database on September 29, 2005. Data sets are from the Geology, Geography, and Water disciplines of the U.S. Geological Survey and cover parts of Beckham, Caddo, Canadian, Comanche, Custer, Dewey, Grady, Kiowa, and Washita Counties in southwestern Oklahoma. A bibliography of past reports from the U.S. Geological Survey and other State and Federal agencies from 1949 to 2004 is included in the atlas. Additionally, reports by Becker (2001), Martin (2002), Fairchild and others (2004), and Miller and Stanley (2005) are provided in electronic format.

ArrayBridge: Interweaving declarative array processing with high-performance computing

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

Xing, Haoyuan; Floratos, Sofoklis; Blanas, Spyros

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aimsmore » to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.« less

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.

libvaxdata: VAX data format conversion routines

USGS Publications Warehouse

Baker, Lawrence M.

2005-01-01

libvaxdata provides a collection of routines for converting numeric data-integer and floating-point-to and from the formats used on a Digital Equipment Corporation1 (DEC) VAX 32-bit minicomputer (Brunner, 1991). Since the VAX numeric data formats are inherited from those used on a DEC PDP-11 16-bit minicomputer, these routines can be used to convert PDP-11 data as well. VAX numeric data formats are also the default data formats used on DEC Alpha 64-bit minicomputers running OpenVMS The libvaxdata routines are callable from Fortran or C. They require that the caller use two's-complement format for integer data and IEEE 754 format (ANSI/IEEE, 1985) for floating-point data. They also require that the 'natural' size of a C int type (integer) is 32 bits. That is the case for most modern 32-bit and 64-bit computer systems. Nevertheless, you may wish to consult the Fortran or C compiler documentation on your system to be sure. Some Fortran compilers support conversion of VAX numeric data on-the-fly when reading or writing unformatted files, either as a compiler option or a run-time I/O option. This feature may be easier to use than the libvaxdata routines. Consult the Fortran compiler documentation on your system to determine if this alternative is available to you. 1Later Compaq Computer Corporation, now Hewlett-Packard Company

Incorporating the APS Catalog of the POSS I and Image Archive in ADS

NASA Technical Reports Server (NTRS)

Humphreys, Roberta M.

1998-01-01

The primary purpose of this contract was to develop the software to both create and access an on-line database of images from digital scans of the Palomar Sky Survey. This required modifying our DBMS (called Star Base) to create an image database from the actual raw pixel data from the scans. The digitized images are processed into a set of coordinate-reference index and pixel files that are stored in run-length files, thus achieving an efficient lossless compression. For efficiency and ease of referencing, each digitized POSS I plate is then divided into 900 subplates. Our custom DBMS maps each query into the corresponding POSS plate(s) and subplate(s). All images from the appropriate subplates are retrieved from disk with byte-offsets taken from the index files. These are assembled on-the-fly into a GIF image file for browser display, and a FITS format image file for retrieval. The FITS images have a pixel size of 0.33 arcseconds. The FITS header contains astrometric and photometric information. This method keeps the disk requirements manageable while allowing for future improvements. When complete, the APS Image Database will contain over 130 Gb of data. A set of web pages query forms are available on-line, as well as an on-line tutorial and documentation. The database is distributed to the Internet by a high-speed SGI server and a high-bandwidth disk system. URL is http://aps.umn.edu/IDB/. The image database software is written in perl and C and has been compiled on SGI computers with MIX5.3. A copy of the written documentation is included and the software is on the accompanying exabyte tape.

QRFXFreeze: Queryable Compressor for RFX.

PubMed

Senthilkumar, Radha; Nandagopal, Gomathi; Ronald, Daphne

2015-01-01

The verbose nature of XML has been mulled over again and again and many compression techniques for XML data have been excogitated over the years. Some of the techniques incorporate support for querying the XML database in its compressed format while others have to be decompressed before they can be queried. XML compression in which querying is directly supported instantaneously with no compromise over time is forced to compromise over space. In this paper, we propose the compressor, QRFXFreeze, which not only reduces the space of storage but also supports efficient querying. The compressor does this without decompressing the compressed XML file. The compressor supports all kinds of XML documents along with insert, update, and delete operations. The forte of QRFXFreeze is that the textual data are semantically compressed and are indexed to reduce the querying time. Experimental results show that the proposed compressor performs much better than other well-known compressors.

Earth-Base: A Free And Open Source, RESTful Earth Sciences Platform

NASA Astrophysics Data System (ADS)

Kishor, P.; Heim, N. A.; Peters, S. E.; McClennen, M.

2012-12-01

This presentation describes the motivation, concept, and architecture behind Earth-Base, a web-based, RESTful data-management, analysis and visualization platform for earth sciences data. Traditionally web applications have been built directly accessing data from a database using a scripting language. While such applications are great at bring results to a wide audience, they are limited in scope to the imagination and capabilities of the application developer. Earth-Base decouples the data store from the web application by introducing an intermediate "data application" tier. The data application's job is to query the data store using self-documented, RESTful URIs, and send the results back formatted as JavaScript Object Notation (JSON). Decoupling the data store from the application allows virtually limitless flexibility in developing applications, both web-based for human consumption or programmatic for machine consumption. It also allows outside developers to use the data in their own applications, potentially creating applications that the original data creator and app developer may not have even thought of. Standardized specifications for URI-based querying and JSON-formatted results make querying and developing applications easy. URI-based querying also allows utilizing distributed datasets easily. Companion mechanisms for querying data snapshots aka time-travel, usage tracking and license management, and verification of semantic equivalence of data are also described. The latter promotes the "What You Expect Is What You Get" (WYEIWYG) principle that can aid in data citation and verification.

Query Health: standards-based, cross-platform population health surveillance

PubMed Central

Klann, Jeffrey G; Buck, Michael D; Brown, Jeffrey; Hadley, Marc; Elmore, Richard; Weber, Griffin M; Murphy, Shawn N

2014-01-01

Objective Understanding population-level health trends is essential to effectively monitor and improve public health. The Office of the National Coordinator for Health Information Technology (ONC) Query Health initiative is a collaboration to develop a national architecture for distributed, population-level health queries across diverse clinical systems with disparate data models. Here we review Query Health activities, including a standards-based methodology, an open-source reference implementation, and three pilot projects. Materials and methods Query Health defined a standards-based approach for distributed population health queries, using an ontology based on the Quality Data Model and Consolidated Clinical Document Architecture, Health Quality Measures Format (HQMF) as the query language, the Query Envelope as the secure transport layer, and the Quality Reporting Document Architecture as the result language. Results We implemented this approach using Informatics for Integrating Biology and the Bedside (i2b2) and hQuery for data analytics and PopMedNet for access control, secure query distribution, and response. We deployed the reference implementation at three pilot sites: two public health departments (New York City and Massachusetts) and one pilot designed to support Food and Drug Administration post-market safety surveillance activities. The pilots were successful, although improved cross-platform data normalization is needed. Discussions This initiative resulted in a standards-based methodology for population health queries, a reference implementation, and revision of the HQMF standard. It also informed future directions regarding interoperability and data access for ONC's Data Access Framework initiative. Conclusions Query Health was a test of the learning health system that supplied a functional methodology and reference implementation for distributed population health queries that has been validated at three sites. PMID:24699371

Query Health: standards-based, cross-platform population health surveillance.

PubMed

Klann, Jeffrey G; Buck, Michael D; Brown, Jeffrey; Hadley, Marc; Elmore, Richard; Weber, Griffin M; Murphy, Shawn N

2014-01-01

Understanding population-level health trends is essential to effectively monitor and improve public health. The Office of the National Coordinator for Health Information Technology (ONC) Query Health initiative is a collaboration to develop a national architecture for distributed, population-level health queries across diverse clinical systems with disparate data models. Here we review Query Health activities, including a standards-based methodology, an open-source reference implementation, and three pilot projects. Query Health defined a standards-based approach for distributed population health queries, using an ontology based on the Quality Data Model and Consolidated Clinical Document Architecture, Health Quality Measures Format (HQMF) as the query language, the Query Envelope as the secure transport layer, and the Quality Reporting Document Architecture as the result language. We implemented this approach using Informatics for Integrating Biology and the Bedside (i2b2) and hQuery for data analytics and PopMedNet for access control, secure query distribution, and response. We deployed the reference implementation at three pilot sites: two public health departments (New York City and Massachusetts) and one pilot designed to support Food and Drug Administration post-market safety surveillance activities. The pilots were successful, although improved cross-platform data normalization is needed. This initiative resulted in a standards-based methodology for population health queries, a reference implementation, and revision of the HQMF standard. It also informed future directions regarding interoperability and data access for ONC's Data Access Framework initiative. Query Health was a test of the learning health system that supplied a functional methodology and reference implementation for distributed population health queries that has been validated at three sites. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

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.

An Examination of Natural Language as a Query Formation Tool for Retrieving Information on E-Health from Pub Med.

ERIC Educational Resources Information Center

Peterson, Gabriel M.; Su, Kuichun; Ries, James E.; Sievert, Mary Ellen C.

2002-01-01

Discussion of Internet use for information searches on health-related topics focuses on a study that examined complexity and variability of natural language in using search terms that express the concept of electronic health (e-health). Highlights include precision of retrieved information; shift in terminology; and queries using the Pub Med…

Integrated databanks access and sequence/structure analysis services at the PBIL.

PubMed

Perrière, Guy; Combet, Christophe; Penel, Simon; Blanchet, Christophe; Thioulouse, Jean; Geourjon, Christophe; Grassot, Julien; Charavay, Céline; Gouy, Manolo; Duret, Laurent; Deléage, Gilbert

2003-07-01

The World Wide Web server of the PBIL (Pôle Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server allows to query nucleotide sequence banks in the EMBL and GenBank formats and protein sequence banks in the SWISS-PROT and PIR formats. The query engine on which our data bank access is based is the ACNUC system. It allows the possibility to build complex queries to access functional zones of biological interest and to retrieve large sequence sets. Of special interest are the unique features provided by this system to query the data banks of gene families developed at the PBIL. The server also provides access to a wide range of sequence analysis methods: similarity search programs, multiple alignments, protein structure prediction and multivariate statistics. An originality of this server is the integration of these two aspects: sequence retrieval and sequence analysis. Indeed, thanks to the introduction of re-usable lists, it is possible to perform treatments on large sets of data. The PBIL server can be reached at: http://pbil.univ-lyon1.fr.

Spatial information semantic query based on SPARQL

NASA Astrophysics Data System (ADS)

Xiao, Zhifeng; Huang, Lei; Zhai, Xiaofang

2009-10-01

How can the efficiency of spatial information inquiries be enhanced in today's fast-growing information age? We are rich in geospatial data but poor in up-to-date geospatial information and knowledge that are ready to be accessed by public users. This paper adopts an approach for querying spatial semantic by building an Web Ontology language(OWL) format ontology and introducing SPARQL Protocol and RDF Query Language(SPARQL) to search spatial semantic relations. It is important to establish spatial semantics that support for effective spatial reasoning for performing semantic query. Compared to earlier keyword-based and information retrieval techniques that rely on syntax, we use semantic approaches in our spatial queries system. Semantic approaches need to be developed by ontology, so we use OWL to describe spatial information extracted by the large-scale map of Wuhan. Spatial information expressed by ontology with formal semantics is available to machines for processing and to people for understanding. The approach is illustrated by introducing a case study for using SPARQL to query geo-spatial ontology instances of Wuhan. The paper shows that making use of SPARQL to search OWL ontology instances can ensure the result's accuracy and applicability. The result also indicates constructing a geo-spatial semantic query system has positive efforts on forming spatial query and retrieval.

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

PubMed

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

2013-01-01

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

[On the seasonality of dermatoses: a retrospective analysis of search engine query data depending on the season].

PubMed

Köhler, M J; Springer, S; Kaatz, M

2014-09-01

The volume of search engine queries about disease-relevant items reflects public interest and correlates with disease prevalence as proven by the example of flu (influenza). Other influences include media attention or holidays. The present work investigates if the seasonality of prevalence or symptom severity of dermatoses correlates with search engine query data. The relative weekly volume of dermatological relevant search terms was assessed by the online tool Google Trends for the years 2009-2013. For each item, the degree of seasonality was calculated via frequency analysis and a geometric approach. Many dermatoses show a marked seasonality, reflected by search engine query volumes. Unexpected seasonal variations of these queries suggest a previously unknown variability of the respective disease prevalence. Furthermore, using the example of allergic rhinitis, a close correlation of search engine query data with actual pollen count can be demonstrated. In many cases, search engine query data are appropriate to estimate seasonal variability in prevalence of common dermatoses. This finding may be useful for real-time analysis and formation of hypotheses concerning pathogenetic or symptom aggravating mechanisms and may thus contribute to improvement of diagnostics and prevention of skin diseases.

Visual graph query formulation and exploration: a new perspective on information retrieval at the edge

NASA Astrophysics Data System (ADS)

Kase, Sue E.; Vanni, Michelle; Knight, Joanne A.; Su, Yu; Yan, Xifeng

2016-05-01

Within operational environments decisions must be made quickly based on the information available. Identifying an appropriate knowledge base and accurately formulating a search query are critical tasks for decision-making effectiveness in dynamic situations. The spreading of graph data management tools to access large graph databases is a rapidly emerging research area of potential benefit to the intelligence community. A graph representation provides a natural way of modeling data in a wide variety of domains. Graph structures use nodes, edges, and properties to represent and store data. This research investigates the advantages of information search by graph query initiated by the analyst and interactively refined within the contextual dimensions of the answer space toward a solution. The paper introduces SLQ, a user-friendly graph querying system enabling the visual formulation of schemaless and structureless graph queries. SLQ is demonstrated with an intelligence analyst information search scenario focused on identifying individuals responsible for manufacturing a mosquito-hosted deadly virus. The scenario highlights the interactive construction of graph queries without prior training in complex query languages or graph databases, intuitive navigation through the problem space, and visualization of results in graphical format.

The value of Retrospective and Concurrent Think Aloud in formative usability testing of a physician data query tool.

PubMed

Peute, Linda W P; de Keizer, Nicolette F; Jaspers, Monique W M

2015-06-01

To compare the performance of the Concurrent (CTA) and Retrospective (RTA) Think Aloud method and to assess their value in a formative usability evaluation of an Intensive Care Registry-physician data query tool designed to support ICU quality improvement processes. Sixteen representative intensive care physicians participated in the usability evaluation study. Subjects were allocated to either the CTA or RTA method by a matched randomized design. Each subject performed six usability-testing tasks of varying complexity in the query tool in a real-working context. Methods were compared with regard to number and type of problems detected. Verbal protocols of CTA and RTA were analyzed in depth to assess differences in verbal output. Standardized measures were applied to assess thoroughness in usability problem detection weighted per problem severity level and method overall effectiveness in detecting usability problems with regard to the time subjects spent per method. The usability evaluation of the data query tool revealed a total of 43 unique usability problems that the intensive care physicians encountered. CTA detected unique usability problems with regard to graphics/symbols, navigation issues, error messages, and the organization of information on the query tool's screens. RTA detected unique issues concerning system match with subjects' language and applied terminology. The in-depth verbal protocol analysis of CTA provided information on intensive care physicians' query design strategies. Overall, CTA performed significantly better than RTA in detecting usability problems. CTA usability problem detection effectiveness was 0.80 vs. 0.62 (p<0.05) respectively, with an average difference of 42% less time spent per subject compared to RTA. In addition, CTA was more thorough in detecting usability problems of a moderate (0.85 vs. 0.7) and severe nature (0.71 vs. 0.57). In this study, the CTA is more effective in usability-problem detection and provided clarification of intensive care physician query design strategies to inform redesign of the query tool. However, CTA does not outperform RTA. The RTA additionally elucidated unique usability problems and new user requirements. Based on the results of this study, we recommend the use of CTA in formative usability evaluation studies of health information technology. However, we recommend further research on the application of RTA in usability studies with regard to user expertise and experience when focusing on user profile customized (re)design. Copyright © 2015 Elsevier Inc. All rights reserved.

12 CFR 1003.4 - Compilation of loan data.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 12 Banks and Banking 8 2012-01-01 2012-01-01 false Compilation of loan data. 1003.4 Section 1003.4....4 Compilation of loan data. (a) Data format and itemization. A financial institution shall collect data regarding applications for, and originations and purchases of, home purchase loans, home...

Taking Proof based Verified Computation a Few Steps Closer to Practicality (extended version)

DTIC Science & Technology

2012-06-27

general s2 + s, in general V’s per-instance CPU costs Issue commit queries (e + 2c) · n/β (e + 2c) · n/β Process commit responses d d Issue PCP...size (# of instances) (§2.3) e: cost of encrypting an element in F d : cost of decrypting an encrypted element f : cost of multiplying in F h: cost of...domain D (such as the integers, Z, or the rationals, Q) to equivalent constraints over a finite field, the programmer or compiler performs 3We suspect

Computing health quality measures using Informatics for Integrating Biology and the Bedside.

PubMed

Klann, Jeffrey G; Murphy, Shawn N

2013-04-19

The Health Quality Measures Format (HQMF) is a Health Level 7 (HL7) standard for expressing computable Clinical Quality Measures (CQMs). Creating tools to process HQMF queries in clinical databases will become increasingly important as the United States moves forward with its Health Information Technology Strategic Plan to Stages 2 and 3 of the Meaningful Use incentive program (MU2 and MU3). Informatics for Integrating Biology and the Bedside (i2b2) is one of the analytical databases used as part of the Office of the National Coordinator (ONC)'s Query Health platform to move toward this goal. Our goal is to integrate i2b2 with the Query Health HQMF architecture, to prepare for other HQMF use-cases (such as MU2 and MU3), and to articulate the functional overlap between i2b2 and HQMF. Therefore, we analyze the structure of HQMF, and then we apply this understanding to HQMF computation on the i2b2 clinical analytical database platform. Specifically, we develop a translator between two query languages, HQMF and i2b2, so that the i2b2 platform can compute HQMF queries. We use the HQMF structure of queries for aggregate reporting, which define clinical data elements and the temporal and logical relationships between them. We use the i2b2 XML format, which allows flexible querying of a complex clinical data repository in an easy-to-understand domain-specific language. The translator can represent nearly any i2b2-XML query as HQMF and execute in i2b2 nearly any HQMF query expressible in i2b2-XML. This translator is part of the freely available reference implementation of the QueryHealth initiative. We analyze limitations of the conversion and find it covers many, but not all, of the complex temporal and logical operators required by quality measures. HQMF is an expressive language for defining quality measures, and it will be important to understand and implement for CQM computation, in both meaningful use and population health. However, its current form might allow complexity that is intractable for current database systems (both in terms of implementation and computation). Our translator, which supports the subset of HQMF currently expressible in i2b2-XML, may represent the beginnings of a practical compromise. It is being pilot-tested in two Query Health demonstration projects, and it can be further expanded to balance computational tractability with the advanced features needed by measure developers.

Computing Health Quality Measures Using Informatics for Integrating Biology and the Bedside

PubMed Central

Murphy, Shawn N

2013-01-01

Background The Health Quality Measures Format (HQMF) is a Health Level 7 (HL7) standard for expressing computable Clinical Quality Measures (CQMs). Creating tools to process HQMF queries in clinical databases will become increasingly important as the United States moves forward with its Health Information Technology Strategic Plan to Stages 2 and 3 of the Meaningful Use incentive program (MU2 and MU3). Informatics for Integrating Biology and the Bedside (i2b2) is one of the analytical databases used as part of the Office of the National Coordinator (ONC)’s Query Health platform to move toward this goal. Objective Our goal is to integrate i2b2 with the Query Health HQMF architecture, to prepare for other HQMF use-cases (such as MU2 and MU3), and to articulate the functional overlap between i2b2 and HQMF. Therefore, we analyze the structure of HQMF, and then we apply this understanding to HQMF computation on the i2b2 clinical analytical database platform. Specifically, we develop a translator between two query languages, HQMF and i2b2, so that the i2b2 platform can compute HQMF queries. Methods We use the HQMF structure of queries for aggregate reporting, which define clinical data elements and the temporal and logical relationships between them. We use the i2b2 XML format, which allows flexible querying of a complex clinical data repository in an easy-to-understand domain-specific language. Results The translator can represent nearly any i2b2-XML query as HQMF and execute in i2b2 nearly any HQMF query expressible in i2b2-XML. This translator is part of the freely available reference implementation of the QueryHealth initiative. We analyze limitations of the conversion and find it covers many, but not all, of the complex temporal and logical operators required by quality measures. Conclusions HQMF is an expressive language for defining quality measures, and it will be important to understand and implement for CQM computation, in both meaningful use and population health. However, its current form might allow complexity that is intractable for current database systems (both in terms of implementation and computation). Our translator, which supports the subset of HQMF currently expressible in i2b2-XML, may represent the beginnings of a practical compromise. It is being pilot-tested in two Query Health demonstration projects, and it can be further expanded to balance computational tractability with the advanced features needed by measure developers. PMID:23603227

An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework.

PubMed

Chen, Yi-An; Tripathi, Lokesh P; Mizuguchi, Kenji

2016-01-01

Data analysis is one of the most critical and challenging steps in drug discovery and disease biology. A user-friendly resource to visualize and analyse high-throughput data provides a powerful medium for both experimental and computational biologists to understand vastly different biological data types and obtain a concise, simplified and meaningful output for better knowledge discovery. We have previously developed TargetMine, an integrated data warehouse optimized for target prioritization. Here we describe how upgraded and newly modelled data types in TargetMine can now survey the wider biological and chemical data space, relevant to drug discovery and development. To enhance the scope of TargetMine from target prioritization to broad-based knowledge discovery, we have also developed a new auxiliary toolkit to assist with data analysis and visualization in TargetMine. This toolkit features interactive data analysis tools to query and analyse the biological data compiled within the TargetMine data warehouse. The enhanced system enables users to discover new hypotheses interactively by performing complicated searches with no programming and obtaining the results in an easy to comprehend output format. Database URL: http://targetmine.mizuguchilab.org. © The Author(s) 2016. Published by Oxford University Press.

An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework

PubMed Central

Chen, Yi-An; Tripathi, Lokesh P.; Mizuguchi, Kenji

2016-01-01

Data analysis is one of the most critical and challenging steps in drug discovery and disease biology. A user-friendly resource to visualize and analyse high-throughput data provides a powerful medium for both experimental and computational biologists to understand vastly different biological data types and obtain a concise, simplified and meaningful output for better knowledge discovery. We have previously developed TargetMine, an integrated data warehouse optimized for target prioritization. Here we describe how upgraded and newly modelled data types in TargetMine can now survey the wider biological and chemical data space, relevant to drug discovery and development. To enhance the scope of TargetMine from target prioritization to broad-based knowledge discovery, we have also developed a new auxiliary toolkit to assist with data analysis and visualization in TargetMine. This toolkit features interactive data analysis tools to query and analyse the biological data compiled within the TargetMine data warehouse. The enhanced system enables users to discover new hypotheses interactively by performing complicated searches with no programming and obtaining the results in an easy to comprehend output format. Database URL: http://targetmine.mizuguchilab.org PMID:26989145

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.

PubMed

Balaur, Irina; Mazein, Alexander; Saqi, Mansoor; Lysenko, Artem; Rawlings, Christopher J; Auffray, Charles

2017-04-01

The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing. The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/ . The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework . ibalaur@eisbm.org. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks

PubMed Central

Mazein, Alexander; Saqi, Mansoor; Lysenko, Artem; Rawlings, Christopher J.; Auffray, Charles

2017-01-01

Abstract Summary: The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing. Availability and Implementation: The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/. The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework. Contact: ibalaur@eisbm.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27993779

Using PeptideAtlas, SRMAtlas and PASSEL – Comprehensive Resources for discovery and targeted proteomics

PubMed Central

Kusebauch, Ulrike; Deutsch, Eric W.; Campbell, David S.; Sun, Zhi; Farrah, Terry; Moritz, Robert L.

2014-01-01

PeptideAtlas, SRMAtlas and PASSEL are web-accessible resources to support discovery and targeted proteomics research. PeptideAtlas is a multi-species compendium of shotgun proteomic data provided by the scientific community, SRMAtlas is a resource of high-quality, complete proteome SRM assays generated in a consistent manner for the targeted identification and quantification of proteins, and PASSEL is a repository that compiles and represents selected reaction monitoring data, all in an easy to use interface. The databases are generated from native mass spectrometry data files that are analyzed in a standardized manner including statistical validation of the results. Each resource offers search functionalities and can be queried by user defined constraints; the query results are provided in tables or are graphically displayed. PeptideAtlas, SRMAtlas and PASSEL are publicly available freely via the website http://www.peptideatlas.org. In this protocol, we describe the use of these resources, we highlight how to submit, search, collate and download data. PMID:24939129

StreamQRE: Modular Specification and Efficient Evaluation of Quantitative Queries over Streaming Data.

PubMed

Mamouras, Konstantinos; Raghothaman, Mukund; Alur, Rajeev; Ives, Zachary G; Khanna, Sanjeev

2017-06-01

Real-time decision making in emerging IoT applications typically relies on computing quantitative summaries of large data streams in an efficient and incremental manner. To simplify the task of programming the desired logic, we propose StreamQRE, which provides natural and high-level constructs for processing streaming data. Our language has a novel integration of linguistic constructs from two distinct programming paradigms: streaming extensions of relational query languages and quantitative extensions of regular expressions. The former allows the programmer to employ relational constructs to partition the input data by keys and to integrate data streams from different sources, while the latter can be used to exploit the logical hierarchy in the input stream for modular specifications. We first present the core language with a small set of combinators, formal semantics, and a decidable type system. We then show how to express a number of common patterns with illustrative examples. Our compilation algorithm translates the high-level query into a streaming algorithm with precise complexity bounds on per-item processing time and total memory footprint. We also show how to integrate approximation algorithms into our framework. We report on an implementation in Java, and evaluate it with respect to existing high-performance engines for processing streaming data. Our experimental evaluation shows that (1) StreamQRE allows more natural and succinct specification of queries compared to existing frameworks, (2) the throughput of our implementation is higher than comparable systems (for example, two-to-four times greater than RxJava), and (3) the approximation algorithms supported by our implementation can lead to substantial memory savings.

StreamQRE: Modular Specification and Efficient Evaluation of Quantitative Queries over Streaming Data*

PubMed Central

Mamouras, Konstantinos; Raghothaman, Mukund; Alur, Rajeev; Ives, Zachary G.; Khanna, Sanjeev

2017-01-01

Real-time decision making in emerging IoT applications typically relies on computing quantitative summaries of large data streams in an efficient and incremental manner. To simplify the task of programming the desired logic, we propose StreamQRE, which provides natural and high-level constructs for processing streaming data. Our language has a novel integration of linguistic constructs from two distinct programming paradigms: streaming extensions of relational query languages and quantitative extensions of regular expressions. The former allows the programmer to employ relational constructs to partition the input data by keys and to integrate data streams from different sources, while the latter can be used to exploit the logical hierarchy in the input stream for modular specifications. We first present the core language with a small set of combinators, formal semantics, and a decidable type system. We then show how to express a number of common patterns with illustrative examples. Our compilation algorithm translates the high-level query into a streaming algorithm with precise complexity bounds on per-item processing time and total memory footprint. We also show how to integrate approximation algorithms into our framework. We report on an implementation in Java, and evaluate it with respect to existing high-performance engines for processing streaming data. Our experimental evaluation shows that (1) StreamQRE allows more natural and succinct specification of queries compared to existing frameworks, (2) the throughput of our implementation is higher than comparable systems (for example, two-to-four times greater than RxJava), and (3) the approximation algorithms supported by our implementation can lead to substantial memory savings. PMID:29151821

Ground Operations Aerospace Language (GOAL). Volume 2: Compiler

NASA Technical Reports Server (NTRS)

1973-01-01

The principal elements and functions of the Ground Operations Aerospace Language (GOAL) compiler are presented. The technique used to transcribe the syntax diagrams into machine processable format for use by the parsing routines is described. An explanation of the parsing technique used to process GOAL source statements is included. The compiler diagnostics and the output reports generated during a GOAL compilation are explained. A description of the GOAL program package is provided.

Language model: Extension to solve inconsistency, incompleteness, and short query in cultural heritage collection

NASA Astrophysics Data System (ADS)

Tan, Kian Lam; Lim, Chen Kim

2017-10-01

With the explosive growth of online information such as email messages, news articles, and scientific literature, many institutions and museums are converting their cultural collections from physical data to digital format. However, this conversion resulted in the issues of inconsistency and incompleteness. Besides, the usage of inaccurate keywords also resulted in short query problem. Most of the time, the inconsistency and incompleteness are caused by the aggregation fault in annotating a document itself while the short query problem is caused by naive user who has prior knowledge and experience in cultural heritage domain. In this paper, we presented an approach to solve the problem of inconsistency, incompleteness and short query by incorporating the Term Similarity Matrix into the Language Model. Our approach is tested on the Cultural Heritage in CLEF (CHiC) collection which consists of short queries and documents. The results show that the proposed approach is effective and has improved the accuracy in retrieval time.

MorphoSaurus--design and evaluation of an interlingua-based, cross-language document retrieval engine for the medical domain.

PubMed

Markó, K; Schulz, S; Hahn, U

2005-01-01

We propose an interlingua-based indexing approach to account for the particular challenges that arise in the design and implementation of cross-language document retrieval systems for the medical domain. Documents, as well as queries, are mapped to a language-independent conceptual layer on which retrieval operations are performed. We contrast this approach with the direct translation of German queries to English ones which, subsequently, are matched against English documents. We evaluate both approaches, interlingua-based and direct translation, on a large medical document collection, the OHSUMED corpus. A substantial benefit for interlingua-based document retrieval using German queries on English texts is found, which amounts to 93% of the (monolingual) English baseline. Most state-of-the-art cross-language information retrieval systems translate user queries to the language(s) of the target documents. In contra-distinction to this approach, translating both documents and user queries into a language-independent, concept-like representation format is more beneficial to enhance cross-language retrieval performance.

EXTENSIBLE DATABASE FRAMEWORK FOR MANAGEMENT OF UNSTRUCTURED AND SEMI-STRUCTURED DOCUMENTS

NASA Technical Reports Server (NTRS)

Gawdiak, Yuri O. (Inventor); La, Tracy T. (Inventor); Lin, Shu-Chun Y. (Inventor); Malof, David A. (Inventor); Tran, Khai Peter B. (Inventor)

2005-01-01

Method and system for querying a collection of Unstructured or semi-structured documents to identify presence of, and provide context and/or content for, keywords and/or keyphrases. The documents are analyzed and assigned a node structure, including an ordered sequence of mutually exclusive node segments or strings. Each node has an associated set of at least four, five or six attributes with node information and can represent a format marker or text, with the last node in any node segment usually being a text node. A keyword (or keyphrase) is specified. and the last node in each node segment is searched for a match with the keyword. When a match is found at a query node, or at a node determined with reference to a query node, the system displays the context andor the content of the query node.

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases

PubMed Central

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

2013-01-01

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

miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST

PubMed Central

Kim, You Jung; Boyd, Andrew; Athey, Brian D.; Patel, Jignesh M.

2005-01-01

A common task in many modern bioinformatics applications is to match a set of nucleotide query sequences against a large sequence dataset. Exis-ting tools, such as BLAST, are designed to evaluate a single query at a time and can be unacceptably slow when the number of sequences in the query set is large. In this paper, we present a new algorithm, called miBLAST, that evaluates such batch workloads efficiently. At the core, miBLAST employs a q-gram filtering and an index join for efficiently detecting similarity between the query sequences and database sequences. This set-oriented technique, which indexes both the query and the database sets, results in substantial performance improvements over existing methods. Our results show that miBLAST is significantly faster than BLAST in many cases. For example, miBLAST aligned 247 965 oligonucleotide sequences in the Affymetrix probe set against the Human UniGene in 1.26 days, compared with 27.27 days with BLAST (an improvement by a factor of 22). The relative performance of miBLAST increases for larger word sizes; however, it decreases for longer queries. miBLAST employs the familiar BLAST statistical model and output format, guaranteeing the same accuracy as BLAST and facilitating a seamless transition for existing BLAST users. PMID:16061938

Usage and administration manual for a geodatabase compendium of water-resources data-Rio Grande Basin from the Rio Arriba-Sandoval County line, New Mexico, to Presidio, Texas, 1889-2009

USGS Publications Warehouse

Burley, Thomas E.

2011-01-01

The U.S. Geological Survey, in cooperation with the New Mexico Interstate Stream Commission, developed a geodatabase compendium (hereinafter referred to as the 'geodatabase') of available water-resources data for the reach of the Rio Grande from Rio Arriba-Sandoval County line, New Mexico, to Presidio, Texas. Since 1889, a wealth of water-resources data has been collected in the Rio Grande Basin from Rio Arriba-Sandoval County line, New Mexico, to Presidio, Texas, for a variety of purposes. Collecting agencies, researchers, and organizations have included the U.S. Geological Survey, Bureau of Reclamation, International Boundary and Water Commission, State agencies, irrigation districts, municipal water utilities, universities, and other entities. About 1,750 data records were recently (2010) evaluated to enhance their usability by compiling them into a single geospatial relational database (geodatabase). This report is intended as a user's manual and administration guide for the geodatabase. All data available, including water quality, water level, and discharge data (both instantaneous and daily) from January 1, 1889, through December 17, 2009, were compiled for the study area. A flexible and efficient geodatabase design was used, enhancing the ability of the geodatabase to handle data from diverse sources and helping to ensure sustainability of the geodatabase with long-term maintenance. Geodatabase tables include daily data values, site locations and information, sample event information, and parameters, as well as data sources and collecting agencies. The end products of this effort are a comprehensive water-resources geodatabase that enables the visualization of primary sampling sites for surface discharges, groundwater elevations, and water-quality and associated data for the study area. In addition, repeatable data processing scripts, Structured Query Language queries for loading prepared data sources, and a detailed process for refreshing all data in the compendium have been developed. The geodatabase functionality allows users to explore spatial characteristics of the data, conduct spatial analyses, and pose questions to the geodatabase in the form of queries. Users can also customize and extend the geodatabase, combine it with other databases, or use the geodatabase design for other water-resources applications.

Isostatic gravity map and principal facts for 694 gravity stations in Yellowstone National Park and vicinity, Wyoming, Montana, and Idaho

USGS Publications Warehouse

Carle, S.F.; Glen, J.M.; Langenheim, V.E.; Smith, R.B.; Oliver, H.W.

1990-01-01

The report presents the principal facts for gravity stations compiled for Yellowstone National Park and vicinity. The gravity data were compiled from three sources: Defense Mapping Agency, University of Utah, and U.S. Geological Survey. Part A of the report is a paper copy describing how the compilation was done and presenting the data in tabular format as well as a map; part B is a 5-1/4 inch floppy diskette containing only the data files in ASCII format. Requirements for part B: IBM PC or compatible, DOS v. 2.0 or higher. Files contained on this diskette: DOD.ISO -- File containing the principal facts of the 514 gravity stations obtained from the Defense Mapping Agency. The data are in Plouff format* (see file PFTAB.TEX). UTAH.ISO -- File containing the principal facts of 153 gravity stations obtained from the University of Utah. Data are in Plouff format. USGS.ISO -- File containing the principal facts of 27 gravity stations collected by the U.S. Geological Survey in July 1987. Data are in Plouff format. PFTAB.TXT -- File containing explanation of principal fact format. ACC.TXT -- File containing explanation of accuracy codes.

Land Treatment Digital Library

USGS Publications Warehouse

Pilliod, David S.; Welty, Justin L.

2013-01-01

The Land Treatment Digital Library (LTDL) was created by the U.S. Geological Survey to catalog legacy land treatment information on Bureau of Land Management lands in the western United States. The LTDL can be used by federal managers and scientists for compiling information for data-calls, producing maps, generating reports, and conducting analyses at varying spatial and temporal scales. The LTDL currently houses thousands of treatments from BLM lands across 10 states. Users can browse a map to find information on individual treatments, perform more complex queries to identify a set of treatments, and view graphs of treatment summary statistics.

Activity recognition using Video Event Segmentation with Text (VEST)

NASA Astrophysics Data System (ADS)

Holloway, Hillary; Jones, Eric K.; Kaluzniacki, Andrew; Blasch, Erik; Tierno, Jorge

2014-06-01

Multi-Intelligence (multi-INT) data includes video, text, and signals that require analysis by operators. Analysis methods include information fusion approaches such as filtering, correlation, and association. In this paper, we discuss the Video Event Segmentation with Text (VEST) method, which provides event boundaries of an activity to compile related message and video clips for future interest. VEST infers meaningful activities by clustering multiple streams of time-sequenced multi-INT intelligence data and derived fusion products. We discuss exemplar results that segment raw full-motion video (FMV) data by using extracted commentary message timestamps, FMV metadata, and user-defined queries.

GELLO: an object-oriented query and expression language for clinical decision support.

PubMed

Sordo, Margarita; Ogunyemi, Omolola; Boxwala, Aziz A; Greenes, Robert A

2003-01-01

GELLO is a purpose-specific, object-oriented (OO) query and expression language. GELLO is the result of a concerted effort of the Decision Systems Group (DSG) working with the HL7 Clinical Decision Support Technical Committee (CDSTC) to provide the HL7 community with a common format for data encoding and manipulation. GELLO will soon be submitted for ballot to the HL7 CDSTC for consideration as a standard.

Thermodynamic data for modeling acid mine drainage problems: compilation and estimation of data for selected soluble iron-sulfate minerals

USGS Publications Warehouse

Hemingway, Bruch S.; Seal, Robert R.; Chou, I-Ming

2002-01-01

Enthalpy of formation, Gibbs energy of formation, and entropy values have been compiled from the literature for the hydrated ferrous sulfate minerals melanterite, rozenite, and szomolnokite, and a variety of other hydrated sulfate compounds. On the basis of this compilation, it appears that there is no evidence for an excess enthalpy of mixing for sulfate-H2O systems, except for the first H2O molecule of crystallization. The enthalpy and Gibbs energy of formation of each H2O molecule of crystallization, except the first, in the iron(II) sulfate - H2O system is -295.15 and -238.0 kJ?mol-1, respectively. The absence of an excess enthalpy of mixing is used as the basis for estimating thermodynamic values for a variety of ferrous, ferric, and mixed-valence sulfate salts of relevance to acid-mine drainage systems.

PIML: the Pathogen Information Markup Language.

PubMed

He, Yongqun; Vines, Richard R; Wattam, Alice R; Abramochkin, Georgiy V; Dickerman, Allan W; Eckart, J Dana; Sobral, Bruno W S

2005-01-01

A vast amount of information about human, animal and plant pathogens has been acquired, stored and displayed in varied formats through different resources, both electronically and otherwise. However, there is no community standard format for organizing this information or agreement on machine-readable format(s) for data exchange, thereby hampering interoperation efforts across information systems harboring such infectious disease data. The Pathogen Information Markup Language (PIML) is a free, open, XML-based format for representing pathogen information. XSLT-based visual presentations of valid PIML documents were developed and can be accessed through the PathInfo website or as part of the interoperable web services federation known as ToolBus/PathPort. Currently, detailed PIML documents are available for 21 pathogens deemed of high priority with regard to public health and national biological defense. A dynamic query system allows simple queries as well as comparisons among these pathogens. Continuing efforts are being taken to include other groups' supporting PIML and to develop more PIML documents. All the PIML-related information is accessible from http://www.vbi.vt.edu/pathport/pathinfo/

Data collection and compilation for a geodatabase of groundwater, surface-water, water-quality, geophysical, and geologic data, Pecos County Region, Texas, 1930-2011

USGS Publications Warehouse

Pearson, Daniel K.; Bumgarner, Johnathan R.; Houston, Natalie A.; Stanton, Gregory P.; Teeple, Andrew; Thomas, Jonathan V.

2012-01-01

The U.S. Geological Survey, in cooperation with Middle Pecos Groundwater Conservation District, Pecos County, City of Fort Stockton, Brewster County, and Pecos County Water Control and Improvement District No. 1, compiled groundwater, surface-water, water-quality, geophysical, and geologic data for site locations in the Pecos County region, Texas, and developed a geodatabase to facilitate use of this information. Data were compiled for an approximately 4,700 square mile area of the Pecos County region, Texas. The geodatabase contains data from 8,242 sampling locations; it was designed to organize and store field-collected geochemical and geophysical data, as well as digital database resources from the U.S. Geological Survey, Middle Pecos Groundwater Conservation District, Texas Water Development Board, Texas Commission on Environmental Quality,and numerous other State and local databases. The geodatabase combines these disparate database resources into a simple data model. Site locations are geospatially enabled and stored in a geodatabase feature class for cartographic visualization and spatial analysis within a Geographic Information System. The sampling locations are related to hydrogeologic information through the use of geodatabase relationship classes. The geodatabase relationship classes provide the ability to perform complex spatial and data-driven queries to explore data stored in the geodatabase.

Novel Algorithm for Classification of Medical Images

NASA Astrophysics Data System (ADS)

Bhushan, Bharat; Juneja, Monika

2010-11-01

Content-based image retrieval (CBIR) methods in medical image databases have been designed to support specific tasks, such as retrieval of medical images. These methods cannot be transferred to other medical applications since different imaging modalities require different types of processing. To enable content-based queries in diverse collections of medical images, the retrieval system must be familiar with the current Image class prior to the query processing. Further, almost all of them deal with the DICOM imaging format. In this paper a novel algorithm based on energy information obtained from wavelet transform for the classification of medical images according to their modalities is described. For this two types of wavelets have been used and have been shown that energy obtained in either case is quite distinct for each of the body part. This technique can be successfully applied to different image formats. The results are shown for JPEG imaging format.

ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding.

PubMed

Guhlin, Joseph; Silverstein, Kevin A T; Zhou, Peng; Tiffin, Peter; Young, Nevin D

2017-08-10

Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data. The Omics Database Generator (ODG) allows users to create customized databases that utilize published genomics data integrated with experimental data which can be queried using a flexible graph database. When provided with omics and experimental data, ODG will create a comparative, multi-dimensional graph database. ODG can import definitions and annotations from other sources such as InterProScan, the Gene Ontology, ENZYME, UniPathway, and others. This annotation data can be especially useful for studying new or understudied species for which transcripts have only been predicted, and rapidly give additional layers of annotation to predicted genes. In better studied species, ODG can perform syntenic annotation translations or rapidly identify characteristics of a set of genes or nucleotide locations, such as hits from an association study. ODG provides a web-based user-interface for configuring the data import and for querying the database. Queries can also be run from the command-line and the database can be queried directly through programming language hooks available for most languages. ODG supports most common genomic formats as well as generic, easy to use tab-separated value format for user-provided annotations. ODG is a user-friendly database generation and query tool that adapts to the supplied data to produce a comparative genomic database or multi-layered annotation database. ODG provides rapid comparative genomic annotation and is therefore particularly useful for non-model or understudied species. For species for which more data are available, ODG can be used to conduct complex multi-omics, pattern-matching queries.

Benchmarking distributed data warehouse solutions for storing genomic variant information

PubMed Central

Wiewiórka, Marek S.; Wysakowicz, Dawid P.; Okoniewski, Michał J.

2017-01-01

Abstract Genomic-based personalized medicine encompasses storing, analysing and interpreting genomic variants as its central issues. At a time when thousands of patientss sequenced exomes and genomes are becoming available, there is a growing need for efficient database storage and querying. The answer could be the application of modern distributed storage systems and query engines. However, the application of large genomic variant databases to this problem has not been sufficiently far explored so far in the literature. To investigate the effectiveness of modern columnar storage [column-oriented Database Management System (DBMS)] and query engines, we have developed a prototypic genomic variant data warehouse, populated with large generated content of genomic variants and phenotypic data. Next, we have benchmarked performance of a number of combinations of distributed storages and query engines on a set of SQL queries that address biological questions essential for both research and medical applications. In addition, a non-distributed, analytical database (MonetDB) has been used as a baseline. Comparison of query execution times confirms that distributed data warehousing solutions outperform classic relational DBMSs. Moreover, pre-aggregation and further denormalization of data, which reduce the number of distributed join operations, significantly improve query performance by several orders of magnitude. Most of distributed back-ends offer a good performance for complex analytical queries, while the Optimized Row Columnar (ORC) format paired with Presto and Parquet with Spark 2 query engines provide, on average, the lowest execution times. Apache Kudu on the other hand, is the only solution that guarantees a sub-second performance for simple genome range queries returning a small subset of data, where low-latency response is expected, while still offering decent performance for running analytical queries. In summary, research and clinical applications that require the storage and analysis of variants from thousands of samples can benefit from the scalability and performance of distributed data warehouse solutions. Database URL: https://github.com/ZSI-Bio/variantsdwh PMID:29220442

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).

Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research.

PubMed

Samwald, Matthias; Lim, Ernest; Masiar, Peter; Marenco, Luis; Chen, Huajun; Morse, Thomas; Mutalik, Pradeep; Shepherd, Gordon; Miller, Perry; Cheung, Kei-Hoi

2009-01-01

The amount of biomedical data available in Semantic Web formats has been rapidly growing in recent years. While these formats are machine-friendly, user-friendly web interfaces allowing easy querying of these data are typically lacking. We present "Entrez Neuron", a pilot neuron-centric interface that allows for keyword-based queries against a coherent repository of OWL ontologies. These ontologies describe neuronal structures, physiology, mathematical models and microscopy images. The returned query results are organized hierarchically according to brain architecture. Where possible, the application makes use of entities from the Open Biomedical Ontologies (OBO) and the 'HCLS knowledgebase' developed by the W3C Interest Group for Health Care and Life Science. It makes use of the emerging RDFa standard to embed ontology fragments and semantic annotations within its HTML-based user interface. The application and underlying ontologies demonstrate how Semantic Web technologies can be used for information integration within a curated information repository and between curated information repositories. It also demonstrates how information integration can be accomplished on the client side, through simple copying and pasting of portions of documents that contain RDFa markup.

Netmeld v. 1.0

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

BERG, MICHAEL; RILEY, MARSHALL

System assessments typically yield large quantities of data from disparate sources for an analyst to scrutinize for issues. Netmeld is used to parse input from different file formats, store the data in a common format, allow users to easily query it, and enable analysts to tie different analysis tools together using a common back-end.

[Design and implementation of Chinese materia medica resources survey results display system].

PubMed

Wang, Hui; Zhang, Xiao-Bo; Ge, Xiao-Guang; Jin, Yan; Wang, Ling; Zhao, Yan-Ping; Jing, Zhi-Xian; Guo, Lan-Ping; Huang, Lu-Qi

2017-11-01

From the beginning of the fourth national census of traditional Chinese medicine resources in 2011, a large amount of data have been collected and compiled, including wild medicinal plant resource data, cultivation of medicinal plant information, traditional knowledge, and specimen information. The traditional paper-based recording method is inconvenient for query and application. The B/S architecture, JavaWeb framework and SOA are used to design and develop the fourth national census results display platform. Through the data integration and sorting, the users are to provide with integrated data services and data query display solutions. The platform realizes the fine data classification, and has the simple data retrieval and the university statistical analysis function. The platform uses Echarts components, Geo Server, Open Layers and other technologies to provide a variety of data display forms such as charts, maps and other visualization forms, intuitive reflects the number, distribution and type of Chinese material medica resources. It meets the data mapping requirements of different levels of users, and provides support for management decision-making. Copyright© by the Chinese Pharmaceutical Association.

Flora-On: Occurrence data of the vascular flora of mainland Portugal.

PubMed

Pereira, Ana Júlia; Francisco, Ana; Porto, Miguel

2016-01-01

The Flora-On dataset currently includes 253,310 occurrence records for the class Embryopsidae (vascular plants), comprising data collated via the platform http://flora-on.pt/ relating to observation records of vascular plants across mainland Portugal. Observations are uploaded directly to the database primarily by experienced botanists and naturalists, typically on a weekly basis, and consist of geo-referenced data points for species (or infraspecific taxa) along with their date of observation and phenological state. The Flora-On project aims to compile and make publicly accessible chorological, ecological, morphological and photographic information for the entire vascular flora of Portugal. The project's website offers powerful query and visualization capabilities, of which we highlight the probabilistic bioclimatic and phenological queries which operate based on the empirical density distributions of species in those variables. Flora-On was created and continues to be maintained by volunteers who are Associate members of Sociedade Portuguesa de Botânica (Botanical Society of Portugal). Given its focus on research-grade and current data, the Flora-On project represents a significant contribution to the knowledge of the present distribution and status of the Portuguese flora.

Retrieving high-resolution images over the Internet from an anatomical image database

NASA Astrophysics Data System (ADS)

Strupp-Adams, Annette; Henderson, Earl

1999-12-01

The Visible Human Data set is an important contribution to the national collection of anatomical images. To enhance the availability of these images, the National Library of Medicine has supported the design and development of a prototype object-oriented image database which imports, stores, and distributes high resolution anatomical images in both pixel and voxel formats. One of the key database modules is its client-server Internet interface. This Web interface provides a query engine with retrieval access to high-resolution anatomical images that range in size from 100KB for browser viewable rendered images, to 1GB for anatomical structures in voxel file formats. The Web query and retrieval client-server system is composed of applet GUIs, servlets, and RMI application modules which communicate with each other to allow users to query for specific anatomical structures, and retrieve image data as well as associated anatomical images from the database. Selected images can be downloaded individually as single files via HTTP or downloaded in batch-mode over the Internet to the user's machine through an applet that uses Netscape's Object Signing mechanism. The image database uses ObjectDesign's object-oriented DBMS, ObjectStore that has a Java interface. The query and retrieval systems has been tested with a Java-CDE window system, and on the x86 architecture using Windows NT 4.0. This paper describes the Java applet client search engine that queries the database; the Java client module that enables users to view anatomical images online; the Java application server interface to the database which organizes data returned to the user, and its distribution engine that allow users to download image files individually and/or in batch-mode.

Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases

PubMed Central

Santana, Filipe; Schober, Daniel; Medeiros, Zulma; Freitas, Fred; Schulz, Stefan

2011-01-01

Motivation: Ontology-like domain knowledge is frequently published in a tabular format embedded in scientific publications. We explore the re-use of such tabular content in the process of building NTDO, an ontology of neglected tropical diseases (NTDs), where the representation of the interdependencies between hosts, pathogens and vectors plays a crucial role. Results: As a proof of concept we analyzed a tabular compilation of knowledge about pathogens, vectors and geographic locations involved in the transmission of NTDs. After a thorough ontological analysis of the domain of interest, we formulated a comprehensive design pattern, rooted in the biomedical domain upper level ontology BioTop. This pattern was implemented in a VBA script which takes cell contents of an Excel spreadsheet and transforms them into OWL-DL. After minor manual post-processing, the correctness and completeness of the ontology was tested using pre-formulated competence questions as description logics (DL) queries. The expected results could be reproduced by the ontology. The proposed approach is recommended for optimizing the acquisition of ontological domain knowledge from tabular representations. Availability and implementation: Domain examples, source code and ontology are freely available on the web at http://www.cin.ufpe.br/~ntdo. Contact: fss3@cin.ufpe.br PMID:21685092

Techniques for Efficiently Managing Large Geosciences Data Sets

NASA Astrophysics Data System (ADS)

Kruger, A.; Krajewski, W. F.; Bradley, A. A.; Smith, J. A.; Baeck, M. L.; Steiner, M.; Lawrence, R. E.; Ramamurthy, M. K.; Weber, J.; Delgreco, S. A.; Domaszczynski, P.; Seo, B.; Gunyon, C. A.

2007-12-01

We have developed techniques and software tools for efficiently managing large geosciences data sets. While the techniques were developed as part of an NSF-Funded ITR project that focuses on making NEXRAD weather data and rainfall products available to hydrologists and other scientists, they are relevant to other geosciences disciplines that deal with large data sets. Metadata, relational databases, data compression, and networking are central to our methodology. Data and derived products are stored on file servers in a compressed format. URLs to, and metadata about the data and derived products are managed in a PostgreSQL database. Virtually all access to the data and products is through this database. Geosciences data normally require a number of processing steps to transform the raw data into useful products: data quality assurance, coordinate transformations and georeferencing, applying calibration information, and many more. We have developed the concept of crawlers that manage this scientific workflow. Crawlers are unattended processes that run indefinitely, and at set intervals query the database for their next assignment. A database table functions as a roster for the crawlers. Crawlers perform well-defined tasks that are, except for perhaps sequencing, largely independent from other crawlers. Once a crawler is done with its current assignment, it updates the database roster table, and gets its next assignment by querying the database. We have developed a library that enables one to quickly add crawlers. The library provides hooks to external (i.e., C-language) compiled codes, so that developers can work and contribute independently. Processes called ingesters inject data into the system. The bulk of the data are from a real-time feed using UCAR/Unidata's IDD/LDM software. An exciting recent development is the establishment of a Unidata HYDRO feed that feeds value-added metadata over the IDD/LDM. Ingesters grab the metadata and populate the PostgreSQL tables. These and other concepts we have developed have enabled us to efficiently manage a 70 Tb (and growing) data weather radar data set.

Querying and Computing with BioCyc Databases

PubMed Central

Krummenacker, Markus; Paley, Suzanne; Mueller, Lukas; Yan, Thomas; Karp, Peter D.

2006-01-01

Summary We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases: access through multiple file formats, access through Application Program Interfaces (APIs) for LISP, Perl and Java, and SQL access through the BioWarehouse relational database. Availability The Pathway Tools software and 20 BioCyc DBs in Tiers 1 and 2 are freely available to academic users; fees apply to some types of commercial use. For download instructions see http://BioCyc.org/download.shtml PMID:15961440

BP Spill Sampling and Monitoring Data

EPA Pesticide Factsheets

This dataset analyzes waste from the the British Petroleum Deepwater Horizon Rig Explosion Emergency Response, providing opportunity to query data sets by metadata criteria and find resulting raw datasets in CSV format.The data query tool allows users to download EPA's air, water and sediment sampling and monitoring data that has been collected in response to the BP oil spill. All sampling and monitoring data that has been collected to date is available for download as raw structured data.The query tools enables CSV file creation to be refined based on the following search criteria: date range (between April 28, 2010 and 9/29/2010); location by zip, city, or county; media (solid waste, weathered oil, air, surface water, liquid waste, tar, sediment, water); substance categories (based on media selection) and substances (based on substance category selection).

The Geodetic Seamless Archive Centers Service Layer: A System Architecture for Federating Geodesy Data Repositories

NASA Astrophysics Data System (ADS)

McWhirter, J.; Boler, F. M.; Bock, Y.; Jamason, P.; Squibb, M. B.; Noll, C. E.; Blewitt, G.; Kreemer, C. W.

2010-12-01

Three geodesy Archive Centers, Scripps Orbit and Permanent Array Center (SOPAC), NASA's Crustal Dynamics Data Information System (CDDIS) and UNAVCO are engaged in a joint effort to define and develop a common Web Service Application Programming Interface (API) for accessing geodetic data holdings. This effort is funded by the NASA ROSES ACCESS Program to modernize the original GPS Seamless Archive Centers (GSAC) technology which was developed in the 1990s. A new web service interface, the GSAC-WS, is being developed to provide uniform and expanded mechanisms through which users can access our data repositories. In total, our respective archives hold tens of millions of files and contain a rich collection of site/station metadata. Though we serve similar user communities, we currently provide a range of different access methods, query services and metadata formats. This leads to a lack of consistency in the userís experience and a duplication of engineering efforts. The GSAC-WS API and its reference implementation in an underlying Java-based GSAC Service Layer (GSL) supports metadata and data queries into site/station oriented data archives. The general nature of this API makes it applicable to a broad range of data systems. The overall goals of this project include providing consistent and rich query interfaces for end users and client programs, the development of enabling technology to facilitate third party repositories in developing these web service capabilities and to enable the ability to perform data queries across a collection of federated GSAC-WS enabled repositories. A fundamental challenge faced in this project is to provide a common suite of query services across a heterogeneous collection of data yet enabling each repository to expose their specific metadata holdings. To address this challenge we are developing a "capabilities" based service where a repository can describe its specific query and metadata capabilities. Furthermore, the architecture of the GSL is based on a model-view paradigm that decouples the underlying data model semantics from particular representations of the data model. This will allow for the GSAC-WS enabled repositories to evolve their service offerings to incorporate new metadata definition formats (e.g., ISO-19115, FGDC, JSON, etc.) and new techniques for accessing their holdings. Building on the core GSAC-WS implementations the project is also developing a federated/distributed query service. This service will seamlessly integrate with the GSAC Service Layer and will support data and metadata queries across a collection of federated GSAC repositories.

Entrez Neuron RDFa: a pragmatic Semantic Web application for data integration in neuroscience research

PubMed Central

Samwald, Matthias; Lim, Ernest; Masiar, Peter; Marenco, Luis; Chen, Huajun; Morse, Thomas; Mutalik, Pradeep; Shepherd, Gordon; Miller, Perry; Cheung, Kei-Hoi

2013-01-01

The amount of biomedical data available in Semantic Web formats has been rapidly growing in recent years. While these formats are machine-friendly, user-friendly web interfaces allowing easy querying of these data are typically lacking. We present “Entrez Neuron”, a pilot neuron-centric interface that allows for keyword-based queries against a coherent repository of OWL ontologies. These ontologies describe neuronal structures, physiology, mathematical models and microscopy images. The returned query results are organized hierarchically according to brain architecture. Where possible, the application makes use of entities from the Open Biomedical Ontologies (OBO) and the ‘HCLS knowledgebase’ developed by the W3C Interest Group for Health Care and Life Science. It makes use of the emerging RDFa standard to embed ontology fragments and semantic annotations within its HTML-based user interface. The application and underlying ontologies demonstrates how Semantic Web technologies can be used for information integration within a curated information repository and between curated information repositories. It also demonstrates how information integration can be accomplished on the client side, through simple copying and pasting of portions of documents that contain RDFa markup. PMID:19745321

StarView: The object oriented design of the ST DADS user interface

NASA Technical Reports Server (NTRS)

Williams, J. D.; Pollizzi, J. A.

1992-01-01

StarView is the user interface being developed for the Hubble Space Telescope Data Archive and Distribution Service (ST DADS). ST DADS is the data archive for HST observations and a relational database catalog describing the archived data. Users will use StarView to query the catalog and select appropriate datasets for study. StarView sends requests for archived datasets to ST DADS which processes the requests and returns the database to the user. StarView is designed to be a powerful and extensible user interface. Unique features include an internal relational database to navigate query results, a form definition language that will work with both CRT and X interfaces, a data definition language that will allow StarView to work with any relational database, and the ability to generate adhoc queries without requiring the user to understand the structure of the ST DADS catalog. Ultimately, StarView will allow the user to refine queries in the local database for improved performance and merge in data from external sources for correlation with other query results. The user will be able to create a query from single or multiple forms, merging the selected attributes into a single query. Arbitrary selection of attributes for querying is supported. The user will be able to select how query results are viewed. A standard form or table-row format may be used. Navigation capabilities are provided to aid the user in viewing query results. Object oriented analysis and design techniques were used in the design of StarView to support the mechanisms and concepts required to implement these features. One such mechanism is the Model-View-Controller (MVC) paradigm. The MVC allows the user to have multiple views of the underlying database, while providing a consistent mechanism for interaction regardless of the view. This approach supports both CRT and X interfaces while providing a common mode of user interaction. Another powerful abstraction is the concept of a Query Model. This concept allows a single query to be built form a single or multiple forms before it is submitted to ST DADS. Supporting this concept is the adhoc query generator which allows the user to select and qualify an indeterminate number attributes from the database. The user does not need any knowledge of how the joins across various tables are to be resolved. The adhoc generator calculates the joins automatically and generates the correct SQL query.

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.

Asking better questions: How presentation formats influence information search.

PubMed

Wu, Charley M; Meder, Björn; Filimon, Flavia; Nelson, Jonathan D

2017-08-01

While the influence of presentation formats have been widely studied in Bayesian reasoning tasks, we present the first systematic investigation of how presentation formats influence information search decisions. Four experiments were conducted across different probabilistic environments, where subjects (N = 2,858) chose between 2 possible search queries, each with binary probabilistic outcomes, with the goal of maximizing classification accuracy. We studied 14 different numerical and visual formats for presenting information about the search environment, constructed across 6 design features that have been prominently related to improvements in Bayesian reasoning accuracy (natural frequencies, posteriors, complement, spatial extent, countability, and part-to-whole information). The posterior variants of the icon array and bar graph formats led to the highest proportion of correct responses, and were substantially better than the standard probability format. Results suggest that presenting information in terms of posterior probabilities and visualizing natural frequencies using spatial extent (a perceptual feature) were especially helpful in guiding search decisions, although environments with a mixture of probabilistic and certain outcomes were challenging across all formats. Subjects who made more accurate probability judgments did not perform better on the search task, suggesting that simple decision heuristics may be used to make search decisions without explicitly applying Bayesian inference to compute probabilities. We propose a new take-the-difference (TTD) heuristic that identifies the accuracy-maximizing query without explicit computation of posterior probabilities. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

cPath: open source software for collecting, storing, and querying biological pathways.

PubMed

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-11-13

Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

40 CFR 610.17 - Application format.

Code of Federal Regulations, 2010 CFR

2010-07-01

... application format, in order to allow the Administrator to compile relevant data on specific devices and to... be allowed for analysis of the application and preparation of a response. As indicated in other...

40 CFR 610.17 - Application format.

Code of Federal Regulations, 2011 CFR

2011-07-01

... application format, in order to allow the Administrator to compile relevant data on specific devices and to... be allowed for analysis of the application and preparation of a response. As indicated in other...

Compilation of historical water-quality data for selected springs in Texas, by ecoregion

USGS Publications Warehouse

Heitmuller, Franklin T.; Williams, Iona P.

2006-01-01

Springs are important hydrologic features in Texas. A database of about 2,000 historically documented springs and available spring-flow measurements previously has been compiled and published, but water-quality data remain scattered in published sources. This report by the U.S. Geological Survey, in cooperation with the Texas Parks and Wildlife Department, documents the compilation of data for 232 springs in Texas on the basis of a set of criteria and the development of a water-quality database for the selected springs. The selection of springs for compilation of historical water-quality data in Texas was made using existing digital and hard-copy data, responses to mailed surveys, selection criteria established by various stakeholders, geographic information systems, and digital database queries. Most springs were selected by computing the highest mean spring flows for each Texas level III ecoregion. A brief assessment of the water-quality data for springs in Texas shows that few data are available in the Arizona/New Mexico Mountains, High Plains, East Central Texas Plains, Western Gulf Coastal Plain, and South Central Plains ecoregions. Water-quality data are more abundant for the Chihuahuan Deserts, Edwards Plateau, and Texas Blackland Prairies ecoregions. Selected constituent concentrations in Texas springs, including silica, calcium, magnesium, sodium, potassium, strontium, sulfate, chloride, fluoride, nitrate (nitrogen), dissolved solids, and hardness (as calcium carbonate) are comparatively high in the Chihuahuan Deserts, Southwestern Tablelands, Central Great Plains, and Cross Timbers ecoregions, mostly as a result of subsurface geology. Comparatively low concentrations of selected constituents in Texas springs are associated with the Arizona/New Mexico Mountains, Southern Texas Plains, East Central Texas Plains, and South Central Plains ecoregions.

BP Spill Sampling and Monitoring Data April-September 2010 - Data Download Tool

EPA Pesticide Factsheets

This dataset analyzes waste from the the British Petroleum Deepwater Horizon Rig Explosion Emergency Response, providing opportunity to query data sets by metadata criteria and find resulting raw datasets in CSV format.The data query tool allows users to download air, water and sediment sampling and monitoring data that has been collected in response to the BP oil spill. All sampling and monitoring data that has been collected to date is available for download as raw structured data.The query tools enables CSV file creation to be refined based on the following search criteria: date range (between April 28, 2010 and 9/29/2010); location by zip, city, or county; media (solid waste, weathered oil, air, surface water, liquid waste, tar, sediment, water); substance categories (based on media selection) and substances (based on substance category selection).

OpenSearch technology for geospatial resources discovery

NASA Astrophysics Data System (ADS)

Papeschi, Fabrizio; Enrico, Boldrini; Mazzetti, Paolo

2010-05-01

In 2005, the term Web 2.0 has been coined by Tim O'Reilly to describe a quickly growing set of Web-based applications that share a common philosophy of "mutually maximizing collective intelligence and added value for each participant by formalized and dynamic information sharing". Around this same period, OpenSearch a new Web 2.0 technology, was developed. More properly, OpenSearch is a collection of technologies that allow publishing of search results in a format suitable for syndication and aggregation. It is a way for websites and search engines to publish search results in a standard and accessible format. Due to its strong impact on the way the Web is perceived by users and also due its relevance for businesses, Web 2.0 has attracted the attention of both mass media and the scientific community. This explosive growth in popularity of Web 2.0 technologies like OpenSearch, and practical applications of Service Oriented Architecture (SOA) resulted in an increased interest in similarities, convergence, and a potential synergy of these two concepts. SOA is considered as the philosophy of encapsulating application logic in services with a uniformly defined interface and making these publicly available via discovery mechanisms. Service consumers may then retrieve these services, compose and use them according to their current needs. A great degree of similarity between SOA and Web 2.0 may be leading to a convergence between the two paradigms. They also expose divergent elements, such as the Web 2.0 support to the human interaction in opposition to the typical SOA machine-to-machine interaction. According to these considerations, the Geospatial Information (GI) domain, is also moving first steps towards a new approach of data publishing and discovering, in particular taking advantage of the OpenSearch technology. A specific GI niche is represented by the OGC Catalog Service for Web (CSW) that is part of the OGC Web Services (OWS) specifications suite, which provides a set of services for discovery, access, and processing of geospatial resources in a SOA framework. GI-cat is a distributed CSW framework implementation developed by the ESSI Lab of the Italian National Research Council (CNR-IMAA) and the University of Florence. It provides brokering and mediation functionalities towards heterogeneous resources and inventories, exposing several standard interfaces for query distribution. This work focuses on a new GI-cat interface which allows the catalog to be queried according to the OpenSearch syntax specification, thus filling the gap between the SOA architectural design of the CSW and the Web 2.0. At the moment, there is no OGC standard specification about this topic, but an official change request has been proposed in order to enable the OGC catalogues to support OpenSearch queries. In this change request, an OpenSearch extension is proposed providing a standard mechanism to query a resource based on temporal and geographic extents. Two new catalog operations are also proposed, in order to publish a suitable OpenSearch interface. This extended interface is implemented by the modular GI-cat architecture adding a new profiling module called "OpenSearch profiler". Since GI-cat also acts as a clearinghouse catalog, another component called "OpenSearch accessor" is added in order to access OpenSearch compliant services. An important role in the GI-cat extension, is played by the adopted mapping strategy. Two different kind of mappings are required: query, and response elements mapping. Query mapping is provided in order to fit the simple OpenSearch query syntax to the complex CSW query expressed by the OGC Filter syntax. GI-cat internal data model is based on the ISO-19115 profile, that is more complex than the simple XML syndication formats, such as RSS 2.0 and Atom 1.0, suggested by OpenSearch. Once response elements are available, in order to be presented, they need to be translated from the GI-cat internal data model, to the above mentioned syndication formats; the mapping processing, is bidirectional. When GI-cat is used to access OpenSearch compliant services, the CSW query must be mapped to the OpenSearch query, and the response elements, must be translated according to the GI-cat internal data model. As results of such extensions, GI-cat provides a user friendly facade to the complex CSW interface, thus enabling it to be queried, for example, using a browser toolbar.

SATRAT: Staphylococcus aureus transcript regulatory network analysis tool.

PubMed

Gopal, Tamilselvi; Nagarajan, Vijayaraj; Elasri, Mohamed O

2015-01-01

Staphylococcus aureus is a commensal organism that primarily colonizes the nose of healthy individuals. S. aureus causes a spectrum of infections that range from skin and soft-tissue infections to fatal invasive diseases. S. aureus uses a large number of virulence factors that are regulated in a coordinated fashion. The complex regulatory mechanisms have been investigated in numerous high-throughput experiments. Access to this data is critical to studying this pathogen. Previously, we developed a compilation of microarray experimental data to enable researchers to search, browse, compare, and contrast transcript profiles. We have substantially updated this database and have built a novel exploratory tool-SATRAT-the S. aureus transcript regulatory network analysis tool, based on the updated database. This tool is capable of performing deep searches using a query and generating an interactive regulatory network based on associations among the regulators of any query gene. We believe this integrated regulatory network analysis tool would help researchers explore the missing links and identify novel pathways that regulate virulence in S. aureus. Also, the data model and the network generation code used to build this resource is open sourced, enabling researchers to build similar resources for other bacterial systems.

PACS and electronic health records

NASA Astrophysics Data System (ADS)

Cohen, Simona; Gilboa, Flora; Shani, Uri

2002-05-01

Electronic Health Record (EHR) is a major component of the health informatics domain. An important part of the EHR is the medical images obtained over a patient's lifetime and stored in diverse PACS. The vision presented in this paper is that future medical information systems will convert data from various medical sources -- including diverse modalities, PACS, HIS, CIS, RIS, and proprietary systems -- to HL7 standard XML documents. Then, the various documents are indexed and compiled to EHRs, upon which complex queries can be posed. We describe the conversion of data retrieved from PACS systems through DICOM to HL7 standard XML documents. This enables the EHR system to answer queries such as 'Get all chest images of patients at the age of 20-30, that have blood type 'A' and are allergic to pine trees', which a single PACS cannot answer. The integration of data from multiple sources makes our approach capable of delivering such answers. It enables the correlation of medical, demographic, clinical, and even genetic information. In addition, by fully indexing all the tagged data in DICOM objects, it becomes possible to offer access to huge amounts of valuable data, which can be better exploited in the specific radiology domain.

Flora-On: Occurrence data of the vascular flora of mainland Portugal

PubMed Central

Pereira, Ana Júlia; Francisco, Ana; Porto, Miguel

2016-01-01

Abstract The Flora-On dataset currently includes 253,310 occurrence records for the class Embryopsidae (vascular plants), comprising data collated via the platform http://flora-on.pt/ relating to observation records of vascular plants across mainland Portugal. Observations are uploaded directly to the database primarily by experienced botanists and naturalists, typically on a weekly basis, and consist of geo-referenced data points for species (or infraspecific taxa) along with their date of observation and phenological state. The Flora-On project aims to compile and make publicly accessible chorological, ecological, morphological and photographic information for the entire vascular flora of Portugal. The project’s website offers powerful query and visualization capabilities, of which we highlight the probabilistic bioclimatic and phenological queries which operate based on the empirical density distributions of species in those variables. Flora-On was created and continues to be maintained by volunteers who are Associate members of Sociedade Portuguesa de Botânica (Botanical Society of Portugal). Given its focus on research-grade and current data, the Flora-On project represents a significant contribution to the knowledge of the present distribution and status of the Portuguese flora. PMID:27698587

Archetype-based data warehouse environment to enable the reuse of electronic health record data.

PubMed

Marco-Ruiz, Luis; Moner, David; Maldonado, José A; Kolstrup, Nils; Bellika, Johan G

2015-09-01

The reuse of data captured during health care delivery is essential to satisfy the demands of clinical research and clinical decision support systems. A main barrier for the reuse is the existence of legacy formats of data and the high granularity of it when stored in an electronic health record (EHR) system. Thus, we need mechanisms to standardize, aggregate, and query data concealed in the EHRs, to allow their reuse whenever they are needed. To create a data warehouse infrastructure using archetype-based technologies, standards and query languages to enable the interoperability needed for data reuse. The work presented makes use of best of breed archetype-based data transformation and storage technologies to create a workflow for the modeling, extraction, transformation and load of EHR proprietary data into standardized data repositories. We converted legacy data and performed patient-centered aggregations via archetype-based transformations. Later, specific purpose aggregations were performed at a query level for particular use cases. Laboratory test results of a population of 230,000 patients belonging to Troms and Finnmark counties in Norway requested between January 2013 and November 2014 have been standardized. Test records normalization has been performed by defining transformation and aggregation functions between the laboratory records and an archetype. These mappings were used to automatically generate open EHR compliant data. These data were loaded into an archetype-based data warehouse. Once loaded, we defined indicators linked to the data in the warehouse to monitor test activity of Salmonella and Pertussis using the archetype query language. Archetype-based standards and technologies can be used to create a data warehouse environment that enables data from EHR systems to be reused in clinical research and decision support systems. With this approach, existing EHR data becomes available in a standardized and interoperable format, thus opening a world of possibilities toward semantic or concept-based reuse, query and communication of clinical data. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

CrossQuery: a web tool for easy associative querying of transcriptome data.

PubMed

Wagner, Toni U; Fischer, Andreas; Thoma, Eva C; Schartl, Manfred

2011-01-01

Enormous amounts of data are being generated by modern methods such as transcriptome or exome sequencing and microarray profiling. Primary analyses such as quality control, normalization, statistics and mapping are highly complex and need to be performed by specialists. Thereafter, results are handed back to biomedical researchers, who are then confronted with complicated data lists. For rather simple tasks like data filtering, sorting and cross-association there is a need for new tools which can be used by non-specialists. Here, we describe CrossQuery, a web tool that enables straight forward, simple syntax queries to be executed on transcriptome sequencing and microarray datasets. We provide deep-sequencing data sets of stem cell lines derived from the model fish Medaka and microarray data of human endothelial cells. In the example datasets provided, mRNA expression levels, gene, transcript and sample identification numbers, GO-terms and gene descriptions can be freely correlated, filtered and sorted. Queries can be saved for later reuse and results can be exported to standard formats that allow copy-and-paste to all widespread data visualization tools such as Microsoft Excel. CrossQuery enables researchers to quickly and freely work with transcriptome and microarray data sets requiring only minimal computer skills. Furthermore, CrossQuery allows growing association of multiple datasets as long as at least one common point of correlated information, such as transcript identification numbers or GO-terms, is shared between samples. For advanced users, the object-oriented plug-in and event-driven code design of both server-side and client-side scripts allow easy addition of new features, data sources and data types.

1 CFR 10.3 - Format.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 1 General Provisions 1 2010-01-01 2010-01-01 false Format. 10.3 Section 10.3 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER SPECIAL EDITIONS OF THE FEDERAL REGISTER PRESIDENTIAL PAPERS Regular Publication § 10.3 Format. The Daily Compilation of Presidential Documents is published online on...

1 CFR 10.3 - Format.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 1 General Provisions 1 2011-01-01 2011-01-01 false Format. 10.3 Section 10.3 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER SPECIAL EDITIONS OF THE FEDERAL REGISTER PRESIDENTIAL PAPERS Regular Publication § 10.3 Format. The Daily Compilation of Presidential Documents is published online on...

1 CFR 10.3 - Format.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 1 General Provisions 1 2014-01-01 2012-01-01 true Format. 10.3 Section 10.3 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER SPECIAL EDITIONS OF THE FEDERAL REGISTER PRESIDENTIAL PAPERS Regular Publication § 10.3 Format. The Daily Compilation of Presidential Documents is published online on...

1 CFR 10.3 - Format.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 1 General Provisions 1 2013-01-01 2012-01-01 true Format. 10.3 Section 10.3 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER SPECIAL EDITIONS OF THE FEDERAL REGISTER PRESIDENTIAL PAPERS Regular Publication § 10.3 Format. The Daily Compilation of Presidential Documents is published online on...

1 CFR 10.3 - Format.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 1 General Provisions 1 2012-01-01 2012-01-01 false Format. 10.3 Section 10.3 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER SPECIAL EDITIONS OF THE FEDERAL REGISTER PRESIDENTIAL PAPERS Regular Publication § 10.3 Format. The Daily Compilation of Presidential Documents is published online on...

Generation of large scale urban environments to support advanced sensor and seeker simulation

NASA Astrophysics Data System (ADS)

Giuliani, Joseph; Hershey, Daniel; McKeown, David, Jr.; Willis, Carla; Van, Tan

2009-05-01

One of the key aspects for the design of a next generation weapon system is the need to operate in cluttered and complex urban environments. Simulation systems rely on accurate representation of these environments and require automated software tools to construct the underlying 3D geometry and associated spectral and material properties that are then formatted for various objective seeker simulation systems. Under an Air Force Small Business Innovative Research (SBIR) contract, we have developed an automated process to generate 3D urban environments with user defined properties. These environments can be composed from a wide variety of source materials, including vector source data, pre-existing 3D models, and digital elevation models, and rapidly organized into a geo-specific visual simulation database. This intermediate representation can be easily inspected in the visible spectrum for content and organization and interactively queried for accuracy. Once the database contains the required contents, it can then be exported into specific synthetic scene generation runtime formats, preserving the relationship between geometry and material properties. To date an exporter for the Irma simulation system developed and maintained by AFRL/Eglin has been created and a second exporter to Real Time Composite Hardbody and Missile Plume (CHAMP) simulation system for real-time use is currently being developed. This process supports significantly more complex target environments than previous approaches to database generation. In this paper we describe the capabilities for content creation for advanced seeker processing algorithms simulation and sensor stimulation, including the overall database compilation process and sample databases produced and exported for the Irma runtime system. We also discuss the addition of object dynamics and viewer dynamics within the visual simulation into the Irma runtime environment.

A compilation and analysis of helicopter handling qualities data. Volume 1: Data compilation

NASA Technical Reports Server (NTRS)

Heffley, R. K.; Jewell, W. F.; Lehman, J. M.; Vanwinkle, R. A.

1979-01-01

A collection of basic descriptive data, stability derivatives and transfer functions for six degrees of freedom, quasi-static model is introduced. The data are arranged in a common, compact format for each of the five helicopters represented. The vehicles studied include the BO-105, AH-1h, and the CH53D.

Indexing the medical open access literature for textual and content-based visual retrieval.

PubMed

Eggel, Ivan; Müller, Henning

2010-01-01

Over the past few years an increasing amount of scientific journals have been created in an open access format. Particularly in the medical field the number of openly accessible journals is enormous making a wide body of knowledge available for analysis and retrieval. Part of the trend towards open access publications can be linked to funding bodies such as the NIH¹ (National Institutes of Health) and the Swiss National Science Foundation (SNF²) requiring funded projects to make all articles of funded research available publicly. This article describes an approach to make part of the knowledge of open access journals available for retrieval including the textual information but also the images contained in the articles. For this goal all articles of 24 journals related to medical informatics and medical imaging were crawled from the web pages of BioMed Central. Text and images of the PDF (Portable Document Format) files were indexed separately and a web-based retrieval interface allows for searching via keyword queries or by visual similarity queries. Starting point for a visual similarity query can be an image on the local hard disk that is uploaded or any image found via the textual search. Search for similar documents is also possible.

The Arden Syntax standard for clinical decision support: experiences and directions.

PubMed

Samwald, Matthias; Fehre, Karsten; de Bruin, Jeroen; Adlassnig, Klaus-Peter

2012-08-01

Arden Syntax is a widely recognized standard for representing clinical and scientific knowledge in an executable format. It has a history that reaches back until 1989 and is currently maintained by the Health Level 7 (HL7) organization. We created a production-ready development environment, compiler, rule engine and application server for Arden Syntax. Over the course of several years, we have applied this Arden - Syntax - based CDS system in a wide variety of clinical problem domains, such as hepatitis serology interpretation, monitoring of nosocomial infections or the prediction of metastatic events in melanoma patients. We found the Arden Syntax standard to be very suitable for the practical implementation of CDS systems. Among the advantages of Arden Syntax are its status as an actively developed HL7 standard, the readability of the syntax, and various syntactic features such as flexible list handling. A major challenge we encountered was the technical integration of our CDS systems in existing, heterogeneous health information systems. To address this issue, we are currently working on incorporating the HL7 standard GELLO, which provides a standardized interface and query language for accessing data in health information systems. We hope that these planned extensions of the Arden Syntax might eventually help in realizing the vision of a global, interoperable and shared library of clinical decision support knowledge. Copyright © 2012 Elsevier Inc. All rights reserved.

Identification of contaminant trends and data gaps for terrestrial vertebrates residing in northeastern estuaries of the United States

USGS Publications Warehouse

Rattner, B.A.; Pearson, J.L.; Golden, N.H.; Erwin, R.M.; Ottinger, M.A.

1998-01-01

The Biomonitoring of Environmental Status and Trends (BEST) program of the Department of the Interior is focused to identify and understand effects of contaminant stressors on biological resources under their stewardship. One BEST program activity involves evaluation of retrospective data to assess and predict the condition of biota in Atlantic coast estuaries. A 'Contaminant Exposure and Effects--Terrestrial Vertebrates' database (CEE-TV) has been compiled through computerized literature searches of Fish and Wildlife Reviews, BIOSIS, AGRICOLA, and TOXLINE, review of existing databases (e.g., US EPA Ecological Incident Information System, USGS Diagnostic and Epizootic Databases), and solicitation of unpublished reports from conservation agencies, private groups, and universities. Summary information has been entered into the CEE-TV database, including species, collection date (1965-present), site coordinates, sample matrix, contaminant concentrations, biomarker and bioindicator responses, and reference source, utilizing a 96-field dBase format. Currently, the CEE-TV database contains 3500 georeferenced records representing >200 vertebrate species and > 100,000 individuals residing in estuaries from Maine through Florida. This relational database can be directly queried, imported into the ARC/INFO geographic information system (GIS) to examine spatial tendencies, and used to identify 'hot-spots', generate hypotheses, and focus ecotoxicological assessments. An overview of temporal, phylogenetic, and geographic contaminant exposure and effects information, trends, and data gaps will be presented for terrestrial vertebrates residing in estuaries in the northeast United States.

Design and development of linked data from the National Map

USGS Publications Warehouse

Usery, E. Lynn; Varanka, Dalia E.

2012-01-01

The development of linked data on the World-Wide Web provides the opportunity for the U.S. Geological Survey (USGS) to supply its extensive volumes of geospatial data, information, and knowledge in a machine interpretable form and reach users and applications that heretofore have been unavailable. To pilot a process to take advantage of this opportunity, the USGS is developing an ontology for The National Map and converting selected data from nine research test areas to a Semantic Web format to support machine processing and linked data access. In a case study, the USGS has developed initial methods for legacy vector and raster formatted geometry, attributes, and spatial relationships to be accessed in a linked data environment maintaining the capability to generate graphic or image output from semantic queries. The description of an initial USGS approach to developing ontology, linked data, and initial query capability from The National Map databases is presented.

PlateRunner: A Search Engine to Identify EMR Boilerplates.

PubMed

Divita, Guy; Workman, T Elizabeth; Carter, Marjorie E; Redd, Andrew; Samore, Matthew H; Gundlapalli, Adi V

2016-01-01

Medical text contains boilerplated content, an artifact of pull-down forms from EMRs. Boilerplated content is the source of challenges for concept extraction on clinical text. This paper introduces PlateRunner, a search engine on boilerplates from the US Department of Veterans Affairs (VA) EMR. Boilerplates containing concepts should be identified and reviewed to recognize challenging formats, identify high yield document titles, and fine tune section zoning. This search engine has the capability to filter negated and asserted concepts, save and search query results. This tool can save queries, search results, and documents found for later analysis.

Compendium of Arab exploratory wells and petroleum fields, 1985 edition

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

Not Available

1985-01-01

This book provides a compilation of primary and secondary information giving well name and province, operating company, completion date, exploration technique, bottom home formation, total depth, producing formations, lithology, geologic age, drilling results, and geologic, petrophysical, and production data. It covers all the Arab countries in a new format.

GBA manager: an online tool for querying low-complexity regions in proteins.

PubMed

Bandyopadhyay, Nirmalya; Kahveci, Tamer

2010-01-01

Abstract We developed GBA Manager, an online software that facilitates the Graph-Based Algorithm (GBA) we proposed in our earlier work. GBA identifies the low-complexity regions (LCR) of protein sequences. GBA exploits a similarity matrix, such as BLOSUM62, to compute the complexity of the subsequences of the input protein sequence. It uses a graph-based algorithm to accurately compute the regions that have low complexities. GBA Manager is a user friendly web-service that enables online querying of protein sequences using GBA. In addition to querying capabilities of the existing GBA algorithm, GBA Manager computes the p-values of the LCR identified. The p-value gives an estimate of the possibility that the region appears by chance. GBA Manager presents the output in three different understandable formats. GBA Manager is freely accessible at http://bioinformatics.cise.ufl.edu/GBA/GBA.htm .

Toward privacy-preserving JPEG image retrieval

NASA Astrophysics Data System (ADS)

Cheng, Hang; Wang, Jingyue; Wang, Meiqing; Zhong, Shangping

2017-07-01

This paper proposes a privacy-preserving retrieval scheme for JPEG images based on local variance. Three parties are involved in the scheme: the content owner, the server, and the authorized user. The content owner encrypts JPEG images for privacy protection by jointly using permutation cipher and stream cipher, and then, the encrypted versions are uploaded to the server. With an encrypted query image provided by an authorized user, the server may extract blockwise local variances in different directions without knowing the plaintext content. After that, it can calculate the similarity between the encrypted query image and each encrypted database image by a local variance-based feature comparison mechanism. The authorized user with the encryption key can decrypt the returned encrypted images with plaintext content similar to the query image. The experimental results show that the proposed scheme not only provides effective privacy-preserving retrieval service but also ensures both format compliance and file size preservation for encrypted JPEG images.

Constraints on the Formation and Modification of Lobate Debris Aprons Through Categorized Crater Counts

NASA Astrophysics Data System (ADS)

Berman, D. C.; Crown, D. A.; Joseph, E. C. S.

2012-03-01

Compilation of crater counts using CTX images and analysis of SFD, coupled with categorization of crater morphologies, provides important insights into interpretation of the formation and modification of lobate debris aprons.

cPath: open source software for collecting, storing, and querying biological pathways

PubMed Central

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-01-01

Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. PMID:17101041

Semantator: semantic annotator for converting biomedical text to linked data.

PubMed

Tao, Cui; Song, Dezhao; Sharma, Deepak; Chute, Christopher G

2013-10-01

More than 80% of biomedical data is embedded in plain text. The unstructured nature of these text-based documents makes it challenging to easily browse and query the data of interest in them. One approach to facilitate browsing and querying biomedical text is to convert the plain text to a linked web of data, i.e., converting data originally in free text to structured formats with defined meta-level semantics. In this paper, we introduce Semantator (Semantic Annotator), a semantic-web-based environment for annotating data of interest in biomedical documents, browsing and querying the annotated data, and interactively refining annotation results if needed. Through Semantator, information of interest can be either annotated manually or semi-automatically using plug-in information extraction tools. The annotated results will be stored in RDF and can be queried using the SPARQL query language. In addition, semantic reasoners can be directly applied to the annotated data for consistency checking and knowledge inference. Semantator has been released online and was used by the biomedical ontology community who provided positive feedbacks. Our evaluation results indicated that (1) Semantator can perform the annotation functionalities as designed; (2) Semantator can be adopted in real applications in clinical and transactional research; and (3) the annotated results using Semantator can be easily used in Semantic-web-based reasoning tools for further inference. Copyright © 2013 Elsevier Inc. All rights reserved.

EarthServer: a Summary of Achievements in Technology, Services, and Standards

NASA Astrophysics Data System (ADS)

Baumann, Peter

2015-04-01

Big Data in the Earth sciences, the Tera- to Exabyte archives, mostly are made up from coverage data, according to ISO and OGC defined as the digital representation of some space-time varying phenomenon. Common examples include 1-D sensor timeseries, 2-D remote sensing imagery, 3D x/y/t image timese ries and x/y/z geology data, and 4-D x/y/z/t atmosphere and ocean data. Analytics on such data requires on-demand processing of sometimes significant complexity, such as getting the Fourier transform of satellite images. As network bandwidth limits prohibit transfer of such Big Data it is indispensable to devise protocols allowing clients to task flexible and fast processing on the server. The transatlantic EarthServer initiative, running from 2011 through 2014, has united 11 partners to establish Big Earth Data Analytics. A key ingredient has been flexibility for users to ask whatever they want, not impeded and complicated by system internals. The EarthServer answer to this is to use high-level, standards-based query languages which unify data and metadata search in a simple, yet powerful way. A second key ingredient is scalability. Without any doubt, scalability ultimately can only be achieved through parallelization. In the past, parallelizing cod e has been done at compile time and usually with manual intervention. The EarthServer approach is to perform a samentic-based dynamic distribution of queries fragments based on networks optimization and further criteria. The EarthServer platform is comprised by rasdaman, the pioneer and leading Array DBMS built for any-size multi-dimensional raster data being extended with support for irregular grids and general meshes; in-situ retrieval (evaluation of database queries on existing archive structures, avoiding data import and, hence, duplication); the aforementioned distributed query processing. Additionally, Web clients for multi-dimensional data visualization are being established. Client/server interfaces are strictly based on OGC and W3C standards, in particular the Web Coverage Processing Service (WCPS) which defines a high-level coverage query language. Reviewers have attested EarthServer that "With no doubt the project has been shaping the Big Earth Data landscape through the standardization activities within OGC, ISO and beyond". We present the project approach, its outcomes and impact on standardization and Big Data technology, and vistas for the future.

A Columnar Storage Strategy with Spatiotemporal Index for Big Climate Data

NASA Astrophysics Data System (ADS)

Hu, F.; Bowen, M. K.; Li, Z.; Schnase, J. L.; Duffy, D.; Lee, T. J.; Yang, C. P.

2015-12-01

Large collections of observational, reanalysis, and climate model output data may grow to as large as a 100 PB in the coming years, so climate dataset is in the Big Data domain, and various distributed computing frameworks have been utilized to address the challenges by big climate data analysis. However, due to the binary data format (NetCDF, HDF) with high spatial and temporal dimensions, the computing frameworks in Apache Hadoop ecosystem are not originally suited for big climate data. In order to make the computing frameworks in Hadoop ecosystem directly support big climate data, we propose a columnar storage format with spatiotemporal index to store climate data, which will support any project in the Apache Hadoop ecosystem (e.g. MapReduce, Spark, Hive, Impala). With this approach, the climate data will be transferred into binary Parquet data format, a columnar storage format, and spatial and temporal index will be built and attached into the end of Parquet files to enable real-time data query. Then such climate data in Parquet data format could be available to any computing frameworks in Hadoop ecosystem. The proposed approach is evaluated using the NASA Modern-Era Retrospective Analysis for Research and Applications (MERRA) climate reanalysis dataset. Experimental results show that this approach could efficiently overcome the gap between the big climate data and the distributed computing frameworks, and the spatiotemporal index could significantly accelerate data querying and processing.

Environmental Mission Impact Assessment

DTIC Science & Technology

2008-01-01

System Agency’s (DISA) Federated Search service. The mission impacts can be generated for a general rectangular area, or generated for routes, route...that respond to queries (format- ted according to DISA’s Federated Search specifi- FIGURE 2 EVIS service-oriented architecture design, illustrating the

A comparison of database systems for XML-type data.

PubMed

Risse, Judith E; Leunissen, Jack A M

2010-01-01

In the field of bioinformatics interchangeable data formats based on XML are widely used. XML-type data is also at the core of most web services. With the increasing amount of data stored in XML comes the need for storing and accessing the data. In this paper we analyse the suitability of different database systems for storing and querying large datasets in general and Medline in particular. All reviewed database systems perform well when tested with small to medium sized datasets, however when the full Medline dataset is queried a large variation in query times is observed. There is not one system that is vastly superior to the others in this comparison and, depending on the database size and the query requirements, different systems are most suitable. The best all-round solution is the Oracle 11~g database system using the new binary storage option. Alias-i's Lingpipe is a more lightweight, customizable and sufficiently fast solution. It does however require more initial configuration steps. For data with a changing XML structure Sedna and BaseX as native XML database systems or MySQL with an XML-type column are suitable.

GenoMetric Query Language: a novel approach to large-scale genomic data management.

PubMed

Masseroli, Marco; Pinoli, Pietro; Venco, Francesco; Kaitoua, Abdulrahman; Jalili, Vahid; Palluzzi, Fernando; Muller, Heiko; Ceri, Stefano

2015-06-15

Improvement of sequencing technologies and data processing pipelines is rapidly providing sequencing data, with associated high-level features, of many individual genomes in multiple biological and clinical conditions. They allow for data-driven genomic, transcriptomic and epigenomic characterizations, but require state-of-the-art 'big data' computing strategies, with abstraction levels beyond available tool capabilities. We propose a high-level, declarative GenoMetric Query Language (GMQL) and a toolkit for its use. GMQL operates downstream of raw data preprocessing pipelines and supports queries over thousands of heterogeneous datasets and samples; as such it is key to genomic 'big data' analysis. GMQL leverages a simple data model that provides both abstractions of genomic region data and associated experimental, biological and clinical metadata and interoperability between many data formats. Based on Hadoop framework and Apache Pig platform, GMQL ensures high scalability, expressivity, flexibility and simplicity of use, as demonstrated by several biological query examples on ENCODE and TCGA datasets. The GMQL toolkit is freely available for non-commercial use at http://www.bioinformatics.deib.polimi.it/GMQL/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Data Warehouse to Support Condition Based Maintenance (CBM)

DTIC Science & Technology

2005-05-01

Application ( VBA ) code sequence to import the original MAST-generated CSV and then create a single output table in DBASE IV format. The DBASE IV format...database architecture (Oracle, Sybase, MS- SQL , etc). This design includes table definitions, comments, specification of table attributes, primary and foreign...built queries and applications. Needs the application developers to construct data views. No SQL programming experience. b. Power Database User - knows

A spatial database for landslides in northern Bavaria: A methodological approach

NASA Astrophysics Data System (ADS)

Jäger, Daniel; Kreuzer, Thomas; Wilde, Martina; Bemm, Stefan; Terhorst, Birgit

2018-04-01

Landslide databases provide essential information for hazard modeling, damages on buildings and infrastructure, mitigation, and research needs. This study presents the development of a landslide database system named WISL (Würzburg Information System on Landslides), currently storing detailed landslide data for northern Bavaria, Germany, in order to enable scientific queries as well as comparisons with other regional landslide inventories. WISL is based on free open source software solutions (PostgreSQL, PostGIS) assuring good correspondence of the various softwares and to enable further extensions with specific adaptions of self-developed software. Apart from that, WISL was designed to be particularly compatible for easy communication with other databases. As a central pre-requisite for standardized, homogeneous data acquisition in the field, a customized data sheet for landslide description was compiled. This sheet also serves as an input mask for all data registration procedures in WISL. A variety of "in-database" solutions for landslide analysis provides the necessary scalability for the database, enabling operations at the local server. In its current state, WISL already enables extensive analysis and queries. This paper presents an example analysis of landslides in Oxfordian Limestones in the northeastern Franconian Alb, northern Bavaria. The results reveal widely differing landslides in terms of geometry and size. Further queries related to landslide activity classifies the majority of the landslides as currently inactive, however, they clearly possess a certain potential for remobilization. Along with some active mass movements, a significant percentage of landslides potentially endangers residential areas or infrastructure. The main aspect of future enhancements of the WISL database is related to data extensions in order to increase research possibilities, as well as to transfer the system to other regions and countries.

A geo-spatial data management system for potentially active volcanoes—GEOWARN project

NASA Astrophysics Data System (ADS)

Gogu, Radu C.; Dietrich, Volker J.; Jenny, Bernhard; Schwandner, Florian M.; Hurni, Lorenz

2006-02-01

Integrated studies of active volcanic systems for the purpose of long-term monitoring and forecast and short-term eruption prediction require large numbers of data-sets from various disciplines. A modern database concept has been developed for managing and analyzing multi-disciplinary volcanological data-sets. The GEOWARN project (choosing the "Kos-Yali-Nisyros-Tilos volcanic field, Greece" and the "Campi Flegrei, Italy" as test sites) is oriented toward potentially active volcanoes situated in regions of high geodynamic unrest. This article describes the volcanological database of the spatial and temporal data acquired within the GEOWARN project. As a first step, a spatial database embedded in a Geographic Information System (GIS) environment was created. Digital data of different spatial resolution, and time-series data collected at different intervals or periods, were unified in a common, four-dimensional representation of space and time. The database scheme comprises various information layers containing geographic data (e.g. seafloor and land digital elevation model, satellite imagery, anthropogenic structures, land-use), geophysical data (e.g. from active and passive seismicity, gravity, tomography, SAR interferometry, thermal imagery, differential GPS), geological data (e.g. lithology, structural geology, oceanography), and geochemical data (e.g. from hydrothermal fluid chemistry and diffuse degassing features). As a second step based on the presented database, spatial data analysis has been performed using custom-programmed interfaces that execute query scripts resulting in a graphical visualization of data. These query tools were designed and compiled following scenarios of known "behavior" patterns of dormant volcanoes and first candidate signs of potential unrest. The spatial database and query approach is intended to facilitate scientific research on volcanic processes and phenomena, and volcanic surveillance.

Horizon scanning for new genomic tests.

PubMed

Gwinn, Marta; Grossniklaus, Daurice A; Yu, Wei; Melillo, Stephanie; Wulf, Anja; Flome, Jennifer; Dotson, W David; Khoury, Muin J

2011-02-01

The development of health-related genomic tests is decentralized and dynamic, involving government, academic, and commercial entities. Consequently, it is not easy to determine which tests are in development, currently available, or discontinued. We developed and assessed the usefulness of a systematic approach to identifying new genomic tests on the Internet. We devised targeted queries of Web pages, newspaper articles, and blogs (Google Alerts) to identify new genomic tests. We finalized search and review procedures during a pilot phase that ended in March 2010. Queries continue to run daily and are compiled weekly; selected data are indexed in an online database, the Genomic Applications in Practice and Prevention Finder. After the pilot phase, our scan detected approximately two to three new genomic tests per week. Nearly two thirds of all tests (122/188, 65%) were related to cancer; only 6% were related to hereditary disorders. Although 88 (47%) of the tests, including 2 marketed directly to consumers, were commercially available, only 12 (6%) claimed United States Food and Drug Administration licensure. Systematic surveillance of the Internet provides information about genomic tests that can be used in combination with other resources to evaluate genomic tests. The Genomic Applications in Practice and Prevention Finder makes this information accessible to a wide group of stakeholders.

In-Memory Graph Databases for Web-Scale Data

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

Castellana, Vito G.; Morari, Alessandro; Weaver, Jesse R.

RDF databases have emerged as one of the most relevant way for organizing, integrating, and managing expo- nentially growing, often heterogeneous, and not rigidly structured data for a variety of scientific and commercial fields. In this paper we discuss the solutions integrated in GEMS (Graph database Engine for Multithreaded Systems), a software framework for implementing RDF databases on commodity, distributed-memory high-performance clusters. Unlike the majority of current RDF databases, GEMS has been designed from the ground up to primarily employ graph-based methods. This is reflected in all the layers of its stack. The GEMS framework is composed of: a SPARQL-to-C++more » compiler, a library of data structures and related methods to access and modify them, and a custom runtime providing lightweight software multithreading, network messages aggregation and a partitioned global address space. We provide an overview of the framework, detailing its component and how they have been closely designed and customized to address issues of graph methods applied to large-scale datasets on clusters. We discuss in details the principles that enable automatic translation of the queries (expressed in SPARQL, the query language of choice for RDF databases) to graph methods, and identify differences with respect to other RDF databases.« less

Digital depth horizon compilations of the Alaskan North Slope and adjacent Arctic regions

USGS Publications Warehouse

Saltus, Richard W.; Bird, Kenneth J.

2003-01-01

Data have been digitized and combined to create four detailed depth horizon grids spanning the Alaskan North Slope and adjacent offshore areas. These map horizon compilations were created to aid in petroleum system modeling and related studies. Topography/bathymetry is extracted from a recent Arctic compilation of global onshore DEM and satellite altimetry and ship soundings offshore. The Lower Cretaceous Unconformity (LCU), the top of the Triassic Shublik Formation, and the pre-Carboniferous acoustic basement horizon grids are created from numerous seismic studies, drill hole information, and interpolation. These horizons were selected because they mark critical times in the geologic evolution of the region as it relates to petroleum. The various horizons clearly show the major tectonic elements of this region including the Brooks Range, Colville Trough, Barrow Arch, Hanna Trough, Chukchi Platform, Nuwuk Basin, Kaktovik Basin, and Canada Basin. The gridded data are available in a variety of data formats for use in regional studies.

Open Data, Jupyter Notebooks and Geospatial Data Standards Combined - Opening up large volumes of marine and climate data to other communities

NASA Astrophysics Data System (ADS)

Clements, O.; Siemen, S.; Wagemann, J.

2017-12-01

The EU-funded Earthserver-2 project aims to offer on-demand access to large volumes of environmental data (Earth Observation, Marine, Climate data and Planetary data) via the interface standard Web Coverage Service defined by the Open Geospatial Consortium. Providing access to data via OGC web services (e.g. WCS and WMS) has the potential to open up services to a wider audience, especially to users outside the respective communities. Especially WCS 2.0 with its processing extension Web Coverage Processing Service (WCPS) is highly beneficial to make large volumes accessible to non-expert communities. Users do not have to deal with custom community data formats, such as GRIB for the meteorological community, but can directly access the data in a format they are more familiar with, such as NetCDF, JSON or CSV. Data requests can further directly be integrated into custom processing routines and users are not required to download Gigabytes of data anymore. WCS supports trim (reduction of data extent) and slice (reduction of data dimension) operations on multi-dimensional data, providing users a very flexible on-demand access to the data. WCPS allows the user to craft queries to run on the data using a text-based query language, similar to SQL. These queries can be very powerful, e.g. condensing a three-dimensional data cube into its two-dimensional mean. However, the more processing-intensive the more complex the query. As part of the EarthServer-2 project, we developed a python library that helps users to generate complex WCPS queries with Python, a programming language they are more familiar with. The interactive presentation aims to give practical examples how users can benefit from two specific WCS services from the Marine and Climate community. Use-cases from the two communities will show different approaches to take advantage of a Web Coverage (Processing) Service. The entire content is available with Jupyter Notebooks, as they prove to be a highly beneficial tool to generate reproducible workflows for environmental data analysis.

Digital Bedrock Compilation: A Geodatabase Covering Forest Service Lands in California

NASA Astrophysics Data System (ADS)

Elder, D.; de La Fuente, J. A.; Reichert, M.

2010-12-01

This digital database contains bedrock geologic mapping for Forest Service lands within California. This compilation began in 2004 and the first version was completed in 2005. Second publication of this geodatabase was completed in 2010 and filled major gaps in the southern Sierra Nevada and Modoc/Medicine Lake/Warner Mountains areas. This digital map database was compiled from previously published and unpublished geologic mapping, with source mapping and review from California Geological Survey, the U.S. Geological Survey and others. Much of the source data was itself compilation mapping. This geodatabase is huge, containing ~107,000 polygons and ~ 280,000 arcs. Mapping was compiled from more than one thousand individual sources and covers over 41,000,000 acres (~166,000 km2). It was compiled from source maps at various scales - from ~ 1:4,000 to 1:250,000 and represents the best available geologic mapping at largest scale possible. An estimated 70-80% of the source information was digitized from geologic mapping at 1:62,500 scale or better. Forest Service ACT2 Enterprise Team compiled the bedrock mapping and developed a geodatabase to store this information. This geodatabase supports feature classes for polygons (e.g, map units), lines (e.g., contacts, boundaries, faults and structural lines) and points (e.g., orientation data, structural symbology). Lookup tables provide detailed information for feature class items. Lookup/type tables contain legal values and hierarchical groupings for geologic ages and lithologies. Type tables link coded values with descriptions for line and point attributes, such as line type, line location and point type. This digital mapping is at the core of many quantitative analyses and derivative map products. Queries of the database are used to produce maps and to quantify rock types of interest. These include the following: (1) ultramafic rocks - where hazards from naturally occurring asbestos are high, (2) granitic rocks - increased erosion hazards, (3) limestone, chert, sedimentary rocks - paleontological resources (Potential Fossil Yield Classification maps), (4) calcareous rocks (cave resources, water chemistry), and (5) lava flows - lava tubes (more caves). Map unit groupings (e.g., belts, terranes, tectonic & geomorphic provinces) can also be derived from the geodatabase. Digital geologic mapping was used in ground water modeling to predict effects of tunneling through the San Bernardino Mountains. Bedrock mapping is used in models that characterize watershed sediment regimes and quantify anthropogenic influences. When combined with digital geomorphology mapping, this geodatabase helps to assess landslide hazards.

A novel methodology for querying web images

NASA Astrophysics Data System (ADS)

Prabhakara, Rashmi; Lee, Ching Cheng

2005-01-01

Ever since the advent of Internet, there has been an immense growth in the amount of image data that is available on the World Wide Web. With such a magnitude of image availability, an efficient and effective image retrieval system is required to make use of this information. This research presents an effective image matching and indexing technique that improvises on existing integrated image retrieval methods. The proposed technique follows a two-phase approach, integrating query by topic and query by example specification methods. The first phase consists of topic-based image retrieval using an improved text information retrieval (IR) technique that makes use of the structured format of HTML documents. It consists of a focused crawler that not only provides for the user to enter the keyword for the topic-based search but also, the scope in which the user wants to find the images. The second phase uses the query by example specification to perform a low-level content-based image match for the retrieval of smaller and relatively closer results of the example image. Information related to the image feature is automatically extracted from the query image by the image processing system. A technique that is not computationally intensive based on color feature is used to perform content-based matching of images. The main goal is to develop a functional image search and indexing system and to demonstrate that better retrieval results can be achieved with this proposed hybrid search technique.

A novel methodology for querying web images

NASA Astrophysics Data System (ADS)

Prabhakara, Rashmi; Lee, Ching Cheng

2004-12-01

Ever since the advent of Internet, there has been an immense growth in the amount of image data that is available on the World Wide Web. With such a magnitude of image availability, an efficient and effective image retrieval system is required to make use of this information. This research presents an effective image matching and indexing technique that improvises on existing integrated image retrieval methods. The proposed technique follows a two-phase approach, integrating query by topic and query by example specification methods. The first phase consists of topic-based image retrieval using an improved text information retrieval (IR) technique that makes use of the structured format of HTML documents. It consists of a focused crawler that not only provides for the user to enter the keyword for the topic-based search but also, the scope in which the user wants to find the images. The second phase uses the query by example specification to perform a low-level content-based image match for the retrieval of smaller and relatively closer results of the example image. Information related to the image feature is automatically extracted from the query image by the image processing system. A technique that is not computationally intensive based on color feature is used to perform content-based matching of images. The main goal is to develop a functional image search and indexing system and to demonstrate that better retrieval results can be achieved with this proposed hybrid search technique.

Querying archetype-based EHRs by search ontology-based XPath engineering.

PubMed

Kropf, Stefan; Uciteli, Alexandr; Schierle, Katrin; Krücken, Peter; Denecke, Kerstin; Herre, Heinrich

2018-05-11

Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of using free text searches, that lead to false positive results, the precision can be increased by constraining the search to certain parts of documents. A search ontology-based specification of queries on XML documents defines search concepts and relates them to parts in the XML document structure. Such query specification method is practically introduced and evaluated by applying concrete research questions formulated in natural language on a data collection for information retrieval purposes. The search is performed by search ontology-based XPath engineering that reuses ontologies and XML-related W3C standards. The key result is that the specification of research questions can be supported by the usage of search ontology-based XPath engineering. A deeper recognition of entities and a semantic understanding of the content is necessary for a further improvement of precision and recall. Key limitation is that the application of the introduced process requires skills in ontology and software development. In future, the time consuming ontology development could be overcome by implementing a new clinical role: the clinical ontologist. The introduced Search Ontology XML extension connects Search Terms to certain parts in XML documents and enables an ontology-based definition of queries. Search ontology-based XPath engineering can support research question answering by the specification of complex XPath expressions without deep syntax knowledge about XPaths.

gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances.

PubMed

Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

2016-01-01

Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos).

gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances

PubMed Central

Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

2016-01-01

Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos). PMID:27846272

A comprehensive and scalable database search system for metaproteomics.

PubMed

Chatterjee, Sandip; Stupp, Gregory S; Park, Sung Kyu Robin; Ducom, Jean-Christophe; Yates, John R; Su, Andrew I; Wolan, Dennis W

2016-08-16

Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metaproteomic analysis method (ComPIL) that addresses protein database size limitations. Our approach to overcome this significant limitation in metaproteomics was to design a scalable set of sequence databases assembled for optimal library querying speeds. ComPIL was integrated with a modified version of the search engine ProLuCID (termed "Blazmass") to permit rapid matching of experimental spectra. Proof-of-principle analysis of human HEK293 lysate with a ComPIL database derived from high-quality genomic libraries was able to detect nearly all of the same peptides as a search with a human database (~500x fewer peptides in the database), with a small reduction in sensitivity. We were also able to detect proteins from the adenovirus used to immortalize these cells. We applied our method to a set of healthy human gut microbiome proteomic samples and showed a substantial increase in the number of identified peptides and proteins compared to previous metaproteomic analyses, while retaining a high degree of protein identification accuracy and allowing for a more in-depth characterization of the functional landscape of the samples. The combination of ComPIL with Blazmass allows proteomic searches to be performed with database sizes much larger than previously possible. These large database searches can be applied to complex meta-samples with unknown composition or proteomic samples where unexpected proteins may be identified. The protein database, proteomic search engine, and the proteomic data files for the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis.

Uploading, Searching and Visualizing of Paleomagnetic and Rock Magnetic Data in the Online MagIC Database

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A.; Tauxe, L.; Constable, C.; Donadini, F.

2007-12-01

The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by both rock and paleomagnetic data. The goal of MagIC is to archive all available measurements and derived properties from paleomagnetic studies of directions and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). MagIC is hosted under EarthRef.org at http://earthref.org/MAGIC/ and will soon implement two search nodes, one for paleomagnetism and one for rock magnetism. Currently the PMAG node is operational. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual map interface to browse and select locations. Users can also browse the database by data type or by data compilation to view all contributions associated with well known earlier collections like PINT, GMPDB or PSVRL. The query result set is displayed in a digestible tabular format allowing the user to descend from locations to sites, samples, specimens and measurements. At each stage, the result set can be saved and, where appropriate, can be visualized by plotting global location maps, equal area, XY, age, and depth plots, or typical Zijderveld, hysteresis, magnetization and remanence diagrams. User contributions to the MagIC database are critical to achieving a useful research tool. We have developed a standard data and metadata template (version 2.3) that can be used to format and upload all data at the time of publication in Earth Science journals. Software tools are provided to facilitate population of these templates within Microsoft Excel. These tools allow for the import/export of text files and provide advanced functionality to manage and edit the data, and to perform various internal checks to maintain data integrity and prepare for uploading. The MagIC Contribution Wizard at http://earthref.org/MAGIC/upload.htm executes the upload and takes only a few minutes to process tens of thousands of data records. The standardized MagIC template files are stored in the digital archives of EarthRef.org where they remain available for download by the public (in both text and Excel format). Finally, the contents of these template files are automatically parsed into the online relational database, making the data available for online searches in the paleomagnetic and rock magnetic search nodes. During the upload process the owner has the option of keeping the contribution private so it can be viewed in the context of other data sets and visualized using the suite of MagIC plotting tools. Alternatively, the new data can be password protected and shared with a group of users at the contributor's discretion. Once they are published and the owner is comfortable making the upload publicly accessible, the MagIC Editing Committee reviews the contribution for adherence to the MagIC data model and conventions to ensure a high level of data integrity.

Geologic map of the Patagonia Mountains, Santa Cruz County, Arizona

USGS Publications Warehouse

Graybeal, Frederick T.; Moyer, Lorre A.; Vikre, Peter; Dunlap, Pamela; Wallis, John C.

2015-01-01

Several spatial databases provide data for the geologic map of the Patagonia Mountains in Arizona. The data can be viewed and queried in ArcGIS 10, a geographic information system; a geologic map is also available in PDF format. All products are available online only.

Adding Data Management Services to Parallel File Systems

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

Brandt, Scott

2015-03-04

The objective of this project, called DAMASC for “Data Management in Scientific Computing”, is to coalesce data management with parallel file system management to present a declarative interface to scientists for managing, querying, and analyzing extremely large data sets efficiently and predictably. Managing extremely large data sets is a key challenge of exascale computing. The overhead, energy, and cost of moving massive volumes of data demand designs where computation is close to storage. In current architectures, compute/analysis clusters access data in a physically separate parallel file system and largely leave it scientist to reduce data movement. Over the past decadesmore » the high-end computing community has adopted middleware with multiple layers of abstractions and specialized file formats such as NetCDF-4 and HDF5. These abstractions provide a limited set of high-level data processing functions, but have inherent functionality and performance limitations: middleware that provides access to the highly structured contents of scientific data files stored in the (unstructured) file systems can only optimize to the extent that file system interfaces permit; the highly structured formats of these files often impedes native file system performance optimizations. We are developing Damasc, an enhanced high-performance file system with native rich data management services. Damasc will enable efficient queries and updates over files stored in their native byte-stream format while retaining the inherent performance of file system data storage via declarative queries and updates over views of underlying files. Damasc has four key benefits for the development of data-intensive scientific code: (1) applications can use important data-management services, such as declarative queries, views, and provenance tracking, that are currently available only within database systems; (2) the use of these services becomes easier, as they are provided within a familiar file-based ecosystem; (3) common optimizations, e.g., indexing and caching, are readily supported across several file formats, avoiding effort duplication; and (4) performance improves significantly, as data processing is integrated more tightly with data storage. Our key contributions are: SciHadoop which explores changes to MapReduce assumption by taking advantage of semantics of structured data while preserving MapReduce’s failure and resource management; DataMods which extends common abstractions of parallel file systems so they become programmable such that they can be extended to natively support a variety of data models and can be hooked into emerging distributed runtimes such as Stanford’s Legion; and Miso which combines Hadoop and relational data warehousing to minimize time to insight, taking into account the overhead of ingesting data into data warehousing.« less

FastQuery: A Parallel Indexing System for Scientific Data

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

Chou, Jerry; Wu, Kesheng; Prabhat,

2011-07-29

Modern scientific datasets present numerous data management and analysis challenges. State-of-the- art index and query technologies such as FastBit can significantly improve accesses to these datasets by augmenting the user data with indexes and other secondary information. However, a challenge is that the indexes assume the relational data model but the scientific data generally follows the array data model. To match the two data models, we design a generic mapping mechanism and implement an efficient input and output interface for reading and writing the data and their corresponding indexes. To take advantage of the emerging many-core architectures, we also developmore » a parallel strategy for indexing using threading technology. This approach complements our on-going MPI-based parallelization efforts. We demonstrate the flexibility of our software by applying it to two of the most commonly used scientific data formats, HDF5 and NetCDF. We present two case studies using data from a particle accelerator model and a global climate model. We also conducted a detailed performance study using these scientific datasets. The results show that FastQuery speeds up the query time by a factor of 2.5x to 50x, and it reduces the indexing time by a factor of 16 on 24 cores.« less

Digital Geologic Map of the Wallace 1:100,000 Quadrangle, Idaho

USGS Publications Warehouse

Lewis, Reed S.; Burmester, Russell F.; McFaddan, Mark D.; Derkey, Pamela D.; Oblad, Jon R.

1999-01-01

The geology of the Wallace 1:100,000 quadrangle, Idaho was compiled by Reed S. Lewis in 1997 primarily from published materials including 1983 data from Foster, Harrison's unpublished mapping done from 1975 to 1985, Hietenan's 1963, 1967, 1968, and 1984 mapping, Hobbs and others 1965 mapping, and Vance's 1981 mapping, supplemented by eight weeks of field mapping by Reed S. Lewis, Russell F. Burmester, and Mark D. McFaddan in 1997 and 1998. This geologic map information was inked onto a 1:100,000-scale greenline mylar of the topographic base map for input into a geographic information system (GIS). The resulting digital geologic map GIS can be queried in many ways to produce a variety of geologic maps. Digital base map data files (topography, roads, towns, rivers and lakes, etc.) are not included: they may be obtained from a variety of commercial and government sources. This database is not meant to be used or displayed at any scale larger than 1:100,000 (e.g., 1:62,500 or 1:24,000). The map area is located in north Idaho. The primary sources of map data are shown in figure 2 and additional sources are shown in figure 3. This open-file report describes the geologic map units, the methods used to convert the geologic map data into a digital format, the Arc/Info GIS file structures and relationships, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet. Mapping and compilation was completed by the Idaho Geological Survey under contract with the U.S. Geological Survey (USGS) office in Spokane, Washington. The authors would like to acknowledge the help of the following field assistants: Josh Goodman, Yvonne Issak, Jeremy Johnson and Kevin Myer. Don Winston provided help with our ongoing study of Belt stratigraphy, and Tom Frost assisted with logistical problems and sample collection. Manuscript reviews by Steve Box, Tom Frost, and Brian White are greatly appreciated. We wish to thank Karen S. Bolm of the USGS for reviewing the digital files.

Mycobacteriophage genome database.

PubMed

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

2011-01-01

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

Detailed requirements for a next generation nuclear data structure.

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

Brown, D.

2016-07-05

This document attempts to compile the requirements for the top-levels of a hierarchical arrangement of nuclear data such as found in the ENDF format. This set of requirements will be used to guide the development of a new data structure to replace the legacy ENDF format.

A compiler and validator for flight operations on NASA space missions

NASA Astrophysics Data System (ADS)

Fonte, Sergio; Politi, Romolo; Capria, Maria Teresa; Giardino, Marco; De Sanctis, Maria Cristina

2016-07-01

In NASA missions the management and the programming of the flight systems is performed by a specific scripting language, the SASF (Spacecraft Activity Sequence File). In order to perform a check on the syntax and grammar it is necessary a compiler that stress the errors (eventually) found in the sequence file produced for an instrument on board the flight system. In our experience on Dawn mission, we developed VIRV (VIR Validator), a tool that performs checks on the syntax and grammar of SASF, runs a simulations of VIR acquisitions and eventually finds violation of the flight rules of the sequences produced. The project of a SASF compiler (SSC - Spacecraft Sequence Compiler) is ready to have a new implementation: the generalization for different NASA mission. In fact, VIRV is a compiler for a dialect of SASF; it includes VIR commands as part of SASF language. Our goal is to produce a general compiler for the SASF, in which every instrument has a library to be introduced into the compiler. The SSC can analyze a SASF, produce a log of events, perform a simulation of the instrument acquisition and check the flight rules for the instrument selected. The output of the program can be produced in GRASS GIS format and may help the operator to analyze the geometry of the acquisition.

A Compilation of Global Bio-Optical in Situ Data for Ocean-Colour Satellite Applications

NASA Technical Reports Server (NTRS)

Valente, Andre; Sathyendranath, Shubha; Brotus, Vanda; Groom, Steve; Grant, Michael; Taberner, Malcolm; Antoine, David; Arnone, Robert; Balch, William M.; Barker, Kathryn;

Thematic video indexing to support video database retrieval and query processing

NASA Astrophysics Data System (ADS)

Khoja, Shakeel A.; Hall, Wendy

1999-08-01

This paper presents a novel video database system, which caters for complex and long videos, such as documentaries, educational videos, etc. As compared to relatively structured format videos like CNN news or commercial advertisements, this database system has the capacity to work with long and unstructured videos.

Data Container Study for Handling Array-based Data Using Rasdaman, Hive, Spark, and MongoDB

NASA Astrophysics Data System (ADS)

Xu, M.; Hu, F.; Yu, M.; Scheele, C.; Liu, K.; Huang, Q.; Yang, C. P.; Little, M. M.

2016-12-01

Geoscience communities have come up with various big data storage solutions, such as Rasdaman and Hive, to address the grand challenges for massive Earth observation data management and processing. To examine the readiness of current solutions in supporting big Earth observation, we propose to investigate and compare four popular data container solutions, including Rasdaman, Hive, Spark, and MongoDB. Using different types of spatial and non-spatial queries, datasets stored in common scientific data formats (e.g., NetCDF and HDF), and two applications (i.e. dust storm simulation data mining and MERRA data analytics), we systematically compare and evaluate the feature and performance of these four data containers in terms of data discover and access. The computing resources (e.g. CPU, memory, hard drive, network) consumed while performing various queries and operations are monitored and recorded for the performance evaluation. The initial results show that 1) Rasdaman has the best performance for queries on statistical and operational functions, and supports NetCDF data format better than HDF; 2) Rasdaman clustering configuration is more complex than the others; 3) Hive performs better on single pixel extraction from multiple images; and 4) Except for the single pixel extractions, Spark performs better than Hive and its performance is close to Rasdaman. A comprehensive report will detail the experimental results, and compare their pros and cons regarding system performance, ease of use, accessibility, scalability, compatibility, and flexibility.

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.

PubMed

Kohany, Oleksiy; Gentles, Andrew J; Hankus, Lukasz; Jurka, Jerzy

2006-10-25

Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases. We describe the software tools RepbaseSubmitter and Censor, which are designed to facilitate updating and screening the content of Repbase. RepbaseSubmitter is a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position. Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and sensitivity, and can conduct DNA-DNA, DNA-protein, or translated DNA-translated DNA searches of genomic sequence. Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s), repeat sequences found in the query, and alignments. Censor and RepbaseSubmitter are available as both web-based services and downloadable versions. They can be found at http://www.girinst.org/repbase/submission.html (RepbaseSubmitter) and http://www.girinst.org/censor/index.php (Censor).

Towards Big Earth Data Analytics: The EarthServer Approach

NASA Astrophysics Data System (ADS)

Baumann, Peter

2013-04-01

Big Data in the Earth sciences, the Tera- to Exabyte archives, mostly are made up from coverage data whereby the term "coverage", according to ISO and OGC, is defined as the digital representation of some space-time varying phenomenon. Common examples include 1-D sensor timeseries, 2-D remote sensing imagery, 3D x/y/t image timeseries and x/y/z geology data, and 4-D x/y/z/t atmosphere and ocean data. Analytics on such data requires on-demand processing of sometimes significant complexity, such as getting the Fourier transform of satellite images. As network bandwidth limits prohibit transfer of such Big Data it is indispensable to devise protocols allowing clients to task flexible and fast processing on the server. The EarthServer initiative, funded by EU FP7 eInfrastructures, unites 11 partners from computer and earth sciences to establish Big Earth Data Analytics. One key ingredient is flexibility for users to ask what they want, not impeded and complicated by system internals. The EarthServer answer to this is to use high-level query languages; these have proven tremendously successful on tabular and XML data, and we extend them with a central geo data structure, multi-dimensional arrays. A second key ingredient is scalability. Without any doubt, scalability ultimately can only be achieved through parallelization. In the past, parallelizing code has been done at compile time and usually with manual intervention. The EarthServer approach is to perform a samentic-based dynamic distribution of queries fragments based on networks optimization and further criteria. The EarthServer platform is comprised by rasdaman, an Array DBMS enabling efficient storage and retrieval of any-size, any-type multi-dimensional raster data. In the project, rasdaman is being extended with several functionality and scalability features, including: support for irregular grids and general meshes; in-situ retrieval (evaluation of database queries on existing archive structures, avoiding data import and, hence, duplication); the aforementioned distributed query processing. Additionally, Web clients for multi-dimensional data visualization are being established. Client/server interfaces are strictly based on OGC and W3C standards, in particular the Web Coverage Processing Service (WCPS) which defines a high-level raster query language. We present the EarthServer project with its vision and approaches, relate it to the current state of standardization, and demonstrate it by way of large-scale data centers and their services using rasdaman.

Determining Recommendations for Improvement of Communication Skills Training in Dental Education: A Scoping Review.

PubMed

Ayn, Caitlyn; Robinson, Lynne; Nason, April; Lovas, John

2017-04-01

Professional communication skills have a significant impact on dental patient satisfaction and health outcomes. Communication skills training has been shown to improve the communication skills of dental students. Therefore, strengthening communication skills training in dental education shows promise for improving dental patient satisfaction and outcomes. The aim of this study was to facilitate the development of dental communication skills training through a scoping review with compilation of a list of considerations, design of an example curriculum, and consideration of barriers and facilitators to adoption of such training. A search to identify studies of communication skills training interventions and programs was conducted. Search queries were run in three databases using both text strings and controlled terms (MeSH), yielding 1,833 unique articles. Of these, 35 were full-text reviewed, and 17 were included in the final synthesis. Considerations presented in the articles were compiled into 15 considerations. These considerations were grouped into four themes: the value of communication skills training, the role of instructors, the importance of accounting for diversity, and the structure of communication skills training. An example curriculum reflective of these considerations is presented, and consideration of potential barriers and facilitators to implementation are discussed. Application and evaluation of these considerations are recommended in order to support and inform future communication skills training development.

Adsorptive Removal of Metal Ions from Water using Functionalized Biomaterials.

PubMed

Deshpande, Kanchanmala

2017-01-01

Synthesis and modification of cost-effective sorbents for removing heavy metals from water resources is an area of significance. It had been reported that materials with biological origins, such as agricultural and animal waste, are excellent alternatives to conventional adsorbents due to their higher affinity, capacity and selectivity towards metal ions. These properties of biomaterials help to reduce or detoxify metal ions concentration in contaminated water to acceptable regulatory standards. Synthesis of novel, efficient, cost effective, eco-friendly biomaterials for heavy metal adsorption from water is still an area of challenge. In this comprehensive review, acompilation of patents as well as published articles is carried out to outline the properties of different biomaterials based on their precursors along withdetailed description of biomaterial morphology and various surface modification approaches. A detailed study of the performance of adsorbents and the role of physical and chemical modification in terms of enhancing their potential for metal adsorption from water is compiled here. The factors affecting adsorption behavior i.e., capacity and affinity of e biomaterials is also compiled. This paper presents a concise review of reported studies on the synthesis and modification of biomaterials, their use for heavy metal removal from waters and future prospects of this technology. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The Role of Formative Evaluation in Implementation Research and the QUERI Experience

PubMed Central

Stetler, Cheryl B; Legro, Marcia W; Wallace, Carolyn M; Bowman, Candice; Guihan, Marylou; Hagedorn, Hildi; Kimmel, Barbara; Sharp, Nancy D; Smith, Jeffrey L

2006-01-01

This article describes the importance and role of 4 stages of formative evaluation in our growing understanding of how to implement research findings into practice in order to improve the quality of clinical care. It reviews limitations of traditional approaches to implementation research and presents a rationale for new thinking and use of new methods. Developmental, implementation-focused, progress-focused, and interpretive evaluations are then defined and illustrated with examples from Veterans Health Administration Quality Enhancement Research Initiative projects. This article also provides methodologic details and highlights challenges encountered in actualizing formative evaluation within implementation research. PMID:16637954

The SCEC Unified Community Velocity Model (UCVM) Software Framework for Distributing and Querying Seismic Velocity Models

NASA Astrophysics Data System (ADS)

Maechling, P. J.; Taborda, R.; Callaghan, S.; Shaw, J. H.; Plesch, A.; Olsen, K. B.; Jordan, T. H.; Goulet, C. A.

2017-12-01

Crustal seismic velocity models and datasets play a key role in regional three-dimensional numerical earthquake ground-motion simulation, full waveform tomography, modern physics-based probabilistic earthquake hazard analysis, as well as in other related fields including geophysics, seismology, and earthquake engineering. The standard material properties provided by a seismic velocity model are P- and S-wave velocities and density for any arbitrary point within the geographic volume for which the model is defined. Many seismic velocity models and datasets are constructed by synthesizing information from multiple sources and the resulting models are delivered to users in multiple file formats, such as text files, binary files, HDF-5 files, structured and unstructured grids, and through computer applications that allow for interactive querying of material properties. The Southern California Earthquake Center (SCEC) has developed the Unified Community Velocity Model (UCVM) software framework to facilitate the registration and distribution of existing and future seismic velocity models to the SCEC community. The UCVM software framework is designed to provide a standard query interface to multiple, alternative velocity models, even if the underlying velocity models are defined in different formats or use different geographic projections. The UCVM framework provides a comprehensive set of open-source tools for querying seismic velocity model properties, combining regional 3D models and 1D background models, visualizing 3D models, and generating computational models in the form of regular grids or unstructured meshes that can be used as inputs for ground-motion simulations. The UCVM framework helps researchers compare seismic velocity models and build equivalent simulation meshes from alternative velocity models. These capabilities enable researchers to evaluate the impact of alternative velocity models in ground-motion simulations and seismic hazard analysis applications. In this poster, we summarize the key components of the UCVM framework and describe the impact it has had in various computational geoscientific applications.

HAL/S-FC and HAL/S-360 compiler system program description

NASA Technical Reports Server (NTRS)

1976-01-01

The compiler is a large multi-phase design and can be broken into four phases: Phase 1 inputs the source language and does a syntactic and semantic analysis generating the source listing, a file of instructions in an internal format (HALMAT) and a collection of tables to be used in subsequent phases. Phase 1.5 massages the code produced by Phase 1, performing machine independent optimization. Phase 2 inputs the HALMAT produced by Phase 1 and outputs machine language object modules in a form suitable for the OS-360 or FCOS linkage editor. Phase 3 produces the SDF tables. The four phases described are written in XPL, a language specifically designed for compiler implementation. In addition to the compiler, there is a large library containing all the routines that can be explicitly called by the source language programmer plus a large collection of routines for implementing various facilities of the language.

Topographic mapping of the Moon

USGS Publications Warehouse

Wu, S.S.C.

1985-01-01

Contour maps of the Moon have been compiled by photogrammetric methods that use stereoscopic combinations of all available metric photographs from the Apollo 15, 16, and 17 missions. The maps utilize the same format as the existing NASA shaded-relief Lunar Planning Charts (LOC-1, -2, -3, and -4), which have a scale of 1:2 750 000. The map contour interval is 500m. A control net derived from Apollo photographs by Doyle and others was used for the compilation. Contour lines and elevations are referred to the new topographic datum of the Moon, which is defined in terms of spherical harmonics from the lunar gravity field. Compilation of all four LOC charts was completed on analytical plotters from 566 stereo models of Apollo metric photographs that cover approximately 20% of the Moon. This is the first step toward compiling a global topographic map of the Moon at a scale of 1:5 000 000. ?? 1985 D. Reidel Publishing Company.

A relational database in neurosurgery.

PubMed

Sicurello, F; Marchetti, M R; Cazzaniga, P

1995-01-01

This paper describes teh automatic procedure for a clinical record management in a Neurosurgery ward. The automated record allows the storage, querying and effective management of clinical data. This is useful during the patient stay and also for data processing and analysis aiming at clinical research and statistical studies. The clinical record is problem-oriented. It contains a minimum data set regarding every patient and a data set which is defined by a classification nomenclature (using an inner protocol). The main parts of the clinical record are the following tables: PERSONAL DATA: contains the fields relating to personal and admission data of the patient. The compilation of some fields is compulsory because they serve as input for the automated discharge letter. This table is used as an identifier for patient retrieval. composed of five different tables according to the kind of data. They are: familiar anamnesis, physiological anamnesis, past and next pathology anamnesis, and trauma anamnesis. GENERAL OBJECTIVITY: contains the general physical information of a patient. The field hold default values, which quickens the compilation and assures the recording of normal values. NEUROLOGICAL EXAMINATION: contains information about the neurological status of the patient. Also in this table, ther are default values in the fields. COMA: contains standardized ata and classifications. The multiple choices are automated and driven and belong to homogeneous classes. SURGICAL OPERATIONS: the information recording is made defining the general kind of operation and then defining the peculiar kind of operation. INSTRUMENTAL EXAMINATIONS: some examination results are recorded in a free structure, while other ones (TAC, etc.) follow codified structure. In order to identify a pathology by means of TAC, it is enough to record three values corresponding to three variables. THis classification fully describes a lot of neurosurgical pathologies. DISCHARGE: contains conclusions, therapies, result, and hospital course. Medical language is closer to the natural one and presents some abiguities. In order to solve this problem, a classification nomenclature was used for diagnosis definition. DISCHARGE LETTER: the document given to the patient when he is discharged. It extracts data from the previously described modules and contains standard headings. The information stored int he database is structured (e.g., diagnosis, name, surname, etc.) and access to this data takes place when the user wants to search the database, using particular queries where the identifying data of a patient is put as conditions for the research (SELECT age, name WHERE diagnosis="TRAUMA"). Logical operators and relational algebra of the relational DBMS allows more complex queries ((diagnosis="TRAUMA" AND age="19") OR sex="M"). The queries are deterministic, because data management uses a classification nomenclature. Data retrieval takes place through a matching, and the DBMS answers directly to the queries. The information retrieval speed depends upon the kind of system that is used; in our case retrieval time is low because the accesses to disk are few even for big databases. In medicine, clinical records can have a hierarchical structure and/or a relational one. Nevertheless, the hierarchical model presents a disadvantage: it is not very flexible because it is linked to a pre-defined structure; as a matter of fact, the definition of path is established in the beginning and not during the execution. Thus, a better representation of the system at a logical level requries a relational DBMS which exploits the relationships between entities in a vertical and horizontal way. That is why the developers adopted a mixed strategy which exploits the advantages of both models and which is provided by M Technology with SQL language (M/SQL). For the future, it is important to have at one's disposal multimedia technologies, which integrate different kinds of information (alp

Industrial Arts Technology Bibliography; An Annotated Reference for Librarians.

ERIC Educational Resources Information Center

New York State Education Dept., Albany. Bureau of Secondary Curriculum Development.

This compilation is designed to assist librarians in selecting books for supplementing the expanding program of industrial arts education. The books were selected for the major subject areas of a broad industrial arts program, on the basis of reflected interest of students, content, format, and readability. The format and coding used in the…

SAFE: SPARQL Federation over RDF Data Cubes with Access Control.

PubMed

Khan, Yasar; Saleem, Muhammad; Mehdi, Muntazir; Hogan, Aidan; Mehmood, Qaiser; Rebholz-Schuhmann, Dietrich; Sahay, Ratnesh

2017-02-01

Several query federation engines have been proposed for accessing public Linked Open Data sources. However, in many domains, resources are sensitive and access to these resources is tightly controlled by stakeholders; consequently, privacy is a major concern when federating queries over such datasets. In the Healthcare and Life Sciences (HCLS) domain real-world datasets contain sensitive statistical information: strict ownership is granted to individuals working in hospitals, research labs, clinical trial organisers, etc. Therefore, the legal and ethical concerns on (i) preserving the anonymity of patients (or clinical subjects); and (ii) respecting data ownership through access control; are key challenges faced by the data analytics community working within the HCLS domain. Likewise statistical data play a key role in the domain, where the RDF Data Cube Vocabulary has been proposed as a standard format to enable the exchange of such data. However, to the best of our knowledge, no existing approach has looked to optimise federated queries over such statistical data. We present SAFE: a query federation engine that enables policy-aware access to sensitive statistical datasets represented as RDF data cubes. SAFE is designed specifically to query statistical RDF data cubes in a distributed setting, where access control is coupled with source selection, user profiles and their access rights. SAFE proposes a join-aware source selection method that avoids wasteful requests to irrelevant and unauthorised data sources. In order to preserve anonymity and enforce stricter access control, SAFE's indexing system does not hold any data instances-it stores only predicates and endpoints. The resulting data summary has a significantly lower index generation time and size compared to existing engines, which allows for faster updates when sources change. We validate the performance of the system with experiments over real-world datasets provided by three clinical organisations as well as legacy linked datasets. We show that SAFE enables granular graph-level access control over distributed clinical RDF data cubes and efficiently reduces the source selection and overall query execution time when compared with general-purpose SPARQL query federation engines in the targeted setting.

MYCIN II: design and implementation of a therapy reference with complex content-based indexing.

PubMed Central

Kim, D. K.; Fagan, L. M.; Jones, K. T.; Berrios, D. C.; Yu, V. L.

1998-01-01

We describe the construction of MYCIN II, a prototype system that provides for content-based markup and search of a forthcoming clinical therapeutics textbook, Antimicrobial Therapy and Vaccines. Existing commercial search technology for digital references utilizes generic tools such as textword-based searches with geographical or statistical refinements. We suggest that the drawbacks of such systems significantly restrict their use in everyday clinical practice. This is in spite of the fact that there is a great need for the information contained within these same references. The system we describe is intended to supplement keyword searching so that certain important questions can be asked easily and can be answered reliably (in terms of precision and recall). Our method attacks this problem in a restricted domain of knowledge-clinical infectious disease. For example, we would like to be able to answer the class of questions exemplified by the following query: "What antimicrobial agents can be used to treat endocarditis caused by Eikenella corrodens?" We have compiled and analyzed a list of such questions to develop a concept-based markup scheme. This scheme was then applied within an HTML markup to electronically "highlight" passages from three textbook chapters. We constructed a functioning web-based search interface. Our system also provides semi-automated querying of PubMed using our concept markup and the user's actions as a guide. PMID:9929205

MYCIN II: design and implementation of a therapy reference with complex content-based indexing.

PubMed

Kim, D K; Fagan, L M; Jones, K T; Berrios, D C; Yu, V L

1998-01-01

We describe the construction of MYCIN II, a prototype system that provides for content-based markup and search of a forthcoming clinical therapeutics textbook, Antimicrobial Therapy and Vaccines. Existing commercial search technology for digital references utilizes generic tools such as textword-based searches with geographical or statistical refinements. We suggest that the drawbacks of such systems significantly restrict their use in everyday clinical practice. This is in spite of the fact that there is a great need for the information contained within these same references. The system we describe is intended to supplement keyword searching so that certain important questions can be asked easily and can be answered reliably (in terms of precision and recall). Our method attacks this problem in a restricted domain of knowledge-clinical infectious disease. For example, we would like to be able to answer the class of questions exemplified by the following query: "What antimicrobial agents can be used to treat endocarditis caused by Eikenella corrodens?" We have compiled and analyzed a list of such questions to develop a concept-based markup scheme. This scheme was then applied within an HTML markup to electronically "highlight" passages from three textbook chapters. We constructed a functioning web-based search interface. Our system also provides semi-automated querying of PubMed using our concept markup and the user's actions as a guide.

An evolution-based DNA-binding residue predictor using a dynamic query-driven learning scheme.

PubMed

Chai, H; Zhang, J; Yang, G; Ma, Z

2016-11-15

DNA-binding proteins play a pivotal role in various biological activities. Identification of DNA-binding residues (DBRs) is of great importance for understanding the mechanism of gene regulations and chromatin remodeling. Most traditional computational methods usually construct their predictors on static non-redundant datasets. They excluded many homologous DNA-binding proteins so as to guarantee the generalization capability of their models. However, those ignored samples may potentially provide useful clues when studying protein-DNA interactions, which have not obtained enough attention. In view of this, we propose a novel method, namely DQPred-DBR, to fill the gap of DBR predictions. First, a large-scale extensible sample pool was compiled. Second, evolution-based features in the form of a relative position specific score matrix and covariant evolutionary conservation descriptors were used to encode the feature space. Third, a dynamic query-driven learning scheme was designed to make more use of proteins with known structure and functions. In comparison with a traditional static model, the introduction of dynamic models could obviously improve the prediction performance. Experimental results from the benchmark and independent datasets proved that our DQPred-DBR had promising generalization capability. It was capable of producing decent predictions and outperforms many state-of-the-art methods. For the convenience of academic use, our proposed method was also implemented as a web server at .

Constraining Stellar Population Models. I. Age, Metallicity and Abundance Pattern Compilation for Galactic Globular Clusters

NASA Astrophysics Data System (ADS)

Roediger, Joel C.; Courteau, Stéphane; Graves, Genevieve; Schiavon, Ricardo P.

2014-01-01

We present an extensive literature compilation of age, metallicity, and chemical abundance pattern information for the 41 Galactic globular clusters (GGCs) studied by Schiavon et al. Our compilation constitutes a notable improvement over previous similar work, particularly in terms of chemical abundances. Its primary purpose is to enable detailed evaluations of and refinements to stellar population synthesis models designed to recover the above information for unresolved stellar systems based on their integrated spectra. However, since the Schiavon sample spans a wide range of the known GGC parameter space, our compilation may also benefit investigations related to a variety of astrophysical endeavors, such as the early formation of the Milky Way, the chemical evolution of GGCs, and stellar evolution and nucleosynthesis. For instance, we confirm with our compiled data that the GGC system has a bimodal metallicity distribution and is uniformly enhanced in the α elements. When paired with the ages of our clusters, we find evidence that supports a scenario whereby the Milky Way obtained its globular clusters through two channels: in situ formation and accretion of satellite galaxies. The distributions of C, N, O, and Na abundances and the dispersions thereof per cluster corroborate the known fact that all GGCs studied so far with respect to multiple stellar populations have been found to harbor them. Finally, using data on individual stars, we verify that stellar atmospheres become progressively polluted by CN(O)-processed material after they leave the main sequence. We also uncover evidence which suggests that the α elements Mg and Ca may originate from more than one nucleosynthetic production site. We estimate that our compilation incorporates all relevant analyses from the literature up to mid-2012. As an aid to investigators in the fields named above, we provide detailed electronic tables of the data upon which our work is based at http://www.astro.queensu.ca/people/Stephane_Courteau/roediger2013/index.html.

samiDB: A Prototype Data Archive for Big Science Exploration

NASA Astrophysics Data System (ADS)

Konstantopoulos, I. S.; Green, A. W.; Cortese, L.; Foster, C.; Scott, N.

2015-04-01

samiDB is an archive, database, and query engine to serve the spectra, spectral hypercubes, and high-level science products that make up the SAMI Galaxy Survey. Based on the versatile Hierarchical Data Format (HDF5), samiDB does not depend on relational database structures and hence lightens the setup and maintenance load imposed on science teams by metadata tables. The code, written in Python, covers the ingestion, querying, and exporting of data as well as the automatic setup of an HTML schema browser. samiDB serves as a maintenance-light data archive for Big Science and can be adopted and adapted by science teams that lack the means to hire professional archivists to set up the data back end for their projects.

TopFed: TCGA tailored federated query processing and linking to LOD.

PubMed

Saleem, Muhammad; Padmanabhuni, Shanmukha S; Ngomo, Axel-Cyrille Ngonga; Iqbal, Aftab; Almeida, Jonas S; Decker, Stefan; Deus, Helena F

2014-01-01

The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to catalogue genetic mutations responsible for cancer using genome analysis techniques. One of the aims of this project is to create a comprehensive and open repository of cancer related molecular analysis, to be exploited by bioinformaticians towards advancing cancer knowledge. However, devising bioinformatics applications to analyse such large dataset is still challenging, as it often requires downloading large archives and parsing the relevant text files. Therefore, it is making it difficult to enable virtual data integration in order to collect the critical co-variates necessary for analysis. We address these issues by transforming the TCGA data into the Semantic Web standard Resource Description Format (RDF), link it to relevant datasets in the Linked Open Data (LOD) cloud and further propose an efficient data distribution strategy to host the resulting 20.4 billion triples data via several SPARQL endpoints. Having the TCGA data distributed across multiple SPARQL endpoints, we enable biomedical scientists to query and retrieve information from these SPARQL endpoints by proposing a TCGA tailored federated SPARQL query processing engine named TopFed. We compare TopFed with a well established federation engine FedX in terms of source selection and query execution time by using 10 different federated SPARQL queries with varying requirements. Our evaluation results show that TopFed selects on average less than half of the sources (with 100% recall) with query execution time equal to one third to that of FedX. With TopFed, we aim to offer biomedical scientists a single-point-of-access through which distributed TCGA data can be accessed in unison. We believe the proposed system can greatly help researchers in the biomedical domain to carry out their research effectively with TCGA as the amount and diversity of data exceeds the ability of local resources to handle its retrieval and parsing.

Towards ontology-driven navigation of the lipid bibliosphere

PubMed Central

Baker, Christopher JO; Kanagasabai, Rajaraman; Ang, Wee Tiong; Veeramani, Anitha; Low, Hong-Sang; Wenk, Markus R

2008-01-01

Background The indexing of scientific literature and content is a relevant and contemporary requirement within life science information systems. Navigating information available in legacy formats continues to be a challenge both in enterprise and academic domains. The emergence of semantic web technologies and their fusion with artificial intelligence techniques has provided a new toolkit with which to address these data integration challenges. In the emerging field of lipidomics such navigation challenges are barriers to the translation of scientific results into actionable knowledge, critical to the treatment of diseases such as Alzheimer's syndrome, Mycobacterium infections and cancer. Results We present a literature-driven workflow involving document delivery and natural language processing steps generating tagged sentences containing lipid, protein and disease names, which are instantiated to custom designed lipid ontology. We describe the design challenges in capturing lipid nomenclature, the mandate of the ontology and its role as query model in the navigation of the lipid bibliosphere. We illustrate the extent of the description logic-based A-box query capability provided by the instantiated ontology using a graphical query composer to query sentences describing lipid-protein and lipid-disease correlations. Conclusion As scientists accept the need to readjust the manner in which we search for information and derive knowledge we illustrate a system that can constrain the literature explosion and knowledge navigation problems. Specifically we have focussed on solving this challenge for lipidomics researchers who have to deal with the lack of standardized vocabulary, differing classification schemes, and a wide array of synonyms before being able to derive scientific insights. The use of the OWL-DL variant of the Web Ontology Language (OWL) and description logic reasoning is pivotal in this regard, providing the lipid scientist with advanced query access to the results of text mining algorithms instantiated into the ontology. The visual query paradigm assists in the adoption of this technology. PMID:18315858

Towards ontology-driven navigation of the lipid bibliosphere.

PubMed

Baker, Christopher Jo; Kanagasabai, Rajaraman; Ang, Wee Tiong; Veeramani, Anitha; Low, Hong-Sang; Wenk, Markus R

2008-01-01

The indexing of scientific literature and content is a relevant and contemporary requirement within life science information systems. Navigating information available in legacy formats continues to be a challenge both in enterprise and academic domains. The emergence of semantic web technologies and their fusion with artificial intelligence techniques has provided a new toolkit with which to address these data integration challenges. In the emerging field of lipidomics such navigation challenges are barriers to the translation of scientific results into actionable knowledge, critical to the treatment of diseases such as Alzheimer's syndrome, Mycobacterium infections and cancer. We present a literature-driven workflow involving document delivery and natural language processing steps generating tagged sentences containing lipid, protein and disease names, which are instantiated to custom designed lipid ontology. We describe the design challenges in capturing lipid nomenclature, the mandate of the ontology and its role as query model in the navigation of the lipid bibliosphere. We illustrate the extent of the description logic-based A-box query capability provided by the instantiated ontology using a graphical query composer to query sentences describing lipid-protein and lipid-disease correlations. As scientists accept the need to readjust the manner in which we search for information and derive knowledge we illustrate a system that can constrain the literature explosion and knowledge navigation problems. Specifically we have focussed on solving this challenge for lipidomics researchers who have to deal with the lack of standardized vocabulary, differing classification schemes, and a wide array of synonyms before being able to derive scientific insights. The use of the OWL-DL variant of the Web Ontology Language (OWL) and description logic reasoning is pivotal in this regard, providing the lipid scientist with advanced query access to the results of text mining algorithms instantiated into the ontology. The visual query paradigm assists in the adoption of this technology.

PROTICdb: a web-based application to store, track, query, and compare plant proteome data.

PubMed

Ferry-Dumazet, Hélène; Houel, Gwenn; Montalent, Pierre; Moreau, Luc; Langella, Olivier; Negroni, Luc; Vincent, Delphine; Lalanne, Céline; de Daruvar, Antoine; Plomion, Christophe; Zivy, Michel; Joets, Johann

2005-05-01

PROTICdb is a web-based application, mainly designed to store and analyze plant proteome data obtained by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry (MS). The purposes of PROTICdb are (i) to store, track, and query information related to proteomic experiments, i.e., from tissue sampling to protein identification and quantitative measurements, and (ii) to integrate information from the user's own expertise and other sources into a knowledge base, used to support data interpretation (e.g., for the determination of allelic variants or products of post-translational modifications). Data insertion into the relational database of PROTICdb is achieved either by uploading outputs of image analysis and MS identification software, or by filling web forms. 2-D PAGE annotated maps can be displayed, queried, and compared through a graphical interface. Links to external databases are also available. Quantitative data can be easily exported in a tabulated format for statistical analyses. PROTICdb is based on the Oracle or the PostgreSQL Database Management System and is freely available upon request at the following URL: http://moulon.inra.fr/ bioinfo/PROTICdb.

ScotlandsPlaces XML: Bespoke XML or XML Mapping?

ERIC Educational Resources Information Center

Beamer, Ashley; Gillick, Mark

2010-01-01

Purpose: The purpose of this paper is to investigate web services (in the form of parameterised URLs), specifically in the context of the ScotlandsPlaces project. This involves cross-domain querying, data retrieval and display via the development of a bespoke XML standard rather than existing XML formats and mapping between them.…

A Practical Ontology Query Expansion Algorithm for Semantic-Aware Learning Objects Retrieval

ERIC Educational Resources Information Center

Lee, Ming-Che; Tsai, Kun Hua; Wang, Tzone I.

2008-01-01

Following the rapid development of Internet, particularly web page interaction technology, distant e-learning has become increasingly realistic and popular. To solve the problems associated with sharing and reusing teaching materials in different e-learning systems, several standard formats, including SCORM, IMS, LOM, and AICC, etc., recently have…

SEGY to ASCII: Conversion and Plotting Program

USGS Publications Warehouse

Goldman, Mark R.

1999-01-01

This report documents a computer program to convert standard 4 byte, IBM floating point SEGY files to ASCII xyz format. The program then optionally plots the seismic data using the GMT plotting package. The material for this publication is contained in a standard tar file (of99-126.tar) that is uncompressed and 726 K in size. It can be downloaded by any Unix machine. Move the tar file to the directory you wish to use it in, then type 'tar xvf of99-126.tar' The archive files (and diskette) contain a NOTE file, a README file, a version-history file, source code, a makefile for easy compilation, and an ASCII version of the documentation. The archive files (and diskette) also contain example test files, including a typical SEGY file along with the resulting ASCII xyz and postscript files. Requirements for compiling the source code into an executable are a C++ compiler. The program has been successfully compiled using Gnu's g++ version 2.8.1, and use of other compilers may require modifications to the existing source code. The g++ compiler is a free, high quality C++ compiler and may be downloaded from the ftp site: ftp://ftp.gnu.org/gnu Requirements for plotting the seismic data is the existence of the GMT plotting package. The GMT plotting package may be downloaded from the web site: http://www.soest.hawaii.edu/gmt/

A compilation of global bio-optical in situ data for ocean-colour satellite applications

NASA Astrophysics Data System (ADS)

Valente, André; Sathyendranath, Shubha; Brotas, Vanda; Groom, Steve; Grant, Michael; Taberner, Malcolm; Antoine, David; Arnone, Robert; Balch, William M.; Barker, Kathryn; Barlow, Ray; Bélanger, Simon; Berthon, Jean-François; Beşiktepe, Şükrü; Brando, Vittorio; Canuti, Elisabetta; Chavez, Francisco; Claustre, Hervé; Crout, Richard; Frouin, Robert; García-Soto, Carlos; Gibb, Stuart W.; Gould, Richard; Hooker, Stanford; Kahru, Mati; Klein, Holger; Kratzer, Susanne; Loisel, Hubert; McKee, David; Mitchell, Brian G.; Moisan, Tiffany; Muller-Karger, Frank; O'Dowd, Leonie; Ondrusek, Michael; Poulton, Alex J.; Repecaud, Michel; Smyth, Timothy; Sosik, Heidi M.; Twardowski, Michael; Voss, Kenneth; Werdell, Jeremy; Wernand, Marcel; Zibordi, Giuseppe

2016-06-01

A compiled set of in situ data is important to evaluate the quality of ocean-colour satellite-data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT, GeP&CO), span between 1997 and 2012, and have a global distribution. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties and spectral diffuse attenuation coefficients. The data were from multi-project archives acquired via the open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) were preserved throughout the work and made available in the final table. Using all the data in a validation exercise increases the number of matchups and enhances the representativeness of different marine regimes. By making available the metadata, it is also possible to analyse each set of data separately. The compiled data are available at doi:10.1594/PANGAEA.854832 (Valente et al., 2015).

Web image retrieval using an effective topic and content-based technique

NASA Astrophysics Data System (ADS)

Lee, Ching-Cheng; Prabhakara, Rashmi

2005-03-01

There has been an exponential growth in the amount of image data that is available on the World Wide Web since the early development of Internet. With such a large amount of information and image available and its usefulness, an effective image retrieval system is thus greatly needed. In this paper, we present an effective approach with both image matching and indexing techniques that improvise on existing integrated image retrieval methods. This technique follows a two-phase approach, integrating query by topic and query by example specification methods. In the first phase, The topic-based image retrieval is performed by using an improved text information retrieval (IR) technique that makes use of the structured format of HTML documents. This technique consists of a focused crawler that not only provides for the user to enter the keyword for the topic-based search but also, the scope in which the user wants to find the images. In the second phase, we use query by example specification to perform a low-level content-based image match in order to retrieve smaller and relatively closer results of the example image. From this, information related to the image feature is automatically extracted from the query image. The main objective of our approach is to develop a functional image search and indexing technique and to demonstrate that better retrieval results can be achieved.

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

Schmieman, E.; Johns, W.E.

This document was compiled by a group of about 12 graduate students in the Department of Mechanical Engineering and Material Science at Washington State University and was funded by the U.S. Department of Energy. The literature search resulting in the compilation of this bibliography was designed to be an exhaustive search for research and development work involving the vitrification of mixed wastes, published by domestic and foreign researchers, primarily during 1989-1994. The search techniques were dominated by electronic methods and this bibliography is also available in electronic format, Windows Reference Manager.

GeneBee-net: Internet-based server for analyzing biopolymers

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

Brodsky, L.I.; Ivanov, V.V.; Nikolaev, V.K.

This work describes a network server for searching databanks of biopolymer structures and performing other biocomputing procedures; it is available via direct Internet connection. Basic server procedures are dedicated to homology (similarity) search of sequence and 3D structure of proteins. The homologies found could be used to build multiple alignments, predict protein and RNA secondary structure, and construct phylogenetic trees. In addition to traditional methods of sequence similarity search, the authors propose {open_quotes}non-matrix{close_quotes} (correlational) search. An analogous approach is used to identify regions of similar tertiary structure of proteins. Algorithm concepts and usage examples are presented for new methods. Servicemore » logic is based upon interaction of a client program and server procedures. The client program allows the compilation of queries and the processing of results of an analysis.« less

Creating Access to Data of Worldwide Volcanic Unrest

NASA Astrophysics Data System (ADS)

Venezky, D. Y.; Newhall, C. G.; Malone, S. D.

2003-12-01

We are creating a pilot database (WOVOdat - the World Organization of Volcano Observatories database) using an open source database and content generation software, allowing web access to data of worldwide volcanic seismicity, ground deformation, fumarolic activity, and other changes within or adjacent to a volcanic system. After three years of discussions with volcano observatories of the WOVO community and institutional databases such as IRIS, UNAVCO, and the Smithsonian's Global Volcanism Program about how to link global data of volcanic unrest for use during crisis situations and for research, we are now developing the pilot database. We already have created the core tables and have written simple queries that access some of the available data using pull-down menus on a website. Over the next year, we plan to complete schema realization, expand querying capabilities, and then open the pilot database for a multi-year data-loading process. Many of the challenges we are encountering are common to multidisciplinary projects and include determining standard data formats, choosing levels of data detail (raw vs. minimally processed data, summary intervals vs. continuous data, etc.), and organizing the extant but variable data into a useable schema. Additionally, we are working on how best to enter the varied data into the database (scripts for digital data and web-entry tools for non-digital data) and what standard sets of queries are most important. An essential during an evolving volcanic crisis would be: `Has any volcano shown the behavior being observed here and what happened?'. We believe that with a systematic aggregation of all datasets on volcanic unrest, we should be able to find patterns that were previously inaccessible or unrecognized. The second WOVOdat workshop in 2002 provided a recent forum for discussion of data formats, database access, and schemas. The formats and units for the discussed parameters can be viewed at http://www.wovo.org/WOVOdat/parameters.htm. Comments, suggestions, and participation in all aspects of the WOVOdat project are welcome and appreciated.

Family Myths, Beliefs, and Customs as a Research/Educational Tool to Explore Identity Formation

ERIC Educational Resources Information Center

Herman, William E.

2008-01-01

This paper outlines a qualitative research tool designed to explore personal identity formation as described by Erik Erikson and offers self-reflective and anonymous evaluative comments made by college students after completing this task. Subjects compiled a list of 200 myths, customs, fables, rituals, and beliefs from their family of origin and…

An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence

PubMed Central

Sahoo, Satya S.; Bodenreider, Olivier; Rutter, Joni L.; Skinner, Karen J.; Sheth, Amit P.

2008-01-01

Objectives This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. Methods We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Results Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Conclusion Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. Resource page http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/ PMID:18395495

An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence.

PubMed

Sahoo, Satya S; Bodenreider, Olivier; Rutter, Joni L; Skinner, Karen J; Sheth, Amit P

2008-10-01

This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. RESOURCE PAGE: http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/

K-12 Professional Learning Communities (PLCs) in a Rural School District on the High Plains of Texas: Mechanism for Teacher Support of Innovative Formative Assessment and Instruction with Technology (iFAIT)

ERIC Educational Resources Information Center

Talkmitt, Marcia Joy

2013-01-01

The purpose of this study was to explore the evolution of collaborative practices of PLCs as they emerge when using technology based formative assessment via iFAIT or innovative Formative Assessment with Instruction and Technology developed by the researcher using audience response systems and the online data compiler, Eduphoria!. This study used…

Availability of Ada and C++ Compilers, Tools, Education and Training

DTIC Science & Technology

1991-07-01

executable mini-specs, to support import of existing code. Automated database population/change propagation. 9. Documentation generation: via FrameMaker . 10...formats. 12. Links to other tools: i. Atherton’s Software Backplane. ii. 4GLS iii. Interleaf and FrameMaker publishing. 13. Output formats: PostScript...by end 󈨟. 11. Output formats: ASCII, PostScript, Interleaf, HPGL, Troff, nroff, FrameMaker , WordPerfect. 12. User interface: Menu and mouse

Mercury Toolset for Spatiotemporal Metadata

NASA Technical Reports Server (NTRS)

Wilson, Bruce E.; Palanisamy, Giri; Devarakonda, Ranjeet; Rhyne, B. Timothy; Lindsley, Chris; Green, James

2010-01-01

Mercury (http://mercury.ornl.gov) is a set of tools for federated harvesting, searching, and retrieving metadata, particularly spatiotemporal metadata. Version 3.0 of the Mercury toolset provides orders of magnitude improvements in search speed, support for additional metadata formats, integration with Google Maps for spatial queries, facetted type search, support for RSS (Really Simple Syndication) delivery of search results, and enhanced customization to meet the needs of the multiple projects that use Mercury. It provides a single portal to very quickly search for data and information contained in disparate data management systems, each of which may use different metadata formats. Mercury harvests metadata and key data from contributing project servers distributed around the world and builds a centralized index. The search interfaces then allow the users to perform a variety of fielded, spatial, and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury periodically (typically daily) harvests metadata sources through a collection of interfaces and re-indexes these metadata to provide extremely rapid search capabilities, even over collections with tens of millions of metadata records. A number of both graphical and application interfaces have been constructed within Mercury, to enable both human users and other computer programs to perform queries. Mercury was also designed to support multiple different projects, so that the particular fields that can be queried and used with search filters are easy to configure for each different project.

Mercury Toolset for Spatiotemporal Metadata

NASA Astrophysics Data System (ADS)

Devarakonda, Ranjeet; Palanisamy, Giri; Green, James; Wilson, Bruce; Rhyne, B. Timothy; Lindsley, Chris

2010-06-01

Mercury (http://mercury.ornl.gov) is a set of tools for federated harvesting, searching, and retrieving metadata, particularly spatiotemporal metadata. Version 3.0 of the Mercury toolset provides orders of magnitude improvements in search speed, support for additional metadata formats, integration with Google Maps for spatial queries, facetted type search, support for RSS (Really Simple Syndication) delivery of search results, and enhanced customization to meet the needs of the multiple projects that use Mercury. It provides a single portal to very quickly search for data and information contained in disparate data management systems, each of which may use different metadata formats. Mercury harvests metadata and key data from contributing project servers distributed around the world and builds a centralized index. The search interfaces then allow the users to perform a variety of fielded, spatial, and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury periodically (typically daily)harvests metadata sources through a collection of interfaces and re-indexes these metadata to provide extremely rapid search capabilities, even over collections with tens of millions of metadata records. A number of both graphical and application interfaces have been constructed within Mercury, to enable both human users and other computer programs to perform queries. Mercury was also designed to support multiple different projects, so that the particular fields that can be queried and used with search filters are easy to configure for each different project.

DET/MPS - THE GSFC ENERGY BALANCE PROGRAM, DIRECT ENERGY TRANSFER/MULTIMISSION SPACECRAFT MODULAR POWER SYSTEM (DEC VAX VMS VERSION)

NASA Technical Reports Server (NTRS)

Jagielski, J. M.

1994-01-01

The DET/MPS programs model and simulate the Direct Energy Transfer and Multimission Spacecraft Modular Power System in order to aid both in design and in analysis of orbital energy balance. Typically, the DET power system has the solar array directly to the spacecraft bus, and the central building block of MPS is the Standard Power Regulator Unit. DET/MPS allows a minute-by-minute simulation of the power system's performance as it responds to various orbital parameters, focusing its output on solar array output and battery characteristics. While this package is limited in terms of orbital mechanics, it is sufficient to calculate eclipse and solar array data for circular or non-circular orbits. DET/MPS can be adjusted to run one or sequential orbits up to about one week, simulated time. These programs have been used on a variety of Goddard Space Flight Center spacecraft projects. DET/MPS is written in FORTRAN 77 with some VAX-type extensions. Any FORTRAN 77 compiler that includes VAX extensions should be able to compile and run the program with little or no modifications. The compiler must at least support free-form (or tab-delineated) source format and 'do do-while end-do' control structures. DET/MPS is available for three platforms: GSC-13374, for DEC VAX series computers running VMS, is available in DEC VAX Backup format on a 9-track 1600 BPI tape (standard distribution) or TK50 tape cartridge; GSC-13443, for UNIX-based computers, is available on a .25 inch streaming magnetic tape cartridge in UNIX tar format; and GSC-13444, for Macintosh computers running AU/X with either the NKR FORTRAN or AbSoft MacFORTRAN II compilers, is available on a 3.5 inch 800K Macintosh format diskette. Source code and test data are supplied. The UNIX version of DET requires 90K of main memory for execution. DET/MPS was developed in 1990. A/UX and Macintosh are registered trademarks of Apple Computer, Inc. VMS, DEC VAX and TK50 are trademarks of Digital Equipment Corporation. UNIX is a registered trademark of AT&T Bell Laboratories.

DET/MPS - THE GSFC ENERGY BALANCE PROGRAM, DIRECT ENERGY TRANSFER/MULTIMISSION SPACECRAFT MODULAR POWER SYSTEM (UNIX VERSION)

NASA Technical Reports Server (NTRS)

Jagielski, J. M.

1994-01-01

The DET/MPS programs model and simulate the Direct Energy Transfer and Multimission Spacecraft Modular Power System in order to aid both in design and in analysis of orbital energy balance. Typically, the DET power system has the solar array directly to the spacecraft bus, and the central building block of MPS is the Standard Power Regulator Unit. DET/MPS allows a minute-by-minute simulation of the power system's performance as it responds to various orbital parameters, focusing its output on solar array output and battery characteristics. While this package is limited in terms of orbital mechanics, it is sufficient to calculate eclipse and solar array data for circular or non-circular orbits. DET/MPS can be adjusted to run one or sequential orbits up to about one week, simulated time. These programs have been used on a variety of Goddard Space Flight Center spacecraft projects. DET/MPS is written in FORTRAN 77 with some VAX-type extensions. Any FORTRAN 77 compiler that includes VAX extensions should be able to compile and run the program with little or no modifications. The compiler must at least support free-form (or tab-delineated) source format and 'do do-while end-do' control structures. DET/MPS is available for three platforms: GSC-13374, for DEC VAX series computers running VMS, is available in DEC VAX Backup format on a 9-track 1600 BPI tape (standard distribution) or TK50 tape cartridge; GSC-13443, for UNIX-based computers, is available on a .25 inch streaming magnetic tape cartridge in UNIX tar format; and GSC-13444, for Macintosh computers running AU/X with either the NKR FORTRAN or AbSoft MacFORTRAN II compilers, is available on a 3.5 inch 800K Macintosh format diskette. Source code and test data are supplied. The UNIX version of DET requires 90K of main memory for execution. DET/MPS was developed in 1990. A/UX and Macintosh are registered trademarks of Apple Computer, Inc. VMS, DEC VAX and TK50 are trademarks of Digital Equipment Corporation. UNIX is a registered trademark of AT&T Bell Laboratories.

DET/MPS - THE GSFC ENERGY BALANCE PROGRAM, DIRECT ENERGY TRANSFER/MULTIMISSION SPACECRAFT MODULAR POWER SYSTEM (MACINTOSH A/UX VERSION)

NASA Technical Reports Server (NTRS)

Jagielski, J. M.

1994-01-01

The DET/MPS programs model and simulate the Direct Energy Transfer and Multimission Spacecraft Modular Power System in order to aid both in design and in analysis of orbital energy balance. Typically, the DET power system has the solar array directly to the spacecraft bus, and the central building block of MPS is the Standard Power Regulator Unit. DET/MPS allows a minute-by-minute simulation of the power system's performance as it responds to various orbital parameters, focusing its output on solar array output and battery characteristics. While this package is limited in terms of orbital mechanics, it is sufficient to calculate eclipse and solar array data for circular or non-circular orbits. DET/MPS can be adjusted to run one or sequential orbits up to about one week, simulated time. These programs have been used on a variety of Goddard Space Flight Center spacecraft projects. DET/MPS is written in FORTRAN 77 with some VAX-type extensions. Any FORTRAN 77 compiler that includes VAX extensions should be able to compile and run the program with little or no modifications. The compiler must at least support free-form (or tab-delineated) source format and 'do do-while end-do' control structures. DET/MPS is available for three platforms: GSC-13374, for DEC VAX series computers running VMS, is available in DEC VAX Backup format on a 9-track 1600 BPI tape (standard distribution) or TK50 tape cartridge; GSC-13443, for UNIX-based computers, is available on a .25 inch streaming magnetic tape cartridge in UNIX tar format; and GSC-13444, for Macintosh computers running AU/X with either the NKR FORTRAN or AbSoft MacFORTRAN II compilers, is available on a 3.5 inch 800K Macintosh format diskette. Source code and test data are supplied. The UNIX version of DET requires 90K of main memory for execution. DET/MPS was developed in 1990. A/UX and Macintosh are registered trademarks of Apple Computer, Inc. VMS, DEC VAX and TK50 are trademarks of Digital Equipment Corporation. UNIX is a registered trademark of AT&T Bell Laboratories.

PrionScan: an online database of predicted prion domains in complete proteomes.

PubMed

Espinosa Angarica, Vladimir; Angulo, Alfonso; Giner, Arturo; Losilla, Guillermo; Ventura, Salvador; Sancho, Javier

2014-02-05

Prions are a particular type of amyloids related to a large variety of important processes in cells, but also responsible for serious diseases in mammals and humans. The number of experimentally characterized prions is still low and corresponds to a handful of examples in microorganisms and mammals. Prion aggregation is mediated by specific protein domains with a remarkable compositional bias towards glutamine/asparagine and against charged residues and prolines. These compositional features have been used to predict new prion proteins in the genomes of different organisms. Despite these efforts, there are only a few available data sources containing prion predictions at a genomic scale. Here we present PrionScan, a new database of predicted prion-like domains in complete proteomes. We have previously developed a predictive methodology to identify and score prionogenic stretches in protein sequences. In the present work, we exploit this approach to scan all the protein sequences in public databases and compile a repository containing relevant information of proteins bearing prion-like domains. The database is updated regularly alongside UniprotKB and in its present version contains approximately 28000 predictions in proteins from different functional categories in more than 3200 organisms from all the taxonomic subdivisions. PrionScan can be used in two different ways: database query and analysis of protein sequences submitted by the users. In the first mode, simple queries allow to retrieve a detailed description of the properties of a defined protein. Queries can also be combined to generate more complex and specific searching patterns. In the second mode, users can submit and analyze their own sequences. It is expected that this database would provide relevant insights on prion functions and regulation from a genome-wide perspective, allowing researches performing cross-species prion biology studies. Our database might also be useful for guiding experimentalists in the identification of new candidates for further experimental characterization.

Computer assisted data analysis in intensive care: the ICDEV project--development of a scientific database system for intensive care (Intensive Care Data Evaluation Project).

PubMed

Metnitz, P G; Laback, P; Popow, C; Laback, O; Lenz, K; Hiesmayr, M

1995-01-01

Patient Data Management Systems (PDMS) for ICUs collect, present and store clinical data. Various intentions make analysis of those digitally stored data desirable, such as quality control or scientific purposes. The aim of the Intensive Care Data Evaluation project (ICDEV), was to provide a database tool for the analysis of data recorded at various ICUs at the University Clinics of Vienna. General Hospital of Vienna, with two different PDMSs used: CareVue 9000 (Hewlett Packard, Andover, USA) at two ICUs (one medical ICU and one neonatal ICU) and PICIS Chart+ (PICIS, Paris, France) at one Cardiothoracic ICU. CONCEPT AND METHODS: Clinically oriented analysis of the data collected in a PDMS at an ICU was the beginning of the development. After defining the database structure we established a client-server based database system under Microsoft Windows NI and developed a user friendly data quering application using Microsoft Visual C++ and Visual Basic; ICDEV was successfully installed at three different ICUs, adjustment to the different PDMS configurations were done within a few days. The database structure developed by us enables a powerful query concept representing an 'EXPERT QUESTION COMPILER' which may help to answer almost any clinical questions. Several program modules facilitate queries at the patient, group and unit level. Results from ICDEV-queries are automatically transferred to Microsoft Excel for display (in form of configurable tables and graphs) and further processing. The ICDEV concept is configurable for adjustment to different intensive care information systems and can be used to support computerized quality control. However, as long as there exists no sufficient artifact recognition or data validation software for automatically recorded patient data, the reliability of these data and their usage for computer assisted quality control remain unclear and should be further studied.

User's Manual for the New England Water-Use Data System (NEWUDS)

USGS Publications Warehouse

Horn, Marilee A.

2003-01-01

Water is used in a variety of ways that need to be understood for effective management of water resources. Water-use activities need to be categorized and included in a database management system to understand current water uses and to provide information to water-resource management policy decisionmakers. The New England Water-Use Data System (NEWUDS) is a complex database developed to store water-use information that allows water to be tracked from a point of water-use activity (called a 'Site'), such as withdrawal from a resource (reservoir or aquifer), to a second Site, such as distribution to a user (business or irrigator). NEWUDS conceptual model consists of 10 core entities: system, owner, address, location, site, data source, resource, conveyance, transaction/rate, and alias, with tables available to store user-defined details. Three components--site (with both a From Site and a To Site), a conveyance that connects them, and a transaction/rate associated with the movement of water over a specific time interval form the core of the basic NEWUDS network model. The most important step in correctly translating real-world water-use activities into a storable format in NEWUDS depends on choosing the appropriate sites and linking them correctly in a network to model the flow of water from the initial From Site to the final To Site. Ten water-use networks representing real-world activities are described--three withdrawal networks, three return networks, two user networks, two complex community-system networks. Ten case studies of water use, one for each network, also are included in this manual to illustrate how to compile, store, and retrieve the appropriate data. The sequence of data entry into tables is critical because there are many foreign keys. The recommended core entity sequence is (1) system, (2) owner, (3) address, (4) location, (5) site, (6) data source, (7) resource, (8) conveyance, (9) transaction, and (10) rate; with (11) alias and (12) user-defined detail subject areas populated as needed. After each step in data entry, quality-assurance queries should be run to ensure the data are correctly entered so that it can be retrieved accurately. The point of data storage is retrieval. Several retrieval queries that focus on retrieving only relevant data to specific questions are presented in this manual as examples for the NEWUDS user.

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.

Solving the challenges of data preprocessing, uploading, archiving, retrieval, analysis and visualization for large heterogeneous paleo- and rock magnetic datasets

NASA Astrophysics Data System (ADS)

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

2011-12-01

The Magnetics Information Consortium (MagIC) provides an archive for the wealth of rock- and paleomagnetic data and interpretations from studies on natural and synthetic samples. As with many fields, most peer-reviewed paleo- and rock magnetic publications only include high level results. However, access to the raw data from which these results were derived is critical for compilation studies and when updating results based on new interpretation and analysis methods. MagIC provides a detailed metadata model with places for everything from raw measurements to their interpretations. Prior to MagIC, these raw data were extremely cumbersome to collect because they mostly existed in a lab's proprietary format on investigator's personal computers or undigitized in field notebooks. MagIC has developed a suite of offline and online tools to enable the paleomagnetic, rock magnetic, and affiliated scientific communities to easily contribute both their previously published data and data supporting an article undergoing peer-review, to retrieve well-annotated published interpretations and raw data, and to analyze and visualize large collections of published data online. Here we present the technology we chose (including VBA in Excel spreadsheets, Python libraries, FastCGI JSON webservices, Oracle procedures, and jQuery user interfaces) and how we implemented it in order to serve the scientific community as seamlessly as possible. These tools are now in use in labs worldwide, have helped archive many valuable legacy studies and datasets, and routinely enable new contributions to the MagIC Database (http://earthref.org/MAGIC/).

Contaminant exposure and effects--terrestrial vertebrates database: Trends and data gaps for Atlantic Coast estuaries

USGS Publications Warehouse

Rattner, B.A.; Pearson, J.L.; Golden, N.H.; Cohen, J.B.; Erwin, R.M.; Ottinger, M.A.

2000-01-01

In order to examine the condition of biota in Atlantic coast estuaries, a ?Contaminant Exposure and Effects--Terrestrial Vertebrates? database (CEE-TV) has been compiled through computerized search of published literature, review of existing databases, and solicitation of unpublished reports from conservation agencies, private groups, and universities. Summary information has been entered into the database, including species, collection date (1965-present), site coordinates, estuary name, hydrologic unit catalogue code, sample matrix, contaminant concentrations, biomarker and bioindicator responses, and reference source, utilizing a 98-field character and numeric format. Currently, the CEE-TV database contains 3699 georeferenced records representing 190 vertebrate species and >145,000 individuals residing in estuaries from Maine through Florida. This relational database can be directly queried, imported into a Geographic Information System to examine spatial patterns, identify data gaps and areas of concern, generate hypotheses, and focus ecotoxicological field assessments. Information on birds made up the vast majority (83%) of the database, with only a modicum of data on amphibians (75,000 chemical compounds in commerce, only 118 commonly measured environmental contaminants were quantified in tissues of terrestrial vertebrates. There were no CEE-TV data records in 15 of the 67 estuaries located along the Atlantic coast and Florida Gulf coast. The CEE-TV database has a number of potential applications including focusing biomonitoring efforts to generate critically needed ecotoxicological data in the numerous ?gaps? along the coast, reducing uncertainty about contaminant risk, identifying areas for mitigation, restoration or special management, and ranking ecological conditions of estuaries.

Compilation of fatigue, fatigue-crack propagation, and fracture data for 2024 and 7075 aluminum, Ti-6Al-4V titanium, and 300M steel. Volume 1: Description of data and data storage on magnetic tape. Volume 2: Data tape (7-track magnetic tape)

NASA Technical Reports Server (NTRS)

Rice, R. C.; Reynolds, J. L.

1976-01-01

Fatigue, fatigue-crack-propagation, and fracture data compiled and stored on magnetic tape are documented. Data for 202 and 7075 aluminum alloys, Ti-6Al-4V titanium alloy, and 300M steel are included in the compilation. Approximately 4,500 fatigue, 6,500 fatigue-crack-propagation, and 1,500 fracture data points are stored on magnetic tape. Descriptions of the data, an index to the data on the magnetic tape, information on data storage format on the tape, a listing of all data source references, and abstracts of other pertinent test information from each data source reference are included.

Space station needs, attributes and architectural options study. Volume 3: Requirements

NASA Technical Reports Server (NTRS)

1983-01-01

A typical system specification format is presented and requirements are compiled. A Program Specification Tree is shown showing a high inclination space station and a low inclination space station with their typical element breakdown, also represented along the top blocks are the interfaces with other systems. The specification format is directed at the Low Inclination space station.

A Dozen Primers on Important Information Standards

ERIC Educational Resources Information Center

Dempsey, Kathy, Comp.

2007-01-01

This is a compilation of 12 primers on important information standards and protocols. These primers are: (1) Atom; (2) COinS; (3) MADS; (4) MARC 21/MARCXML; (5) MIX; (6) MXG; (7) OpenSearch; (8) PREMIS; (9) RESTful HTTP; (10) unAPI; (11) XMPP (aka Jabber); and (12) ZeeRex. The Atom Syndication Format defines a new XML-based syndication format for…

Implementing and evaluating a regional strategy to improve testing rates in VA patients at risk for HIV, utilizing the QUERI process as a guiding framework: QUERI Series.

PubMed

Goetz, Matthew B; Bowman, Candice; Hoang, Tuyen; Anaya, Henry; Osborn, Teresa; Gifford, Allen L; Asch, Steven M

2008-03-19

We describe how we used the framework of the U.S. Department of Veterans Affairs (VA) Quality Enhancement Research Initiative (QUERI) to develop a program to improve rates of diagnostic testing for the Human Immunodeficiency Virus (HIV). This venture was prompted by the observation by the CDC that 25% of HIV-infected patients do not know their diagnosis - a point of substantial importance to the VA, which is the largest provider of HIV care in the United States. Following the QUERI steps (or process), we evaluated: 1) whether undiagnosed HIV infection is a high-risk, high-volume clinical issue within the VA, 2) whether there are evidence-based recommendations for HIV testing, 3) whether there are gaps in the performance of VA HIV testing, and 4) the barriers and facilitators to improving current practice in the VA.Based on our findings, we developed and initiated a QUERI step 4/phase 1 pilot project using the precepts of the Chronic Care Model. Our improvement strategy relies upon electronic clinical reminders to provide decision support; audit/feedback as a clinical information system, and appropriate changes in delivery system design. These activities are complemented by academic detailing and social marketing interventions to achieve provider activation. Our preliminary formative evaluation indicates the need to ensure leadership and team buy-in, address facility-specific barriers, refine the reminder, and address factors that contribute to inter-clinic variances in HIV testing rates. Preliminary unadjusted data from the first seven months of our program show 3-5 fold increases in the proportion of at-risk patients who are offered HIV testing at the VA sites (stations) where the pilot project has been undertaken; no change was seen at control stations. This project demonstrates the early success of the application of the QUERI process to the development of a program to improve HIV testing rates. Preliminary unadjusted results show that the coordinated use of audit/feedback, provider activation, and organizational change can increase HIV testing rates for at-risk patients. We are refining our program prior to extending our work to a small-scale, multi-site evaluation (QUERI step 4/phase 2). We also plan to evaluate the durability/sustainability of the intervention effect, the costs of HIV testing, and the number of newly identified HIV-infected patients. Ultimately, we will evaluate this program in other geographically dispersed stations (QUERI step 4/phases 3 and 4).

Implementing and evaluating a regional strategy to improve testing rates in VA patients at risk for HIV, utilizing the QUERI process as a guiding framework: QUERI Series

PubMed Central

Goetz, Matthew B; Bowman, Candice; Hoang, Tuyen; Anaya, Henry; Osborn, Teresa; Gifford, Allen L; Asch, Steven M

2008-01-01

Background We describe how we used the framework of the U.S. Department of Veterans Affairs (VA) Quality Enhancement Research Initiative (QUERI) to develop a program to improve rates of diagnostic testing for the Human Immunodeficiency Virus (HIV). This venture was prompted by the observation by the CDC that 25% of HIV-infected patients do not know their diagnosis – a point of substantial importance to the VA, which is the largest provider of HIV care in the United States. Methods Following the QUERI steps (or process), we evaluated: 1) whether undiagnosed HIV infection is a high-risk, high-volume clinical issue within the VA, 2) whether there are evidence-based recommendations for HIV testing, 3) whether there are gaps in the performance of VA HIV testing, and 4) the barriers and facilitators to improving current practice in the VA. Based on our findings, we developed and initiated a QUERI step 4/phase 1 pilot project using the precepts of the Chronic Care Model. Our improvement strategy relies upon electronic clinical reminders to provide decision support; audit/feedback as a clinical information system, and appropriate changes in delivery system design. These activities are complemented by academic detailing and social marketing interventions to achieve provider activation. Results Our preliminary formative evaluation indicates the need to ensure leadership and team buy-in, address facility-specific barriers, refine the reminder, and address factors that contribute to inter-clinic variances in HIV testing rates. Preliminary unadjusted data from the first seven months of our program show 3–5 fold increases in the proportion of at-risk patients who are offered HIV testing at the VA sites (stations) where the pilot project has been undertaken; no change was seen at control stations. Discussion This project demonstrates the early success of the application of the QUERI process to the development of a program to improve HIV testing rates. Preliminary unadjusted results show that the coordinated use of audit/feedback, provider activation, and organizational change can increase HIV testing rates for at-risk patients. We are refining our program prior to extending our work to a small-scale, multi-site evaluation (QUERI step 4/phase 2). We also plan to evaluate the durability/sustainability of the intervention effect, the costs of HIV testing, and the number of newly identified HIV-infected patients. Ultimately, we will evaluate this program in other geographically dispersed stations (QUERI step 4/phases 3 and 4). PMID:18353185

Spatial Databases for CalVO Volcanoes: Current Status and Future Directions

NASA Astrophysics Data System (ADS)

Ramsey, D. W.

2013-12-01

The U.S. Geological Survey (USGS) California Volcano Observatory (CalVO) aims to advance scientific understanding of volcanic processes and to lessen harmful impacts of volcanic activity in California and Nevada. Within CalVO's area of responsibility, ten volcanoes or volcanic centers have been identified by a national volcanic threat assessment in support of developing the U.S. National Volcano Early Warning System (NVEWS) as posing moderate, high, or very high threats to surrounding communities based on their recent eruptive histories and their proximity to vulnerable people, property, and infrastructure. To better understand the extent of potential hazards at these and other volcanoes and volcanic centers, the USGS Volcano Science Center (VSC) is continually compiling spatial databases of volcano information, including: geologic mapping, hazards assessment maps, locations of geochemical and geochronological samples, and the distribution of volcanic vents. This digital mapping effort has been ongoing for over 15 years and early databases are being converted to match recent datasets compiled with new data models designed for use in: 1) generating hazard zones, 2) evaluating risk to population and infrastructure, 3) numerical hazard modeling, and 4) display and query on the CalVO as well as other VSC and USGS websites. In these capacities, spatial databases of CalVO volcanoes and their derivative map products provide an integrated and readily accessible framework of VSC hazards science to colleagues, emergency managers, and the general public.

MIPS: a database for protein sequences, homology data and yeast genome information.

PubMed Central

Mewes, H W; Albermann, K; Heumann, K; Liebl, S; Pfeiffer, F

1997-01-01

The MIPS group (Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, collects, processes and distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence Database (,). MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Database. The database is distributed on CD-ROM together with PATCHX, an exhaustive supplement of unique, unverified protein sequences from external sources compiled by MIPS. Through its WWW server (http://www.mips.biochem.mpg.de/ ) MIPS permits internet access to sequence databases, homology data and to yeast genome information. (i) Sequence similarity results from the FASTA program () are stored in the FASTA database for all proteins from PIR-International and PATCHX. The database is dynamically maintained and permits instant access to FASTA results. (ii) Starting with FASTA database queries, proteins have been classified into families and superfamilies (PROT-FAM). (iii) The HPT (hashed position tree) data structure () developed at MIPS is a new approach for rapid sequence and pattern searching. (iv) MIPS provides access to the sequence and annotation of the complete yeast genome (), the functional classification of yeast genes (FunCat) and its graphical display, the 'Genome Browser' (). A CD-ROM based on the JAVA programming language providing dynamic interactive access to the yeast genome and the related protein sequences has been compiled and is available on request. PMID:9016498

MIRNA-DISTILLER: A Stand-Alone Application to Compile microRNA Data from Databases.

PubMed

Rieger, Jessica K; Bodan, Denis A; Zanger, Ulrich M

2011-01-01

MicroRNAs (miRNA) are small non-coding RNA molecules of ∼22 nucleotides which regulate large numbers of genes by binding to seed sequences at the 3'-untranslated region of target gene transcripts. The target mRNA is then usually degraded or translation is inhibited, although thus resulting in posttranscriptional down regulation of gene expression at the mRNA and/or protein level. Due to the bioinformatic difficulties in predicting functional miRNA binding sites, several publically available databases have been developed that predict miRNA binding sites based on different algorithms. The parallel use of different databases is currently indispensable, but highly uncomfortable and time consuming, especially when working with numerous genes of interest. We have therefore developed a new stand-alone program, termed MIRNA-DISTILLER, which allows to compile miRNA data for given target genes from public databases. Currently implemented are TargetScan, microCosm, and miRDB, which may be queried independently, pairwise, or together to calculate the respective intersections. Data are stored locally for application of further analysis tools including freely definable biological parameter filters, customized output-lists for both miRNAs and target genes, and various graphical facilities. The software, a data example file and a tutorial are freely available at http://www.ikp-stuttgart.de/content/language1/html/10415.asp.

MIRNA-DISTILLER: A Stand-Alone Application to Compile microRNA Data from Databases

PubMed Central

Rieger, Jessica K.; Bodan, Denis A.; Zanger, Ulrich M.

2011-01-01

MicroRNAs (miRNA) are small non-coding RNA molecules of ∼22 nucleotides which regulate large numbers of genes by binding to seed sequences at the 3′-untranslated region of target gene transcripts. The target mRNA is then usually degraded or translation is inhibited, although thus resulting in posttranscriptional down regulation of gene expression at the mRNA and/or protein level. Due to the bioinformatic difficulties in predicting functional miRNA binding sites, several publically available databases have been developed that predict miRNA binding sites based on different algorithms. The parallel use of different databases is currently indispensable, but highly uncomfortable and time consuming, especially when working with numerous genes of interest. We have therefore developed a new stand-alone program, termed MIRNA-DISTILLER, which allows to compile miRNA data for given target genes from public databases. Currently implemented are TargetScan, microCosm, and miRDB, which may be queried independently, pairwise, or together to calculate the respective intersections. Data are stored locally for application of further analysis tools including freely definable biological parameter filters, customized output-lists for both miRNAs and target genes, and various graphical facilities. The software, a data example file and a tutorial are freely available at http://www.ikp-stuttgart.de/content/language1/html/10415.asp PMID:22303335

Exploring U.S Cropland - A Web Service based Cropland Data Layer Visualization, Dissemination and Querying System (Invited)

NASA Astrophysics Data System (ADS)

Yang, Z.; Han, W.; di, L.

2010-12-01

The National Agricultural Statistics Service (NASS) of the USDA produces the Cropland Data Layer (CDL) product, which is a raster-formatted, geo-referenced, U.S. crop specific land cover classification. These digital data layers are widely used for a variety of applications by universities, research institutions, government agencies, and private industry in climate change studies, environmental ecosystem studies, bioenergy production & transportation planning, environmental health research and agricultural production decision making. The CDL is also used internally by NASS for crop acreage and yield estimation. Like most geospatial data products, the CDL product is only available by CD/DVD delivery or online bulk file downloading via the National Research Conservation Research (NRCS) Geospatial Data Gateway (external users) or in a printed paper map format. There is no online geospatial information access and dissemination, no crop visualization & browsing, no geospatial query capability, nor online analytics. To facilitate the application of this data layer and to help disseminating the data, a web-service based CDL interactive map visualization, dissemination, querying system is proposed. It uses Web service based service oriented architecture, adopts open standard geospatial information science technology and OGC specifications and standards, and re-uses functions/algorithms from GeoBrain Technology (George Mason University developed). This system provides capabilities of on-line geospatial crop information access, query and on-line analytics via interactive maps. It disseminates all data to the decision makers and users via real time retrieval, processing and publishing over the web through standards-based geospatial web services. A CDL region of interest can also be exported directly to Google Earth for mashup or downloaded for use with other desktop application. This web service based system greatly improves equal-accessibility, interoperability, usability, and data visualization, facilitates crop geospatial information usage, and enables US cropland online exploring capability without any client-side software installation. It also greatly reduces the need for paper map and analysis report printing and media usages, and thus enhances low-carbon Agro-geoinformation dissemination for decision support.

EPA QUICK REFERENCE GUIDES

EPA Science Inventory

EPA Quick Reference Guides are compilations of information on chemical and biological terrorist agents. The information is presented in consistent format and includes agent characteristics, release scenarios, health and safety data, real-time field detection, effect levels, samp...

Protecting personal data in epidemiological research: DataSHIELD and UK law.

PubMed

Wallace, Susan E; Gaye, Amadou; Shoush, Osama; Burton, Paul R

2014-01-01

Data from individual collections, such as biobanks and cohort studies, are now being shared in order to create combined datasets which can be queried to ask complex scientific questions. But this sharing must be done with due regard for data protection principles. DataSHIELD is a new technology that queries nonaggregated, individual-level data in situ but returns query data in an anonymous format. This raises questions of the ability of DataSHIELD to adequately protect participant confidentiality. An ethico-legal analysis was conducted that examined each step of the DataSHIELD process from the perspective of UK case law, regulations, and guidance. DataSHIELD reaches agreed UK standards of protection for the sharing of biomedical data. All direct processing of personal data is conducted within the protected environment of the contributing study; participating studies have scientific, ethics, and data access approvals in place prior to the analysis; studies are clear that their consents conform with this use of data, and participants are informed that anonymisation for further disclosure will take place. DataSHIELD can provide a flexible means of interrogating data while protecting the participants' confidentiality in accordance with applicable legislation and guidance. © 2014 S. Karger AG, Basel.

New Software for Ensemble Creation in the Spitzer-Space-Telescope Operations Database

NASA Technical Reports Server (NTRS)

Laher, Russ; Rector, John

2004-01-01

Some of the computer pipelines used to process digital astronomical images from NASA's Spitzer Space Telescope require multiple input images, in order to generate high-level science and calibration products. The images are grouped into ensembles according to well documented ensemble-creation rules by making explicit associations in the operations Informix database at the Spitzer Science Center (SSC). The advantage of this approach is that a simple database query can retrieve the required ensemble of pipeline input images. New and improved software for ensemble creation has been developed. The new software is much faster than the existing software because it uses pre-compiled database stored-procedures written in Informix SPL (SQL programming language). The new software is also more flexible because the ensemble creation rules are now stored in and read from newly defined database tables. This table-driven approach was implemented so that ensemble rules can be inserted, updated, or deleted without modifying software.

Modeling and Synthesis Support for the North American Carbon Program

NASA Astrophysics Data System (ADS)

Baskaran, L.; Cook, R. B.; Thornton, P. E.; Post, W. M.; Wilson, B. E.; Dadi, U.

2007-12-01

The Modeling and Synthesis Thematic Data Center (MAST-DC) supports the North American Carbon Program by providing data products and data management services needed for modeling and synthesis activities. The overall objective of MAST-DC is to provide advanced data management support to NACP investigators doing modeling and synthesis, thereby freeing those investigators from having to perform data management functions. MAST-DC has compiled a number of data products for North America, including sub-pixel land-water content, daily meteorological data, and soil, land cover, and elevation data. In addition, we have developed an internet-based WebGIS system that enables users to browse, query, display, subset, and download spatial data using a standard web browser. For the mid-continent intensive, MAST-DC is working with a group of data assimilation modelers to generate a consistent set of meteorological data to drive bottom-up models.

VizieR Online Data Catalog: Bright white dwarfs IRAC photometry (Barber+, 2016)

NASA Astrophysics Data System (ADS)

Barber, S. D.; Belardi, C.; Kilic, M.; Gianninas, A.

2017-07-01

Mid-infrared photometry, like the 3.4 and 4.6um photometry available from WISE, is necessary to detect emission from a debris disc orbiting a WD. WISE, however, has poor spatial resolution (6 arcsec beam size) and is known to have a 75 per cent false positive rate for detecting dusty discs around WDs fainter than 14.5(15) mag in W1(W2) (Barber et al. (2014ApJ...786...77B). To mitigate this high rate of spurious detections, we compile higher spatial resolution archival data from the InfraRed Array Camera (IRAC) on the Spitzer Space Telescope. We query the Spitzer Heritage Archive for any observations within 10 arcsec of the 1265 WDs from Gianninas et al. (2011, Cat. J/ApJ/743/138) and find 907 Astronomical Observing Requests (AORs) for 381 WDs. (1 data file).

System and method for anomaly detection

DOEpatents

Scherrer, Chad

2010-06-15

A system and method for detecting one or more anomalies in a plurality of observations is provided. In one illustrative embodiment, the observations are real-time network observations collected from a stream of network traffic. The method includes performing a discrete decomposition of the observations, and introducing derived variables to increase storage and query efficiencies. A mathematical model, such as a conditional independence model, is then generated from the formatted data. The formatted data is also used to construct frequency tables which maintain an accurate count of specific variable occurrence as indicated by the model generation process. The formatted data is then applied to the mathematical model to generate scored data. The scored data is then analyzed to detect anomalies.

Applying Analogical Reasoning Techniques for Teaching XML Document Querying Skills in Database Classes

ERIC Educational Resources Information Center

Mitri, Michel

2012-01-01

XML has become the most ubiquitous format for exchange of data between applications running on the Internet. Most Web Services provide their information to clients in the form of XML. The ability to process complex XML documents in order to extract relevant information is becoming as important a skill for IS students to master as querying…

Beyond Failure: Potentially Mitigating Failed Author Searches in the Online Library Catalog through the Use of Linked Data

ERIC Educational Resources Information Center

Moulaison, Heather Lea; Stanley, Susan Nicole

2013-01-01

Linked data stores house vetted content that can supplement the information available through online library catalogs, potentially mitigating failed author searches if information about the author exists in linked data formats. In this case study, a total of 689 failed author index queries from a large Midwestern academic library's online library…

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

PubMed

Bolleman, Jerven T; Mungall, Christopher J; Strozzi, Francesco; Baran, Joachim; Dumontier, Michel; Bonnal, Raoul J P; Buels, Robert; Hoehndorf, Robert; Fujisawa, Takatomo; Katayama, Toshiaki; Cock, Peter J A

2016-06-13

Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned "omics" areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Our ontology allows users to uniformly describe - and potentially merge - sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.

ProtaBank: A repository for protein design and engineering data.

PubMed

Wang, Connie Y; Chang, Paul M; Ary, Marie L; Allen, Benjamin D; Chica, Roberto A; Mayo, Stephen L; Olafson, Barry D

2018-03-25

We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user-friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Querying Semi-Structured Data

NASA Technical Reports Server (NTRS)

Abiteboul, Serge

1997-01-01

The amount of data of all kinds available electronically has increased dramatically in recent years. The data resides in different forms, ranging from unstructured data in the systems to highly structured in relational database systems. Data is accessible through a variety of interfaces including Web browsers, database query languages, application-specic interfaces, or data exchange formats. Some of this data is raw data, e.g., images or sound. Some of it has structure even if the structure is often implicit, and not as rigid or regular as that found in standard database systems. Sometimes the structure exists but has to be extracted from the data. Sometimes also it exists but we prefer to ignore it for certain purposes such as browsing. We call here semi-structured data this data that is (from a particular viewpoint) neither raw data nor strictly typed, i.e., not table-oriented as in a relational model or sorted-graph as in object databases. As will seen later when the notion of semi-structured data is more precisely de ned, the need for semi-structured data arises naturally in the context of data integration, even when the data sources are themselves well-structured. Although data integration is an old topic, the need to integrate a wider variety of data- formats (e.g., SGML or ASN.1 data) and data found on the Web has brought the topic of semi-structured data to the forefront of research. The main purpose of the paper is to isolate the essential aspects of semi- structured data. We also survey some proposals of models and query languages for semi-structured data. In particular, we consider recent works at Stanford U. and U. Penn on semi-structured data. In both cases, the motivation is found in the integration of heterogeneous data.

A program for the conversion of The National Map data from proprietary format to resource description framework (RDF)

USGS Publications Warehouse

Bulen, Andrew; Carter, Jonathan J.; Varanka, Dalia E.

2011-01-01

To expand data functionality and capabilities for users of The National Map of the U.S. Geological Survey, data sets for six watersheds and three urban areas were converted from the Best Practices vector data model formats to Semantic Web data formats. This report describes and documents the conver-sion process. The report begins with an introduction to basic Semantic Web standards and the background of The National Map. Data were converted from a proprietary format to Geog-raphy Markup Language to capture the geometric footprint of topographic data features. Configuration files were designed to eliminate redundancy and make the conversion more efficient. A SPARQL endpoint was established for data validation and queries. The report concludes by describing the results of the conversion.

Some aspects of modeling hydrocarbon oxidation

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

Gal, D.; Botar, L.; Danoczy, E.

1981-01-01

A modeling procedure for the study of hydrocarbon oxidation is suggested, and its effectiveness for the oxidation of ethylbenzene is demonstrated. As a first step in modeling, systematization involves compilation of possible mechanisms. Then, by introduction of the concept of kinetic communication, the chaotic set of possible mechanisms is systematized into a network. Experimentation serves both as feedback to the systematic arrangement of information and source of new information. Kinetic treatment of the possible mechanism has been accomplished by two different approaches: by classical inductive calculations starting with a small mechanism and using kinetic approximations, and by computer simulation. Themore » authors have compiled a so-called Main Contributory Mechanism, involving processes - within the possible mechanism - which contribute basically to the formation and consumption of the intermediates, to the consumption of the starting compounds and to the formation of the end products. 24 refs.« less

National coal resource assessment non-proprietary data: Location, stratigraphy, and coal quality for selected tertiary coal in the Northern Rocky Mountains and Great Plains region

USGS Publications Warehouse

Flores, Romeo M.; Ochs, A.M.; Stricker, G.D.; Ellis, M.S.; Roberts, S.B.; Keighin, C.W.; Murphy, E.C.; Cavaroc, V.V.; Johnson, R.C.; Wilde, E.M.

1999-01-01

One of the objectives of the National Coal Resource Assessment in the Northern Rocky Mountains and Great Plains region was to compile stratigraphic and coal quality-trace-element data on selected and potentially minable coal beds and zones of the Fort Union Formation (Paleocene) and equivalent formations. In order to implement this objective, drill-hole information was compiled from hard-copy and digital files of the: (1) U.S. Bureau of Land Management (BLM) offices in Casper, Rawlins, and Rock Springs, Wyoming, and in Billings, Montana, (2) State geological surveys of Montana, North Dakota, and Wyoming, (3) Wyoming Department of Environmental Quality in Cheyenne, (4) U.S. Office of Surface Mining in Denver, Colorado, (5) U.S. Geological Survey, National Coal Resource Data System (NCRDS) in Reston, Virginia, (6) U.S. Geological Survey coal publications, (7) university theses, and (8) mining companies.

Ground Operations Aerospace Language (GOAL). Volume 4: Interpretive code translator

NASA Technical Reports Server (NTRS)

1973-01-01

This specification identifies and describes the principal functions and elements of the Interpretive Code Translator which has been developed for use with the GOAL Compiler. This translator enables the user to convert a compliled GOAL program to a highly general binary format which is designed to enable interpretive execution. The translator program provides user controls which are designed to enable the selection of various output types and formats. These controls provide a means for accommodating many of the implementation options which are discussed in the Interpretive Code Guideline document. The technical design approach is given. The relationship between the translator and the GOAL compiler is explained and the principal functions performed by the Translator are described. Specific constraints regarding the use of the Translator are discussed. The control options are described. These options enable the user to select outputs to be generated by the translator and to control vrious aspects of the translation processing.

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature

PubMed Central

McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry BF; Tipton, Keith F

2007-01-01

Background We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. Description The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at . The data are available for download as SQL and XML files via FTP. Conclusion ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List. PMID:17662133

RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources.

PubMed

Anguita, Alberto; Martin, Luis; Garcia-Remesal, Miguel; Maojo, Victor

2013-07-01

This paper presents RDFBuilder, a tool that enables RDF-based access to MAGE-ML-compliant microarray databases. We have developed a system that automatically transforms the MAGE-OM model and microarray data stored in the ArrayExpress database into RDF format. Additionally, the system automatically enables a SPARQL endpoint. This allows users to execute SPARQL queries for retrieving microarray data, either from specific experiments or from more than one experiment at a time. Our system optimizes response times by caching and reusing information from previous queries. In this paper, we describe our methods for achieving this transformation. We show that our approach is complementary to other existing initiatives, such as Bio2RDF, for accessing and retrieving data from the ArrayExpress database. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature.

PubMed

McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry B F; Tipton, Keith F

2007-07-27

We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at http://www.enzyme-database.org. The data are available for download as SQL and XML files via FTP. ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List.

linkedISA: semantic representation of ISA-Tab experimental metadata.

PubMed

González-Beltrán, Alejandra; Maguire, Eamonn; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2014-01-01

Reporting and sharing experimental metadata- such as the experimental design, characteristics of the samples, and procedures applied, along with the analysis results, in a standardised manner ensures that datasets are comprehensible and, in principle, reproducible, comparable and reusable. Furthermore, sharing datasets in formats designed for consumption by humans and machines will also maximize their use. The Investigation/Study/Assay (ISA) open source metadata tracking framework facilitates standards-compliant collection, curation, visualization, storage and sharing of datasets, leveraging on other platforms to enable analysis and publication. The ISA software suite includes several components used in increasingly diverse set of life science and biomedical domains; it is underpinned by a general-purpose format, ISA-Tab, and conversions exist into formats required by public repositories. While ISA-Tab works well mainly as a human readable format, we have also implemented a linked data approach to semantically define the ISA-Tab syntax. We present a semantic web representation of the ISA-Tab syntax that complements ISA-Tab's syntactic interoperability with semantic interoperability. We introduce the linkedISA conversion tool from ISA-Tab to the Resource Description Framework (RDF), supporting mappings from the ISA syntax to multiple community-defined, open ontologies and capitalising on user-provided ontology annotations in the experimental metadata. We describe insights of the implementation and how annotations can be expanded driven by the metadata. We applied the conversion tool as part of Bio-GraphIIn, a web-based application supporting integration of the semantically-rich experimental descriptions. Designed in a user-friendly manner, the Bio-GraphIIn interface hides most of the complexities to the users, exposing a familiar tabular view of the experimental description to allow seamless interaction with the RDF representation, and visualising descriptors to drive the query over the semantic representation of the experimental design. In addition, we defined queries over the linkedISA RDF representation and demonstrated its use over the linkedISA conversion of datasets from Nature' Scientific Data online publication. Our linked data approach has allowed us to: 1) make the ISA-Tab semantics explicit and machine-processable, 2) exploit the existing ontology-based annotations in the ISA-Tab experimental descriptions, 3) augment the ISA-Tab syntax with new descriptive elements, 4) visualise and query elements related to the experimental design. Reasoning over ISA-Tab metadata and associated data will facilitate data integration and knowledge discovery.

Room-temperature storage of medications labeled for refrigeration.

PubMed

Cohen, Victor; Jellinek, Samantha P; Teperikidis, Leftherios; Berkovits, Elliot; Goldman, William M

2007-08-15

Data regarding the recommended maximum duration that refrigerated medications available in hospital pharmacies may be stored safely at room temperature were collected and compiled in a tabular format. During May and June of 2006, the prescribing information for medications labeled for refrigeration as obtained from the supplier were reviewed for data addressing room-temperature storage. Telephone surveys of the products' manufacturers were conducted when this information was not available in the prescribing information. Medications were included in the review if they were labeled to be stored at 2-8 degrees C and purchased by the pharmacy department for uses indicated on the hospital formulary. Frozen antibiotics thawed in the refrigerator and extemporaneously compounded medications were excluded. Information was compiled and arranged in tabular format. The U.S. Pharmacopeia's definition of room temperature (20-25 degrees C [68-77 degrees F]) was used for this review. Of the 189 medications listed in AHFS Drug Information 2006 for storage in a refrigerator, 89 were present in the pharmacy department's refrigerator. Since six manufacturers were unable to provide information for 10 medications, only 79 medications were included in the review. This table may help to avoid unnecessary drug loss and expenditures due to improper storage temperatures. Information regarding the room-temperature storage of 79 medications labeled for refrigerated storage was compiled.

Web Services and Other Enhancements at the Northern California Earthquake Data Center

NASA Astrophysics Data System (ADS)

Neuhauser, D. S.; Zuzlewski, S.; Allen, R. M.

2012-12-01

The Northern California Earthquake Data Center (NCEDC) provides data archive and distribution services for seismological and geophysical data sets that encompass northern California. The NCEDC is enhancing its ability to deliver rapid information through Web Services. NCEDC Web Services use well-established web server and client protocols and REST software architecture to allow users to easily make queries using web browsers or simple program interfaces and to receive the requested data in real-time rather than through batch or email-based requests. Data are returned to the user in the appropriate format such as XML, RESP, or MiniSEED depending on the service, and are compatible with the equivalent IRIS DMC web services. The NCEDC is currently providing the following Web Services: (1) Station inventory and channel response information delivered in StationXML format, (2) Channel response information delivered in RESP format, (3) Time series availability delivered in text and XML formats, (4) Single channel and bulk data request delivered in MiniSEED format. The NCEDC is also developing a rich Earthquake Catalog Web Service to allow users to query earthquake catalogs based on selection parameters such as time, location or geographic region, magnitude, depth, azimuthal gap, and rms. It will return (in QuakeML format) user-specified results that can include simple earthquake parameters, as well as observations such as phase arrivals, codas, amplitudes, and computed parameters such as first motion mechanisms, moment tensors, and rupture length. The NCEDC will work with both IRIS and the International Federation of Digital Seismograph Networks (FDSN) to define a uniform set of web service specifications that can be implemented by multiple data centers to provide users with a common data interface across data centers. The NCEDC now hosts earthquake catalogs and waveforms from the US Department of Energy (DOE) Enhanced Geothermal Systems (EGS) monitoring networks. These data can be accessed through the above web services and through special NCEDC web pages.

Albemarle County/City of Charlottesville transportation planning compact disc.

DOT National Transportation Integrated Search

1998-06-01

This report describes transportation planning data, available in numerous files and formats stored on the accompanying compact disc, that were compiled from planning studies for the Charlottesville/Albemarle area done in 1967, 1979, and 1990. These d...

Cyberspace and Real-World Behavioral Relationships: Towards the Applications of Interest Search Queries to Identify Individuals At-Risk for Suicide

DTIC Science & Technology

2012-06-14

weight fat loss effects diet standard nutrition lose nfpa protein Topic 214: menu restaurant engineering restaurants jones wings seat wild buffalo...Selection ................................................................................... 30 3.5 Raw Data File Format...text mining to descriptions of biological activity and the target of the biological activity (i.e., gene, protein , cell, or microorganism) to predict

Salient Feature Selection Using Feed-Forward Neural Networks and Signal-to-Noise Ratios with a Focus Toward Network Threat Detection and Classification

DTIC Science & Technology

2014-03-27

0.8.0. The virtual machine’s network adapter was set to internal network only to keep any outside traffic from interfering. A MySQL -based query...primary output of Fullstats is the ARFF file format, intended for use with the WEKA Java -based data mining software developed at the University of Waikato

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

PubMed

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

2012-01-01

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

Distributed health data networks: a practical and preferred approach to multi-institutional evaluations of comparative effectiveness, safety, and quality of care.

PubMed

Brown, Jeffrey S; Holmes, John H; Shah, Kiran; Hall, Ken; Lazarus, Ross; Platt, Richard

2010-06-01

Comparative effectiveness research, medical product safety evaluation, and quality measurement will require the ability to use electronic health data held by multiple organizations. There is no consensus about whether to create regional or national combined (eg, "all payer") databases for these purposes, or distributed data networks that leave most Protected Health Information and proprietary data in the possession of the original data holders. Demonstrate functions of a distributed research network that supports research needs and also address data holders concerns about participation. Key design functions included strong local control of data uses and a centralized web-based querying interface. We implemented a pilot distributed research network and evaluated the design considerations, utility for research, and the acceptability to data holders of methods for menu-driven querying. We developed and tested a central, web-based interface with supporting network software. Specific functions assessed include query formation and distribution, query execution and review, and aggregation of results. This pilot successfully evaluated temporal trends in medication use and diagnoses at 5 separate sites, demonstrating some of the possibilities of using a distributed research network. The pilot demonstrated the potential utility of the design, which addressed the major concerns of both users and data holders. No serious obstacles were identified that would prevent development of a fully functional, scalable network. Distributed networks are capable of addressing nearly all anticipated uses of routinely collected electronic healthcare data. Distributed networks would obviate the need for centralized databases, thus avoiding numerous obstacles.

SAM: String-based sequence search algorithm for mitochondrial DNA database queries

PubMed Central

Röck, Alexander; Irwin, Jodi; Dür, Arne; Parsons, Thomas; Parson, Walther

2011-01-01

The analysis of the haploid mitochondrial (mt) genome has numerous applications in forensic and population genetics, as well as in disease studies. Although mtDNA haplotypes are usually determined by sequencing, they are rarely reported as a nucleotide string. Traditionally they are presented in a difference-coded position-based format relative to the corrected version of the first sequenced mtDNA. This convention requires recommendations for standardized sequence alignment that is known to vary between scientific disciplines, even between laboratories. As a consequence, database searches that are vital for the interpretation of mtDNA data can suffer from biased results when query and database haplotypes are annotated differently. In the forensic context that would usually lead to underestimation of the absolute and relative frequencies. To address this issue we introduce SAM, a string-based search algorithm that converts query and database sequences to position-free nucleotide strings and thus eliminates the possibility that identical sequences will be missed in a database query. The mere application of a BLAST algorithm would not be a sufficient remedy as it uses a heuristic approach and does not address properties specific to mtDNA, such as phylogenetically stable but also rapidly evolving insertion and deletion events. The software presented here provides additional flexibility to incorporate phylogenetic data, site-specific mutation rates, and other biologically relevant information that would refine the interpretation of mitochondrial DNA data. The manuscript is accompanied by freeware and example data sets that can be used to evaluate the new software (http://stringvalidation.org). PMID:21056022

Suggested revisions to the annual highway safety work program in Virginia.

DOT National Transportation Integrated Search

1976-01-01

This paper describes some suggested revisions in the format of and method and procedures for compiling the Annual Highway Safety Work Program (AHSWP) required of the states by the National Highway Traffic Safety Administration (NHTSA). Prior to fisca...

Low impact development (LID) and transportation stormwater practices

DOT National Transportation Integrated Search

2010-12-01

The proposed project is a combination of a research/design/best practices compilation and ranking in the format of a : design decision tool that can be used by Region X transportation designers and other researchers with respect to : current, and fut...

Query Auto-Completion Based on Word2vec Semantic Similarity

NASA Astrophysics Data System (ADS)

Shao, Taihua; Chen, Honghui; Chen, Wanyu

2018-04-01

Query auto-completion (QAC) is the first step of information retrieval, which helps users formulate the entire query after inputting only a few prefixes. Regarding the models of QAC, the traditional method ignores the contribution from the semantic relevance between queries. However, similar queries always express extremely similar search intention. In this paper, we propose a hybrid model FS-QAC based on query semantic similarity as well as the query frequency. We choose word2vec method to measure the semantic similarity between intended queries and pre-submitted queries. By combining both features, our experiments show that FS-QAC model improves the performance when predicting the user’s query intention and helping formulate the right query. Our experimental results show that the optimal hybrid model contributes to a 7.54% improvement in terms of MRR against a state-of-the-art baseline using the public AOL query logs.

Inventory of Shale Formations in the US, Including Geologic, Hydrological, and Mechanical Characteristics

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

Dobson, Patrick; Houseworth, James

2013-11-22

The objective of this report is to build upon previous compilations of shale formations within many of the major sedimentary basins in the US by developing GIS data delineating isopach and structural depth maps for many of these units. These data are being incorporated into the LANL digital GIS database being developed for determining host rock distribution and depth/thickness parameters consistent with repository design. Methods were developed to assess hydrological and geomechanical properties and conditions for shale formations based on sonic velocity measurements.

Closing the loop: an interactive action-research conference format for delivering updated medical information while eliciting Latina patient/family experiences and psychosocial needs post-genetic cancer risk assessment.

PubMed

Macdonald, Deborah J; Deri, Julia; Ricker, Charité; Perez, Martin A; Ogaz, Raquel; Feldman, Nancy; Viveros, Lori A; Paz, Benjamin; Weitzel, Jeffrey N; Blazer, Kathleen R

2012-09-01

A patient/family-centered conference was conducted at an underserved community hospital to address Latinas' post-genetic cancer risk assessment (GCRA) medical information and psychosocial support needs, and determine the utility of the action research format. Latinas seen for GCRA were recruited to a half-day conference conducted in Spanish. Content was partly determined from follow-up survey feedback. Written surveys, interactive discussions, and Audience Response System (ARS) queries facilitated the participant-healthcare professional action research process. Analyses included descriptive statistics and thematic analysis. The 71 attendees (41 patients and 27 relatives/friends) were primarily non-US born Spanish-speaking females, mean age 43 years. Among patients, 73 % had a breast cancer history; 85 % had BRCA testing (49 % BRCA+). Nearly all (96 %) attendees completed the conference surveys and ARS queries; ≥48 % participated in interactive discussions. Most (95 %) agreed that the format met their personal interests and expectations and provided useful information and resources. Gaps/challenges identified in the GCRA process included pre-consult anxiety, uncertainty about reason for referral and expected outcomes, and psychosocial needs post-GCRA, such as absorbing and disseminating risk information to relatives and concurrently coping with a recent cancer diagnosis. The combined action research and educational conference format was innovative and effective for responding to continued patient information needs and addressing an important data gap about support needs of Latina patients and family members following genetic cancer risk assessment. Findings informed GCRA process improvements and provide a basis for theory-driven cancer control research.

EquiX-A Search and Query Language for XML.

ERIC Educational Resources Information Center

Cohen, Sara; Kanza, Yaron; Kogan, Yakov; Sagiv, Yehoshua; Nutt, Werner; Serebrenik, Alexander

2002-01-01

Describes EquiX, a search language for XML that combines querying with searching to query the data and the meta-data content of Web pages. Topics include search engines; a data model for XML documents; search query syntax; search query semantics; an algorithm for evaluating a query on a document; and indexing EquiX queries. (LRW)

Digital Geologic Map of the Rosalia 1:100,000 Quadrangle, Washington and Idaho: A Digital Database for the 1990 S.Z. Waggoner Map

USGS Publications Warehouse

Derkey, Pamela D.; Johnson, Bruce R.; Lackaff, Beatrice B.; Derkey, Robert E.

1998-01-01

The geologic map of the Rosalia 1:100,000-scale quadrangle was compiled in 1990 by S.Z. Waggoner of the Washington state Division of Geology and Earth Resources. This data was entered into a geographic information system (GIS) as part of a larger effort to create regional digital geology for the Pacific Northwest. The intent was to provide a digital geospatial database for a previously published black and white paper geologic map. This database can be queried in many ways to produce a variety of geologic maps. Digital base map data files are not included: they may be obtained from a variety of commercial and government sources. This database is not meant to be used or displayed at any scale larger than 1:100,000 (e.g., 1:62,500 or 1:24,000) as it has been somewhat generalized to fit the 1:100,000 scale map. The map area is located in eastern Washington and extends across the state border into western Idaho. This open-file report describes the methods used to convert the geologic map data into a digital format, documents the file structures, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet. We wish to thank J. Eric Schuster of the Washington Division of Geology and Earth Resources for providing the original stable-base mylar and the funding for it to be scanned. We also thank Dick Blank and Barry Moring of the U.S. Geological Survey for reviewing the manuscript and digital files, respectively.

SigReannot-mart: a query environment for expression microarray probe re-annotations.

PubMed

Moreews, François; Rauffet, Gaelle; Dehais, Patrice; Klopp, Christophe

2011-01-01

Expression microarrays are commonly used to study transcriptomes. Most of the arrays are now based on oligo-nucleotide probes. Probe design being a tedious task, it often takes place once at the beginning of the project. The oligo set is then used for several years. During this time period, the knowledge gathered by the community on the genome and the transcriptome increases and gets more precise. Therefore re-annotating the set is essential to supply the biologists with up-to-date annotations. SigReannot-mart is a query environment populated with regularly updated annotations for different oligo sets. It stores the results of the SigReannot pipeline that has mainly been used on farm and aquaculture species. It permits easy extraction in different formats using filters. It is used to compare probe sets on different criteria, to choose the set for a given experiment to mix probe sets in order to create a new one.

ImmunemiR - A Database of Prioritized Immune miRNA Disease Associations and its Interactome.

PubMed

Prabahar, Archana; Natarajan, Jeyakumar

2017-01-01

MicroRNAs are the key regulators of gene expression and their abnormal expression in the immune system may be associated with several human diseases such as inflammation, cancer and autoimmune diseases. Elucidation of miRNA disease association through the interactome will deepen the understanding of its disease mechanisms. A specialized database for immune miRNAs is highly desirable to demonstrate the immune miRNA disease associations in the interactome. miRNAs specific to immune related diseases were retrieved from curated databases such as HMDD, miR2disease and PubMed literature based on MeSH classification of immune system diseases. The additional data such as miRNA target genes, genes coding protein-protein interaction information were compiled from related resources. Further, miRNAs were prioritized to specific immune diseases using random walk ranking algorithm. In total 245 immune miRNAs associated with 92 OMIM disease categories were identified from external databases. The resultant data were compiled as ImmunemiR, a database of prioritized immune miRNA disease associations. This database provides both text based annotation information and network visualization of its interactome. To our knowledge, ImmunemiR is the first available database to provide a comprehensive repository of human immune disease associated miRNAs with network visualization options of its target genes, protein-protein interactions (PPI) and its disease associations. It is freely available at http://www.biominingbu.org/immunemir/. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

GenoQuery: a new querying module for functional annotation in a genomic warehouse

PubMed Central

Lemoine, Frédéric; Labedan, Bernard; Froidevaux, Christine

2008-01-01

Motivation: We have to cope with both a deluge of new genome sequences and a huge amount of data produced by high-throughput approaches used to exploit these genomic features. Crossing and comparing such heterogeneous and disparate data will help improving functional annotation of genomes. This requires designing elaborate integration systems such as warehouses for storing and querying these data. Results: We have designed a relational genomic warehouse with an original multi-layer architecture made of a databases layer and an entities layer. We describe a new querying module, GenoQuery, which is based on this architecture. We use the entities layer to define mixed queries. These mixed queries allow searching for instances of biological entities and their properties in the different databases, without specifying in which database they should be found. Accordingly, we further introduce the central notion of alternative queries. Such queries have the same meaning as the original mixed queries, while exploiting complementarities yielded by the various integrated databases of the warehouse. We explain how GenoQuery computes all the alternative queries of a given mixed query. We illustrate how useful this querying module is by means of a thorough example. Availability: http://www.lri.fr/~lemoine/GenoQuery/ Contact: chris@lri.fr, lemoine@lri.fr PMID:18586731

Sharing and executing linked data queries in a collaborative environment.

PubMed

García Godoy, María Jesús; López-Camacho, Esteban; Navas-Delgado, Ismael; Aldana-Montes, José F

2013-07-01

Life Sciences have emerged as a key domain in the Linked Data community because of the diversity of data semantics and formats available through a great variety of databases and web technologies. Thus, it has been used as the perfect domain for applications in the web of data. Unfortunately, bioinformaticians are not exploiting the full potential of this already available technology, and experts in Life Sciences have real problems to discover, understand and devise how to take advantage of these interlinked (integrated) data. In this article, we present Bioqueries, a wiki-based portal that is aimed at community building around biological Linked Data. This tool has been designed to aid bioinformaticians in developing SPARQL queries to access biological databases exposed as Linked Data, and also to help biologists gain a deeper insight into the potential use of this technology. This public space offers several services and a collaborative infrastructure to stimulate the consumption of biological Linked Data and, therefore, contribute to implementing the benefits of the web of data in this domain. Bioqueries currently contains 215 query entries grouped by database and theme, 230 registered users and 44 end points that contain biological Resource Description Framework information. The Bioqueries portal is freely accessible at http://bioqueries.uma.es. Supplementary data are available at Bioinformatics online.

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

PubMed Central

Sun, Shulei; Chen, Jing; Li, Weizhong; Altintas, Ilkay; Lin, Abel; Peltier, Steve; Stocks, Karen; Allen, Eric E.; Ellisman, Mark; Grethe, Jeffrey; Wooley, John

2011-01-01

The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data. PMID:21045053

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource.

PubMed

Sun, Shulei; Chen, Jing; Li, Weizhong; Altintas, Ilkay; Lin, Abel; Peltier, Steve; Stocks, Karen; Allen, Eric E; Ellisman, Mark; Grethe, Jeffrey; Wooley, John

2011-01-01

The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.

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

Critchlow, Terence J.; Abdulla, Ghaleb; Becla, Jacek

Data management is the organization of information to support efficient access and analysis. For data intensive computing applications, the speed at which relevant data can be accessed is a limiting factor in terms of the size and complexity of computation that can be performed. Data access speed is impacted by the size of the relevant subset of the data, the complexity of the query used to define it, and the layout of the data relative to the query. As the underlying data sets become increasingly complex, the questions asked of it become more involved as well. For example, geospatial datamore » associated with a city is no longer limited to the map data representing its streets, but now also includes layers identifying utility lines, key points, locations and types of businesses within the city limits, tax information for each land parcel, satellite imagery, and possibly even street-level views. As a result, queries have gone from simple questions, such as "how long is Main Street?", to much more complex questions such as "taking all other factors into consideration, are the property values of houses near parks higher than those under power lines, and if so, by what percentage". Answering these questions requires a coherent infrastructure, integrating the relevant data into a format optimized for the questions being asked.« less

EnsMart: A Generic System for Fast and Flexible Access to Biological Data

PubMed Central

Kasprzyk, Arek; Keefe, Damian; Smedley, Damian; London, Darin; Spooner, William; Melsopp, Craig; Hammond, Martin; Rocca-Serra, Philippe; Cox, Tony; Birney, Ewan

2004-01-01

The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to `non-Ensembl' data sets. PMID:14707178

SPARK: Adapting Keyword Query to Semantic Search

NASA Astrophysics Data System (ADS)

Zhou, Qi; Wang, Chong; Xiong, Miao; Wang, Haofen; Yu, Yong

Semantic search promises to provide more accurate result than present-day keyword search. However, progress with semantic search has been delayed due to the complexity of its query languages. In this paper, we explore a novel approach of adapting keywords to querying the semantic web: the approach automatically translates keyword queries into formal logic queries so that end users can use familiar keywords to perform semantic search. A prototype system named 'SPARK' has been implemented in light of this approach. Given a keyword query, SPARK outputs a ranked list of SPARQL queries as the translation result. The translation in SPARK consists of three major steps: term mapping, query graph construction and query ranking. Specifically, a probabilistic query ranking model is proposed to select the most likely SPARQL query. In the experiment, SPARK achieved an encouraging translation result.

Searching for rare diseases in PubMed: a blind comparison of Orphanet expert query and query based on terminological knowledge.

PubMed

Griffon, N; Schuers, M; Dhombres, F; Merabti, T; Kerdelhué, G; Rollin, L; Darmoni, S J

2016-08-02

Despite international initiatives like Orphanet, it remains difficult to find up-to-date information about rare diseases. The aim of this study is to propose an exhaustive set of queries for PubMed based on terminological knowledge and to evaluate it versus the queries based on expertise provided by the most frequently used resource in Europe: Orphanet. Four rare disease terminologies (MeSH, OMIM, HPO and HRDO) were manually mapped to each other permitting the automatic creation of expended terminological queries for rare diseases. For 30 rare diseases, 30 citations retrieved by Orphanet expert query and/or query based on terminological knowledge were assessed for relevance by two independent reviewers unaware of the query's origin. An adjudication procedure was used to resolve any discrepancy. Precision, relative recall and F-measure were all computed. For each Orphanet rare disease (n = 8982), there was a corresponding terminological query, in contrast with only 2284 queries provided by Orphanet. Only 553 citations were evaluated due to queries with 0 or only a few hits. There were no significant differences between the Orpha query and terminological query in terms of precision, respectively 0.61 vs 0.52 (p = 0.13). Nevertheless, terminological queries retrieved more citations more often than Orpha queries (0.57 vs. 0.33; p = 0.01). Interestingly, Orpha queries seemed to retrieve older citations than terminological queries (p < 0.0001). The terminological queries proposed in this study are now currently available for all rare diseases. They may be a useful tool for both precision or recall oriented literature search.

Improving materials and methods for installing inductive loop detectors : final report.

DOT National Transportation Integrated Search

1986-06-01

This report is the final report of this research project. It describes a compiling of materials utilized by various agencies for use in formation of inductive loop detectors. It further lists methods by which different agencies install materials in o...

An advanced web query interface for biological databases

PubMed Central

Latendresse, Mario; Karp, Peter D.

2010-01-01

Although most web-based biological databases (DBs) offer some type of web-based form to allow users to author DB queries, these query forms are quite restricted in the complexity of DB queries that they can formulate. They can typically query only one DB, and can query only a single type of object at a time (e.g. genes) with no possible interaction between the objects—that is, in SQL parlance, no joins are allowed between DB objects. Writing precise queries against biological DBs is usually left to a programmer skillful enough in complex DB query languages like SQL. We present a web interface for building precise queries for biological DBs that can construct much more precise queries than most web-based query forms, yet that is user friendly enough to be used by biologists. It supports queries containing multiple conditions, and connecting multiple object types without using the join concept, which is unintuitive to biologists. This interactive web interface is called the Structured Advanced Query Page (SAQP). Users interactively build up a wide range of query constructs. Interactive documentation within the SAQP describes the schema of the queried DBs. The SAQP is based on BioVelo, a query language based on list comprehension. The SAQP is part of the Pathway Tools software and is available as part of several bioinformatics web sites powered by Pathway Tools, including the BioCyc.org site that contains more than 500 Pathway/Genome DBs. PMID:20624715

BOREAS Elevation Contours over the NSA and SSA in ARC/INFO Generate Format

NASA Technical Reports Server (NTRS)

Knapp, David; Nickeson, Jaime; Hall, Forrest G. (Editor)

2000-01-01

This data set was prepared by BORIS Staff by reformatting the original data into the ARC/INFO Generate format. The original data were received in SIF at a scale of 1:50,000. BORIS staff could not find a format document or commercial software for reading SIF; the BOREAS HYD-08 team pro-vided some C source code that could read some of the SIF files. The data cover the BOREAS NSA and SSA. The original data were compiled from information available in the 1970s and 1980s. The data are available in ARC/INFO Generate format files.

Assessment of Electronic Government Information Products

DTIC Science & Technology

1999-03-30

Center for Environmental Info. & Statistics CM Consumer Handbook for Reducing Solid Waste CM Envirofacts Warehouse CM EPA Online Library System (OLS) CP...Hazardous Waste Site Query (CERCLIS Data) CM Surf Your Watershed CM Test Methods for Evaluating Solid Waste : Physical/Chemical Methods (SW-846) CM...SGML because they consider it "intelligent data" that can automatically generate other formats (e.g., web, BBS, Fax on Demand) through templates and

Integrated Substrate and Thin Film Design Methods

DTIC Science & Technology

1999-02-01

Proper Representation Once the required chemical databases had been converted to the Excel format, VBA macros were written to convert chemical...ternary systems databases were imported from MS Excel to MS Access to implement SQL queries. Further, this database was connected via an ODBC model, to the... VBA macro, corresponding to each of the elements A, B, and C, respectively. The B loop began with the next alphabetical choice of element symbols

A Methodology for Benchmarking Relational Database Machines,

DTIC Science & Technology

1984-01-01

user benchmarks is to compare the multiple users to the best-case performance The data for each query classification coll and the performance...called a benchmark. The term benchmark originates from the markers used by sur - veyors in establishing common reference points for their measure...formatted databases. In order to further simplify the problem, we restrict our study to those DBMs which support the relational model. A sur - vey

Revamping Spacecraft Operational Intelligence with Splunk

NASA Technical Reports Server (NTRS)

Hwang, Victor

2012-01-01

So what is Splunk? Instead of giving the technical details, which you can find online, I'll tell you what it did for me. Splunk slapped everything into one place, with one uniform format, and gave me the ability to forget about all these annoying details of where it is, how to parse it, and all that. Instead, I only need to interact with Splunk to find the data I need. This sounds simple and obvious, but it's surprising what you can do once you all of your data is indexed in one place. By having your data organized, querying becomes much easier. Let's say that I want to search telemetry for a sensor_name gtemp_1 h and to return all data that is at most five minutes old. And because Splunk can hook into a real ]time stream, this data will always be up-to-date. Extending the previous example, I can now aggregate all types of data into one view based in time. In this picture, I've got transaction logs, telemetry, and downlinked files all in one page, organized by time. Even though the raw data looks completely than this, I've defined interfaces that transform it into this uniform format. This gives me a more complete picture for the question what was the spacecraft doing at this particular time? And because querying data is simple, I can start with a big block of data and whiddle it down to what I need, rather than hunting around for the individual pieces of data that I need. When we have all the data we need, we can begin widdling down the data with Splunk's Unix-like search syntax. These three examples highlights my trial-and-error attempts to find large temperature changes. I begin by showing the first 5 temperatures, only to find that they're sorted chronologically, rather than from highest temperatures to lowest temperatures. The next line shows sorting temperatures by their values, but I find that that fs not really what I want either. I want to know the delta temperatures between readings. Looking through Splunk's user manual, I find the delta function, which lets me dynamically generate new information to use in my query. With that extra piece of information, I can now return only the telemetry readings where the temperature changed by at least 10. One other useful feature I'll mention is that all of these queries can be run through Splunk's API. So any scripting language you can think of can plug right in and make these queries. This gives us the ability to build a lot of new tools.

SPARQL Query Re-writing Using Partonomy Based Transformation Rules

NASA Astrophysics Data System (ADS)

Jain, Prateek; Yeh, Peter Z.; Verma, Kunal; Henson, Cory A.; Sheth, Amit P.

Often the information present in a spatial knowledge base is represented at a different level of granularity and abstraction than the query constraints. For querying ontology's containing spatial information, the precise relationships between spatial entities has to be specified in the basic graph pattern of SPARQL query which can result in long and complex queries. We present a novel approach to help users intuitively write SPARQL queries to query spatial data, rather than relying on knowledge of the ontology structure. Our framework re-writes queries, using transformation rules to exploit part-whole relations between geographical entities to address the mismatches between query constraints and knowledge base. Our experiments were performed on completely third party datasets and queries. Evaluations were performed on Geonames dataset using questions from National Geographic Bee serialized into SPARQL and British Administrative Geography Ontology using questions from a popular trivia website. These experiments demonstrate high precision in retrieval of results and ease in writing queries.

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

PubMed

Yokochi, Masashi; Kobayashi, Naohiro; Ulrich, Eldon L; Kinjo, Akira R; Iwata, Takeshi; Ioannidis, Yannis E; Livny, Miron; Markley, John L; Nakamura, Haruki; Kojima, Chojiro; Fujiwara, Toshimichi

2016-05-05

The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. Moreover, a SPARQL endpoint has been deployed. The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes. We have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data exchange across diverse information resources.

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

PubMed Central

2011-01-01

Background Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments. Description MeRy-B, the first platform for plant 1H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues. Conclusion MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php. PMID:21668943

Area racism and birth outcomes among Blacks in the United States.

PubMed

Chae, David H; Clouston, Sean; Martz, Connor D; Hatzenbuehler, Mark L; Cooper, Hannah L F; Turpin, Rodman; Stephens-Davidowitz, Seth; Kramer, Michael R

2018-02-01

There is increasing evidence that racism is a cause of poor health outcomes in the United States, including adverse birth outcomes among Blacks. However, research on the health consequences of racism has faced measurement challenges due to the more subtle nature of contemporary racism, which is not necessarily amenable to assessment through traditionally used survey methods. In this study, we circumvent some of these limitations by examining a previously developed Internet query-based proxy of area racism (Stephens-Davidowitz, 2014) in relation to preterm birth and low birthweight among Blacks. Area racism was measured in 196 designated market areas as the proportion of total Google searches conducted between 2004 and 2007 containing the "n-word." This measure was linked to county-level birth data among Blacks between 2005 and 2008, which were compiled by the National Center for Health Statistics; preterm birth and low birthweight were defined as <37 weeks gestation and <2500 g, respectively. After adjustment for maternal age, Census region, and county-level measures of urbanicity, percent of the Black population, education, and poverty, we found that each standard deviation increase in area racism was associated with relative increases of 5% in the prevalence of preterm birth and 5% in the prevalence of low birthweight among Blacks. Our study provides evidence for the utility of an Internet query-based measure as a proxy for racism at the area-level in epidemiologic studies, and is also suggestive of the role of racism in contributing to poor birth outcomes among Blacks. Copyright © 2017 Elsevier Ltd. All rights reserved.

In Silico target fishing: addressing a "Big Data" problem by ligand-based similarity rankings with data fusion.

PubMed

Liu, Xian; Xu, Yuan; Li, Shanshan; Wang, Yulan; Peng, Jianlong; Luo, Cheng; Luo, Xiaomin; Zheng, Mingyue; Chen, Kaixian; Jiang, Hualiang

2014-01-01

Ligand-based in silico target fishing can be used to identify the potential interacting target of bioactive ligands, which is useful for understanding the polypharmacology and safety profile of existing drugs. The underlying principle of the approach is that known bioactive ligands can be used as reference to predict the targets for a new compound. We tested a pipeline enabling large-scale target fishing and drug repositioning, based on simple fingerprint similarity rankings with data fusion. A large library containing 533 drug relevant targets with 179,807 active ligands was compiled, where each target was defined by its ligand set. For a given query molecule, its target profile is generated by similarity searching against the ligand sets assigned to each target, for which individual searches utilizing multiple reference structures are then fused into a single ranking list representing the potential target interaction profile of the query compound. The proposed approach was validated by 10-fold cross validation and two external tests using data from DrugBank and Therapeutic Target Database (TTD). The use of the approach was further demonstrated with some examples concerning the drug repositioning and drug side-effects prediction. The promising results suggest that the proposed method is useful for not only finding promiscuous drugs for their new usages, but also predicting some important toxic liabilities. With the rapid increasing volume and diversity of data concerning drug related targets and their ligands, the simple ligand-based target fishing approach would play an important role in assisting future drug design and discovery.

Development a computer codes to couple PWR-GALE output and PC-CREAM input

NASA Astrophysics Data System (ADS)

Kuntjoro, S.; Budi Setiawan, M.; Nursinta Adi, W.; Deswandri; Sunaryo, G. R.

2018-02-01

Radionuclide dispersion analysis is part of an important reactor safety analysis. From the analysis it can be obtained the amount of doses received by radiation workers and communities around nuclear reactor. The radionuclide dispersion analysis under normal operating conditions is carried out using the PC-CREAM code, and it requires input data such as source term and population distribution. Input data is derived from the output of another program that is PWR-GALE and written Population Distribution data in certain format. Compiling inputs for PC-CREAM programs manually requires high accuracy, as it involves large amounts of data in certain formats and often errors in compiling inputs manually. To minimize errors in input generation, than it is make coupling program for PWR-GALE and PC-CREAM programs and a program for writing population distribution according to the PC-CREAM input format. This work was conducted to create the coupling programming between PWR-GALE output and PC-CREAM input and programming to written population data in the required formats. Programming is done by using Python programming language which has advantages of multiplatform, object-oriented and interactive. The result of this work is software for coupling data of source term and written population distribution data. So that input to PC-CREAM program can be done easily and avoid formatting errors. Programming sourceterm coupling program PWR-GALE and PC-CREAM is completed, so that the creation of PC-CREAM inputs in souceterm and distribution data can be done easily and according to the desired format.

Applying Semantic Web Concepts to Support Net-Centric Warfare Using the Tactical Assessment Markup Language (TAML)

DTIC Science & Technology

2006-06-01

SPARQL SPARQL Protocol and RDF Query Language SQL Structured Query Language SUMO Suggested Upper Merged Ontology SW... Query optimization algorithms are implemented in the Pellet reasoner in order to ensure querying a knowledge base is efficient . These algorithms...memory as a treelike structure in order for the data to be queried . XML Query (XQuery) is the standard language used when querying XML

Implementation of Quantum Private Queries Using Nuclear Magnetic Resonance

NASA Astrophysics Data System (ADS)

Wang, Chuan; Hao, Liang; Zhao, Lian-Jie

2011-08-01

We present a modified protocol for the realization of a quantum private query process on a classical database. Using one-qubit query and CNOT operation, the query process can be realized in a two-mode database. In the query process, the data privacy is preserved as the sender would not reveal any information about the database besides her query information, and the database provider cannot retain any information about the query. We implement the quantum private query protocol in a nuclear magnetic resonance system. The density matrix of the memory registers are constructed.

A study of medical and health queries to web search engines.

PubMed

Spink, Amanda; Yang, Yin; Jansen, Jim; Nykanen, Pirrko; Lorence, Daniel P; Ozmutlu, Seda; Ozmutlu, H Cenk

2004-03-01

This paper reports findings from an analysis of medical or health queries to different web search engines. We report results: (i). comparing samples of 10000 web queries taken randomly from 1.2 million query logs from the AlltheWeb.com and Excite.com commercial web search engines in 2001 for medical or health queries, (ii). comparing the 2001 findings from Excite and AlltheWeb.com users with results from a previous analysis of medical and health related queries from the Excite Web search engine for 1997 and 1999, and (iii). medical or health advice-seeking queries beginning with the word 'should'. Findings suggest: (i). a small percentage of web queries are medical or health related, (ii). the top five categories of medical or health queries were: general health, weight issues, reproductive health and puberty, pregnancy/obstetrics, and human relationships, and (iii). over time, the medical and health queries may have declined as a proportion of all web queries, as the use of specialized medical/health websites and e-commerce-related queries has increased. Findings provide insights into medical and health-related web querying and suggests some implications for the use of the general web search engines when seeking medical/health information.

Monitoring Moving Queries inside a Safe Region

PubMed Central

Al-Khalidi, Haidar; Taniar, David; Alamri, Sultan

2014-01-01

With mobile moving range queries, there is a need to recalculate the relevant surrounding objects of interest whenever the query moves. Therefore, monitoring the moving query is very costly. The safe region is one method that has been proposed to minimise the communication and computation cost of continuously monitoring a moving range query. Inside the safe region the set of objects of interest to the query do not change; thus there is no need to update the query while it is inside its safe region. However, when the query leaves its safe region the mobile device has to reevaluate the query, necessitating communication with the server. Knowing when and where the mobile device will leave a safe region is widely known as a difficult problem. To solve this problem, we propose a novel method to monitor the position of the query over time using a linear function based on the direction of the query obtained by periodic monitoring of its position. Periodic monitoring ensures that the query is aware of its location all the time. This method reduces the costs associated with communications in client-server architecture. Computational results show that our method is successful in handling moving query patterns. PMID:24696652

RDF-GL: A SPARQL-Based Graphical Query Language for RDF

NASA Astrophysics Data System (ADS)

Hogenboom, Frederik; Milea, Viorel; Frasincar, Flavius; Kaymak, Uzay

This chapter presents RDF-GL, a graphical query language (GQL) for RDF. The GQL is based on the textual query language SPARQL and mainly focuses on SPARQL SELECT queries. The advantage of a GQL over textual query languages is that complexity is hidden through the use of graphical symbols. RDF-GL is supported by a Java-based editor, SPARQLinG, which is presented as well. The editor does not only allow for RDF-GL query creation, but also converts RDF-GL queries to SPARQL queries and is able to subsequently execute these. Experiments show that using the GQL in combination with the editor makes RDF querying more accessible for end users.

TRAVEL FORECASTER

NASA Technical Reports Server (NTRS)

Mauldin, L. E.

1994-01-01

Business travel planning within an organization is often a time-consuming task. Travel Forecaster is a menu-driven, easy-to-use program which plans, forecasts cost, and tracks actual vs. planned cost for business-related travel of a division or branch of an organization and compiles this information into a database to aid the travel planner. The program's ability to handle multiple trip entries makes it a valuable time-saving device. Travel Forecaster takes full advantage of relational data base properties so that information that remains constant, such as per diem rates and airline fares (which are unique for each city), needs entering only once. A typical entry would include selection with the mouse of the traveler's name and destination city from pop-up lists, and typed entries for number of travel days and purpose of the trip. Multiple persons can be selected from the pop-up lists and multiple trips are accommodated by entering the number of days by each appropriate month on the entry form. An estimated travel cost is not required of the user as it is calculated by a Fourth Dimension formula. With this information, the program can produce output of trips by month with subtotal and total cost for either organization or sub-entity of an organization; or produce outputs of trips by month with subtotal and total cost for international-only travel. It will also provide monthly and cumulative formats of planned vs. actual outputs in data or graph form. Travel Forecaster users can do custom queries to search and sort information in the database, and it can create custom reports with the user-friendly report generator. Travel Forecaster 1.1 is a database program for use with Fourth Dimension Runtime 2.1.1. It requires a Macintosh Plus running System 6.0.3 or later, 2Mb of RAM and a hard disk. The standard distribution medium for this package is one 3.5 inch 800K Macintosh format diskette. Travel Forecaster was developed in 1991. Macintosh is a registered trademark of Apple Computer, Inc. Fourth Dimension is a registered trademark of Acius, Inc.

HydroDesktop: An Open Source GIS-Based Platform for Hydrologic Data Discovery, Visualization, and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.; Kadlec, J.; Cao, Y.; Grover, D.; Horsburgh, J. S.; Whiteaker, T.; Goodall, J. L.; Valentine, D. W.

2010-12-01

A growing number of hydrologic information servers are being deployed by government agencies, university networks, and individual researchers using the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS). The CUAHSI HIS Project has developed a standard software stack, called HydroServer, for publishing hydrologic observations data. It includes the Observations Data Model (ODM) database and Water Data Service web services, which together enable publication of data on the Internet in a standard format called Water Markup Language (WaterML). Metadata describing available datasets hosted on these servers is compiled within a central metadata catalog called HIS Central at the San Diego Supercomputer Center and is searchable through a set of predefined web services based queries. Together, these servers and central catalog service comprise a federated HIS of a scale and comprehensiveness never previously available. This presentation will briefly review/introduce the CUAHSI HIS system with special focus on a new HIS software tool called "HydroDesktop" and the open source software development web portal, www.HydroDesktop.org, which supports community development and maintenance of the software. HydroDesktop is a client-side, desktop software application that acts as a search and discovery tool for exploring the distributed network of HydroServers, downloading specific data series, visualizing and summarizing data series and exporting these to formats needed for analysis by external software. HydroDesktop is based on the open source DotSpatial GIS developer toolkit which provides it with map-based data interaction and visualization, and a plug-in interface that can be used by third party developers and researchers to easily extend the software using Microsoft .NET programming languages. HydroDesktop plug-ins that are presently available or currently under development within the project and by third party collaborators include functions for data search and discovery, extensive graphing, data editing and export, HydroServer exploration, integration with the OpenMI workflow and modeling system, and an interface for data analysis through the R statistical package.

Is There Scientific Consensus on Acid Rain? -- Excerpts from Six Governmental Reports.

ERIC Educational Resources Information Center

Environmental Education Report and Newsletter, 1986

1986-01-01

Compiles a series of direct quotations from six governmental reports that reflect a scientific consensus on major aspects of acid deposition. Presents the statements in a question and answer format. Also reviews the sources, extent, and effects of acid rain. (ML)

The anomaly data base of screwworm information

NASA Technical Reports Server (NTRS)

Giddings, L. E.

1976-01-01

Standard statistical processing of anomaly data in the screwworm eradication data system is possible from data compiled on magnetic tapes with the Univac 1108 computer. The format and organization of the data in the data base, which is also available on dedicated disc storage, are described.

Perturbed Equations of Motion for Formation Flight Near the Sun-Earth L2 Point

NASA Technical Reports Server (NTRS)

Segerman, Alan M.; Zedd, Michael F.

2005-01-01

This Memorandum Report consists of a compilation of three individual reports, of increasing complexity, describing investigations of formation flight of spacecraft in the vicinity of the L2 Sun-Earth 1ibration point. The individual reports form the following parts of this compilation: - Introduction to the relative motion of spacecraft about the Sun-Earth L2 Point - Linear and quadratic modelling and solution of the relative motion - Modelling the Perturbations - Elliptical Earth Orbit, Lunar Gravity, Solar Radiation Pressure, Thrusters. The three parts are self-contained, with somewhat, varying notation and terminology. After fair1y significant literature searches: this new work (of Parts 2 and 3) is deemed to be unique because it describes the primary perturbations to the description of relative motion between nearby spacecraft. The effect of the elliptical motion of the Earth about the Sun was verified to be the dominant perturbation to the circular restricted three body problem. Contributions due to lunar gravity and solar radiation pressure are seen to have much smaller effect.

Cumulative query method for influenza surveillance using search engine data.

PubMed

Seo, Dong-Woo; Jo, Min-Woo; Sohn, Chang Hwan; Shin, Soo-Yong; Lee, JaeHo; Yu, Maengsoo; Kim, Won Young; Lim, Kyoung Soo; Lee, Sang-Il

2014-12-16

Internet search queries have become an important data source in syndromic surveillance system. However, there is currently no syndromic surveillance system using Internet search query data in South Korea. The objective of this study was to examine correlations between our cumulative query method and national influenza surveillance data. Our study was based on the local search engine, Daum (approximately 25% market share), and influenza-like illness (ILI) data from the Korea Centers for Disease Control and Prevention. A quota sampling survey was conducted with 200 participants to obtain popular queries. We divided the study period into two sets: Set 1 (the 2009/10 epidemiological year for development set 1 and 2010/11 for validation set 1) and Set 2 (2010/11 for development Set 2 and 2011/12 for validation Set 2). Pearson's correlation coefficients were calculated between the Daum data and the ILI data for the development set. We selected the combined queries for which the correlation coefficients were .7 or higher and listed them in descending order. Then, we created a cumulative query method n representing the number of cumulative combined queries in descending order of the correlation coefficient. In validation set 1, 13 cumulative query methods were applied, and 8 had higher correlation coefficients (min=.916, max=.943) than that of the highest single combined query. Further, 11 of 13 cumulative query methods had an r value of ≥.7, but 4 of 13 combined queries had an r value of ≥.7. In validation set 2, 8 of 15 cumulative query methods showed higher correlation coefficients (min=.975, max=.987) than that of the highest single combined query. All 15 cumulative query methods had an r value of ≥.7, but 6 of 15 combined queries had an r value of ≥.7. Cumulative query method showed relatively higher correlation with national influenza surveillance data than combined queries in the development and validation set.

MCR Container Tools

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

Haas, Nicholas Q; Gillen, Robert E; Karnowski, Thomas P

MathWorks' MATLAB is widely used in academia and industry for prototyping, data analysis, data processing, etc. Many users compile their programs using the MATLAB Compiler to run on workstations/computing clusters via the free MATLAB Compiler Runtime (MCR). The MCR facilitates the execution of code calling Application Programming Interfaces (API) functions from both base MATLAB and MATLAB toolboxes. In a Linux environment, a sizable number of third-party runtime dependencies (i.e. shared libraries) are necessary. Unfortunately, to the MTLAB community's knowledge, these dependencies are not documented, leaving system administrators and/or end-users to find/install the necessary libraries either as runtime errors resulting frommore » them missing or by inspecting the header information of Executable and Linkable Format (ELF) libraries of the MCR to determine which ones are missing from the system. To address various shortcomings, Docker Images based on Community Enterprise Operating System (CentOS) 7, a derivative of Redhat Enterprise Linux (RHEL) 7, containing recent (2015-2017) MCR releases and their dependencies were created. These images, along with a provided sample Docker Compose YAML Script, can be used to create a simulated computing cluster where MATLAB Compiler created binaries can be executed using a sample Slurm Workload Manager script.« less

Data Container Study for Handling array-based data using Hive, Spark, MongoDB, SciDB and Rasdaman

NASA Astrophysics Data System (ADS)

Xu, M.; Hu, F.; Yang, J.; Yu, M.; Yang, C. P.

2017-12-01

Geoscience communities have come up with various big data storage solutions, such as Rasdaman and Hive, to address the grand challenges for massive Earth observation data management and processing. To examine the readiness of current solutions in supporting big Earth observation, we propose to investigate and compare four popular data container solutions, including Rasdaman, Hive, Spark, SciDB and MongoDB. Using different types of spatial and non-spatial queries, datasets stored in common scientific data formats (e.g., NetCDF and HDF), and two applications (i.e. dust storm simulation data mining and MERRA data analytics), we systematically compare and evaluate the feature and performance of these four data containers in terms of data discover and access. The computing resources (e.g. CPU, memory, hard drive, network) consumed while performing various queries and operations are monitored and recorded for the performance evaluation. The initial results show that 1) the popular data container clusters are able to handle large volume of data, but their performances vary in different situations. Meanwhile, there is a trade-off between data preprocessing, disk saving, query-time saving, and resource consuming. 2) ClimateSpark, MongoDB and SciDB perform the best among all the containers in all the queries tests, and Hive performs the worst. 3) These studied data containers can be applied on other array-based datasets, such as high resolution remote sensing data and model simulation data. 4) Rasdaman clustering configuration is more complex than the others. A comprehensive report will detail the experimental results, and compare their pros and cons regarding system performance, ease of use, accessibility, scalability, compatibility, and flexibility.

ClimateSpark: An In-memory Distributed Computing Framework for Big Climate Data Analytics

NASA Astrophysics Data System (ADS)

Hu, F.; Yang, C. P.; Duffy, D.; Schnase, J. L.; Li, Z.

2016-12-01

Massive array-based climate data is being generated from global surveillance systems and model simulations. They are widely used to analyze the environment problems, such as climate changes, natural hazards, and public health. However, knowing the underlying information from these big climate datasets is challenging due to both data- and computing- intensive issues in data processing and analyzing. To tackle the challenges, this paper proposes ClimateSpark, an in-memory distributed computing framework to support big climate data processing. In ClimateSpark, the spatiotemporal index is developed to enable Apache Spark to treat the array-based climate data (e.g. netCDF4, HDF4) as native formats, which are stored in Hadoop Distributed File System (HDFS) without any preprocessing. Based on the index, the spatiotemporal query services are provided to retrieve dataset according to a defined geospatial and temporal bounding box. The data subsets will be read out, and a data partition strategy will be applied to equally split the queried data to each computing node, and store them in memory as climateRDDs for processing. By leveraging Spark SQL and User Defined Function (UDFs), the climate data analysis operations can be conducted by the intuitive SQL language. ClimateSpark is evaluated by two use cases using the NASA Modern-Era Retrospective Analysis for Research and Applications (MERRA) climate reanalysis dataset. One use case is to conduct the spatiotemporal query and visualize the subset results in animation; the other one is to compare different climate model outputs using Taylor-diagram service. Experimental results show that ClimateSpark can significantly accelerate data query and processing, and enable the complex analysis services served in the SQL-style fashion.

Evaluation of Graph Pattern Matching Workloads in Graph Analysis Systems

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

Hong, Seokyong; Lee, Sangkeun; Lim, Seung-Hwan

2016-01-01

Graph analysis has emerged as a powerful method for data scientists to represent, integrate, query, and explore heterogeneous data sources. As a result, graph data management and mining became a popular area of research, and led to the development of plethora of systems in recent years. Unfortunately, the number of emerging graph analysis systems and the wide range of applications, coupled with a lack of apples-to-apples comparisons, make it difficult to understand the trade-offs between different systems and the graph operations for which they are designed. A fair comparison of these systems is a challenging task for the following reasons:more » multiple data models, non-standardized serialization formats, various query interfaces to users, and diverse environments they operate in. To address these key challenges, in this paper we present a new benchmark suite by extending the Lehigh University Benchmark (LUBM) to cover the most common capabilities of various graph analysis systems. We provide the design process of the benchmark, which generalizes the workflow for data scientists to conduct the desired graph analysis on different graph analysis systems. Equipped with this extended benchmark suite, we present performance comparison for nine subgraph pattern retrieval operations over six graph analysis systems, namely NetworkX, Neo4j, Jena, Titan, GraphX, and uRiKA. Through the proposed benchmark suite, this study reveals both quantitative and qualitative findings in (1) implications in loading data into each system; (2) challenges in describing graph patterns for each query interface; and (3) different sensitivity of each system to query selectivity. We envision that this study will pave the road for: (i) data scientists to select the suitable graph analysis systems, and (ii) data management system designers to advance graph analysis systems.« less

A Query Integrator and Manager for the Query Web

PubMed Central

Brinkley, James F.; Detwiler, Landon T.

2012-01-01

We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written in whatever language is appropriate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontology view generation using a combination of graph-based and logical approaches, value set generation for clinical data management, image annotation using terminology obtained from an ontology web service, ontology-driven brain imaging data integration, small-scale clinical data integration, and wider-scale clinical data integration. Such use cases illustrate the current range of applications of QI and lead us to speculate about the potential evolution from smaller groups of interconnected queries into a larger query network that layers over the document and semantic web. The resulting Query Web could greatly aid researchers and others who now have to manually navigate through multiple information sources in order to answer specific questions. PMID:22531831

Using Generalized Annotated Programs to Solve Social Network Diffusion Optimization Problems

DTIC Science & Technology

2013-01-01

as follows: —Let kall be the k value for the SNDOP-ALL query and for each SNDOP query i, let ki be the k for that query. For each query i, set ki... kall − 1. —Number each element of vi ∈ V such that gI(vi) and V C(vi) are true. For the ith SNDOP query, let vi be the corresponding element of V —Let...vertices of S. PROOF. We set up |V | SNDOP-queries as follows: —Let kall be the k value for the SNDOP-ALL query and and for each SNDOP-query i, let ki be

Basic Measures of Progress.

ERIC Educational Resources Information Center

Calkins, Julia; Ling, Thomson; Moore, Eric; Halle, Tamara; Hair, Beth; Moore, Kris; Zaslow, Marty

This document provides a compilation of measures of progress toward school readiness and three contributing conditions as used in several local, state, and national surveys. The report begins with a legend listing the surveys examined, their acronyms, and contact information. The remainder of the report, in tabular format, lists measures of…

ENVIRONMENTAL PROBLEM SOLVING WITH GEOGRAPHIC INFORMATION SYSTEMS: 1994 AND 1999 CONFERENCE PROCEEDINGS

EPA Science Inventory

These two national conferences, held in Cincinnati, Ohio in 1994 and 1999, addressed the area of environmental problem solving with Geographic Information Systems. This CD-ROM is a compilation of the proceedings in PDF format. The emphasis of the conference presentations were on ...

Asbestos in Schools. EPA Bibliographic Series.

ERIC Educational Resources Information Center

Environmental Protection Agency, Washington, DC. Library Information Management and Services Div.

This bibliography was compiled as a response to the requests for information on asbestos in schools. The citations are organized by format and include: (1) Environmental Protection Agency (EPA) reports (annotated); (2) books; (3) articles, proceedings and other reports (annotated); and (4) federal regulations and statutes (annotated). The…

Lab Streaming Layer Enabled Myo Data Collection Software User Manual

DTIC Science & Technology

2017-06-07

time - series data over a local network. LSL handles the networking, time -synchronization, (near-) real- time access as well as, optionally, the... series data collection (e.g., brain activity, heart activity, muscle activity) using the LSL application programming interface (API). Time -synchronized...saved to a single extensible data format (XDF) file. Once the time - series data are collected in a Lab Recorder XDF file, users will be able to query

Baseline and Multimodal UAV GCS Interface Design

DTIC Science & Technology

2011-12-01

information queries). 2 Calhoun et al. (2004) Different musical chords and intervals. Priority level of a late-arriving UAV. 4 Graham and...tactors (the lower levels ones especially) would be on for much longer durations as the UAV’s attitude upset increases. 2.2.2.7.2 Uni- centred Circles...in uni- centred circles. Figure 2.12: Tactor formation for the uni- centred circles of tactors. In this type of display, the tactors which are

Rapid Prototyping of Application Specific Signal Processors Program

DTIC Science & Technology

1992-10-09

EREQ Query optimizer generator from the University of Colorado. In the five year time frame , this trend toward convergence makes it a non- issue ...related issues . TI’s RASSP vision plans to leverage and support CALS as a baseline for addressing data formatting and handling. Previously stated CALS goals ...of the U.S. Gc;:zrnrenL Distibution Statement A. Approved for public release; distribution is unlimited. Prepared By: _-- Texas Instruments Integrated

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.

PubMed

Rideout, Jai Ram; Chase, John H; Bolyen, Evan; Ackermann, Gail; González, Antonio; Knight, Rob; Caporaso, J Gregory

2016-06-13

Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians. As a result, many research groups are shifting toward using cloud-based spreadsheet programs, such as Google Sheets, which support the concurrent editing of a single spreadsheet by different users working on different platforms. Most of the researchers who enter data are not familiar with the formatting requirements of the bioinformatics programs that will be used, so validating and correcting file formats is often a bottleneck prior to beginning bioinformatics analysis. We present Keemei, a Google Sheets Add-on, for validating tabular files used in bioinformatics analyses. Keemei is available free of charge from Google's Chrome Web Store. Keemei can be installed and run on any web browser supported by Google Sheets. Keemei currently supports the validation of two widely used tabular bioinformatics formats, the Quantitative Insights into Microbial Ecology (QIIME) sample metadata mapping file format and the Spatially Referenced Genetic Data (SRGD) format, but is designed to easily support the addition of others. Keemei will save researchers time and frustration by providing a convenient interface for tabular bioinformatics file format validation. By allowing everyone involved with data entry for a project to easily validate their data, it will reduce the validation and formatting bottlenecks that are commonly encountered when human-generated data files are first used with a bioinformatics system. Simplifying the validation of essential tabular data files, such as sample metadata, will reduce common errors and thereby improve the quality and reliability of research outcomes.

Comparative Analysis of Online Health Queries Originating From Personal Computers and Smart Devices on a Consumer Health Information Portal

PubMed Central

Jadhav, Ashutosh; Andrews, Donna; Fiksdal, Alexander; Kumbamu, Ashok; McCormick, Jennifer B; Misitano, Andrew; Nelsen, Laurie; Ryu, Euijung; Sheth, Amit; Wu, Stephen

2014-01-01

Background The number of people using the Internet and mobile/smart devices for health information seeking is increasing rapidly. Although the user experience for online health information seeking varies with the device used, for example, smart devices (SDs) like smartphones/tablets versus personal computers (PCs) like desktops/laptops, very few studies have investigated how online health information seeking behavior (OHISB) may differ by device. Objective The objective of this study is to examine differences in OHISB between PCs and SDs through a comparative analysis of large-scale health search queries submitted through Web search engines from both types of devices. Methods Using the Web analytics tool, IBM NetInsight OnDemand, and based on the type of devices used (PCs or SDs), we obtained the most frequent health search queries between June 2011 and May 2013 that were submitted on Web search engines and directed users to the Mayo Clinic’s consumer health information website. We performed analyses on “Queries with considering repetition counts (QwR)” and “Queries without considering repetition counts (QwoR)”. The dataset contains (1) 2.74 million and 3.94 million QwoR, respectively for PCs and SDs, and (2) more than 100 million QwR for both PCs and SDs. We analyzed structural properties of the queries (length of the search queries, usage of query operators and special characters in health queries), types of search queries (keyword-based, wh-questions, yes/no questions), categorization of the queries based on health categories and information mentioned in the queries (gender, age-groups, temporal references), misspellings in the health queries, and the linguistic structure of the health queries. Results Query strings used for health information searching via PCs and SDs differ by almost 50%. The most searched health categories are “Symptoms” (1 in 3 search queries), “Causes”, and “Treatments & Drugs”. The distribution of search queries for different health categories differs with the device used for the search. Health queries tend to be longer and more specific than general search queries. Health queries from SDs are longer and have slightly fewer spelling mistakes than those from PCs. Users specify words related to women and children more often than that of men and any other age group. Most of the health queries are formulated using keywords; the second-most common are wh- and yes/no questions. Users ask more health questions using SDs than PCs. Almost all health queries have at least one noun and health queries from SDs are more descriptive than those from PCs. Conclusions This study is a large-scale comparative analysis of health search queries to understand the effects of device type (PCs vs SDs) used on OHISB. The study indicates that the device used for online health information search plays an important role in shaping how health information searches by consumers and patients are executed. PMID:25000537

Comparative analysis of online health queries originating from personal computers and smart devices on a consumer health information portal.

PubMed

Jadhav, Ashutosh; Andrews, Donna; Fiksdal, Alexander; Kumbamu, Ashok; McCormick, Jennifer B; Misitano, Andrew; Nelsen, Laurie; Ryu, Euijung; Sheth, Amit; Wu, Stephen; Pathak, Jyotishman

2014-07-04

The number of people using the Internet and mobile/smart devices for health information seeking is increasing rapidly. Although the user experience for online health information seeking varies with the device used, for example, smart devices (SDs) like smartphones/tablets versus personal computers (PCs) like desktops/laptops, very few studies have investigated how online health information seeking behavior (OHISB) may differ by device. The objective of this study is to examine differences in OHISB between PCs and SDs through a comparative analysis of large-scale health search queries submitted through Web search engines from both types of devices. Using the Web analytics tool, IBM NetInsight OnDemand, and based on the type of devices used (PCs or SDs), we obtained the most frequent health search queries between June 2011 and May 2013 that were submitted on Web search engines and directed users to the Mayo Clinic's consumer health information website. We performed analyses on "Queries with considering repetition counts (QwR)" and "Queries without considering repetition counts (QwoR)". The dataset contains (1) 2.74 million and 3.94 million QwoR, respectively for PCs and SDs, and (2) more than 100 million QwR for both PCs and SDs. We analyzed structural properties of the queries (length of the search queries, usage of query operators and special characters in health queries), types of search queries (keyword-based, wh-questions, yes/no questions), categorization of the queries based on health categories and information mentioned in the queries (gender, age-groups, temporal references), misspellings in the health queries, and the linguistic structure of the health queries. Query strings used for health information searching via PCs and SDs differ by almost 50%. The most searched health categories are "Symptoms" (1 in 3 search queries), "Causes", and "Treatments & Drugs". The distribution of search queries for different health categories differs with the device used for the search. Health queries tend to be longer and more specific than general search queries. Health queries from SDs are longer and have slightly fewer spelling mistakes than those from PCs. Users specify words related to women and children more often than that of men and any other age group. Most of the health queries are formulated using keywords; the second-most common are wh- and yes/no questions. Users ask more health questions using SDs than PCs. Almost all health queries have at least one noun and health queries from SDs are more descriptive than those from PCs. This study is a large-scale comparative analysis of health search queries to understand the effects of device type (PCs vs. SDs) used on OHISB. The study indicates that the device used for online health information search plays an important role in shaping how health information searches by consumers and patients are executed.

PAPARA(ZZ)I: An open-source software interface for annotating photographs of the deep-sea

NASA Astrophysics Data System (ADS)

Marcon, Yann; Purser, Autun

PAPARA(ZZ)I is a lightweight and intuitive image annotation program developed for the study of benthic megafauna. It offers functionalities such as free, grid and random point annotation. Annotations may be made following existing classification schemes for marine biota and substrata or with the use of user defined, customised lists of keywords, which broadens the range of potential application of the software to other types of studies (e.g. marine litter distribution assessment). If Internet access is available, PAPARA(ZZ)I can also query and use standardised taxa names directly from the World Register of Marine Species (WoRMS). Program outputs include abundances, densities and size calculations per keyword (e.g. per taxon). These results are written into text files that can be imported into spreadsheet programs for further analyses. PAPARA(ZZ)I is open-source and is available at http://papara-zz-i.github.io. Compiled versions exist for most 64-bit operating systems: Windows, Mac OS X and Linux.

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.

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

USGS Publications Warehouse

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

2008-01-01

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

XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data

PubMed Central

Schweppe, Devin K.; Zheng, Chunxiang; Chavez, Juan D.; Navare, Arti T.; Wu, Xia; Eng, Jimmy K.; Bruce, James E.

2016-01-01

Motivation: Large-scale chemical cross-linking with mass spectrometry (XL-MS) analyses are quickly becoming a powerful means for high-throughput determination of protein structural information and protein–protein interactions. Recent studies have garnered thousands of cross-linked interactions, yet the field lacks an effective tool to compile experimental data or access the network and structural knowledge for these large scale analyses. We present XLinkDB 2.0 which integrates tools for network analysis, Protein Databank queries, modeling of predicted protein structures and modeling of docked protein structures. The novel, integrated approach of XLinkDB 2.0 enables the holistic analysis of XL-MS protein interaction data without limitation to the cross-linker or analytical system used for the analysis. Availability and Implementation: XLinkDB 2.0 can be found here, including documentation and help: http://xlinkdb.gs.washington.edu/. Contact: jimbruce@uw.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153666

SkyQuery - A Prototype Distributed Query and Cross-Matching Web Service for the Virtual Observatory

NASA Astrophysics Data System (ADS)

Thakar, A. R.; Budavari, T.; Malik, T.; Szalay, A. S.; Fekete, G.; Nieto-Santisteban, M.; Haridas, V.; Gray, J.

2002-12-01

We have developed a prototype distributed query and cross-matching service for the VO community, called SkyQuery, which is implemented with hierarchichal Web Services. SkyQuery enables astronomers to run combined queries on existing distributed heterogeneous astronomy archives. SkyQuery provides a simple, user-friendly interface to run distributed queries over the federation of registered astronomical archives in the VO. The SkyQuery client connects to the portal Web Service, which farms the query out to the individual archives, which are also Web Services called SkyNodes. The cross-matching algorithm is run recursively on each SkyNode. Each archive is a relational DBMS with a HTM index for fast spatial lookups. The results of the distributed query are returned as an XML DataSet that is automatically rendered by the client. SkyQuery also returns the image cutout corresponding to the query result. SkyQuery finds not only matches between the various catalogs, but also dropouts - objects that exist in some of the catalogs but not in others. This is often as important as finding matches. We demonstrate the utility of SkyQuery with a brown-dwarf search between SDSS and 2MASS, and a search for radio-quiet quasars in SDSS, 2MASS and FIRST. The importance of a service like SkyQuery for the worldwide astronomical community cannot be overstated: data on the same objects in various archives is mapped in different wavelength ranges and looks very different due to different errors, instrument sensitivities and other peculiarities of each archive. Our cross-matching algorithm preforms a fuzzy spatial join across multiple catalogs. This type of cross-matching is currently often done by eye, one object at a time. A static cross-identification table for a set of archives would become obsolete by the time it was built - the exponential growth of astronomical data means that a dynamic cross-identification mechanism like SkyQuery is the only viable option. SkyQuery was funded by a grant from the NASA AISR program.

The Localized Discovery and Recovery for Query Packet Losses in Wireless Sensor Networks with Distributed Detector Clusters

PubMed Central

Teng, Rui; Leibnitz, Kenji; Miura, Ryu

2013-01-01

An essential application of wireless sensor networks is to successfully respond to user queries. Query packet losses occur in the query dissemination due to wireless communication problems such as interference, multipath fading, packet collisions, etc. The losses of query messages at sensor nodes result in the failure of sensor nodes reporting the requested data. Hence, the reliable and successful dissemination of query messages to sensor nodes is a non-trivial problem. The target of this paper is to enable highly successful query delivery to sensor nodes by localized and energy-efficient discovery, and recovery of query losses. We adopt local and collective cooperation among sensor nodes to increase the success rate of distributed discoveries and recoveries. To enable the scalability in the operations of discoveries and recoveries, we employ a distributed name resolution mechanism at each sensor node to allow sensor nodes to self-detect the correlated queries and query losses, and then efficiently locally respond to the query losses. We prove that the collective discovery of query losses has a high impact on the success of query dissemination and reveal that scalability can be achieved by using the proposed approach. We further study the novel features of the cooperation and competition in the collective recovery at PHY and MAC layers, and show that the appropriate number of detectors can achieve optimal successful recovery rate. We evaluate the proposed approach with both mathematical analyses and computer simulations. The proposed approach enables a high rate of successful delivery of query messages and it results in short route lengths to recover from query losses. The proposed approach is scalable and operates in a fully distributed manner. PMID:23748172

Ontological Approach to Military Knowledge Modeling and Management

DTIC Science & Technology

2004-03-01

federated search mechanism has to reformulate user queries (expressed using the ontology) in the query languages of the different sources (e.g. SQL...ontologies as a common terminology – Unified query to perform federated search • Query processing – Ontology mapping to sources reformulate queries

Research on Extension of Sparql Ontology Query Language Considering the Computation of Indoor Spatial Relations

NASA Astrophysics Data System (ADS)

Li, C.; Zhu, X.; Guo, W.; Liu, Y.; Huang, H.

2015-05-01

A method suitable for indoor complex semantic query considering the computation of indoor spatial relations is provided According to the characteristics of indoor space. This paper designs ontology model describing the space related information of humans, events and Indoor space objects (e.g. Storey and Room) as well as their relations to meet the indoor semantic query. The ontology concepts are used in IndoorSPARQL query language which extends SPARQL syntax for representing and querying indoor space. And four types specific primitives for indoor query, "Adjacent", "Opposite", "Vertical" and "Contain", are defined as query functions in IndoorSPARQL used to support quantitative spatial computations. Also a method is proposed to analysis the query language. Finally this paper adopts this method to realize indoor semantic query on the study area through constructing the ontology model for the study building. The experimental results show that the method proposed in this paper can effectively support complex indoor space semantic query.

VISAGE: Interactive Visual Graph Querying.

PubMed

Pienta, Robert; Navathe, Shamkant; Tamersoy, Acar; Tong, Hanghang; Endert, Alex; Chau, Duen Horng

2016-06-01

Extracting useful patterns from large network datasets has become a fundamental challenge in many domains. We present VISAGE, an interactive visual graph querying approach that empowers users to construct expressive queries, without writing complex code (e.g., finding money laundering rings of bankers and business owners). Our contributions are as follows: (1) we introduce graph autocomplete , an interactive approach that guides users to construct and refine queries, preventing over-specification; (2) VISAGE guides the construction of graph queries using a data-driven approach, enabling users to specify queries with varying levels of specificity, from concrete and detailed (e.g., query by example), to abstract (e.g., with "wildcard" nodes of any types), to purely structural matching; (3) a twelve-participant, within-subject user study demonstrates VISAGE's ease of use and the ability to construct graph queries significantly faster than using a conventional query language; (4) VISAGE works on real graphs with over 468K edges, achieving sub-second response times for common queries.

VISAGE: Interactive Visual Graph Querying

PubMed Central

Pienta, Robert; Navathe, Shamkant; Tamersoy, Acar; Tong, Hanghang; Endert, Alex; Chau, Duen Horng

2017-01-01

Extracting useful patterns from large network datasets has become a fundamental challenge in many domains. We present VISAGE, an interactive visual graph querying approach that empowers users to construct expressive queries, without writing complex code (e.g., finding money laundering rings of bankers and business owners). Our contributions are as follows: (1) we introduce graph autocomplete, an interactive approach that guides users to construct and refine queries, preventing over-specification; (2) VISAGE guides the construction of graph queries using a data-driven approach, enabling users to specify queries with varying levels of specificity, from concrete and detailed (e.g., query by example), to abstract (e.g., with “wildcard” nodes of any types), to purely structural matching; (3) a twelve-participant, within-subject user study demonstrates VISAGE’s ease of use and the ability to construct graph queries significantly faster than using a conventional query language; (4) VISAGE works on real graphs with over 468K edges, achieving sub-second response times for common queries. PMID:28553670

The new Inventory of Italian Glaciers: Present knowledge, applied methods and preliminary results

NASA Astrophysics Data System (ADS)

Smiraglia, Claudio; Diolaiuti, Guglielmina; D'Agata, Carlo; Maragno, Davide; Baroni, Carlo; Mortara, Gianni; Perotti, Luigi; Bondesan, Aldino; Salvatore, Cristina; Vagliasindi, Marco; Vuillermoz, Elisa

2013-04-01

A new Glacier Inventory is an indispensable requirement in Italy due to the importance of evaluating the present glacier coverage and the recent changes driven by climate. Furthermore Alpine glaciers represent a not negligible water and touristic resource then to manage and promote them is needed to know their distribution, size and features. The first Italian Glacier Inventory dates back to 1959-1962. It was compiled by the Italian Glaciological Committee (CGI) in cooperation with the National Research Council (CNR); this first inventory was mainly based on field data coupled with photographs (acquired on the field) and high resolution maps. The Italian glaciation resulted to be spread into 754 ice bodies which altogether were covering 525 km2. Moreover in the Eighties a new inventory was compiled to insert Italian data into the World Glacier Inventory (WGI); aerial photos taken at the end of the Seventies (and in some cases affected by a high and not negligible snow coverage) were used as the main source of data. No other national inventory were compiled after that period. Nevertheless during the last decade the largest part of the Italian Alpine regions have produced regional and local glacier inventories which in several cases are also available and queried through web sites and web GIS application. The actual need is now to obtain a complete, homogeneous and contemporary picture of the Italian Glaciation which encompasses the already available regional and local data and all the new updated information coming from new sources of data (e.g.: orthophotos, satellite imagines, etc..). The challenge was accepted by the University of Milan, the EvK2CNR Committee and the Italian Glaciological Committee who, with the sponsorship of Levissima Spa, are presently working to compile the new updated Italian Glacier Inventory. The first project step is to produce a unique homogeneous glacier database including glacier boundary and surface area and the main fundamental glacier features (following the well-known guidelines of the World Glacier Monitoring Service summarized by Paul et al., 2010). The identification of the Italian glacier bodies and the evaluation of glacier area and main features are performed by analysing aerial orthophotos acquired in the time frame 2007-2012 (pixel size 0.5 m). Moreover the data base will be improved and updated also analysing regional data and by processing and analysing high resolution satellite imagines acquired on the last 2 years. In Lombardy the analysis of the 2007 orthophotos permitted to evaluate a glacier coverage of about 90 km2 of area. This value is about the 75% of the glacier surface area reported for Lombardy glaciers in the Italian Inventory compiled by CGI-CNR in the 1959-62.

Which factors predict the time spent answering queries to a drug information centre?

PubMed Central

Reppe, Linda A.; Spigset, Olav

2010-01-01

Objective To develop a model based upon factors able to predict the time spent answering drug-related queries to Norwegian drug information centres (DICs). Setting and method Drug-related queries received at 5 DICs in Norway from March to May 2007 were randomly assigned to 20 employees until each of them had answered a minimum of five queries. The employees reported the number of drugs involved, the type of literature search performed, and whether the queries were considered judgmental or not, using a specifically developed scoring system. Main outcome measures The scores of these three factors were added together to define a workload score for each query. Workload and its individual factors were subsequently related to the measured time spent answering the queries by simple or multiple linear regression analyses. Results Ninety-six query/answer pairs were analyzed. Workload significantly predicted the time spent answering the queries (adjusted R2 = 0.22, P < 0.001). Literature search was the individual factor best predicting the time spent answering the queries (adjusted R2 = 0.17, P < 0.001), and this variable also contributed the most in the multiple regression analyses. Conclusion The most important workload factor predicting the time spent handling the queries in this study was the type of literature search that had to be performed. The categorisation of queries as judgmental or not, also affected the time spent answering the queries. The number of drugs involved did not significantly influence the time spent answering drug information queries. PMID:20922480

Personalized query suggestion based on user behavior

NASA Astrophysics Data System (ADS)

Chen, Wanyu; Hao, Zepeng; Shao, Taihua; Chen, Honghui

Query suggestions help users refine their queries after they input an initial query. Previous work mainly concentrated on similarity-based and context-based query suggestion approaches. However, models that focus on adapting to a specific user (personalization) can help to improve the probability of the user being satisfied. In this paper, we propose a personalized query suggestion model based on users’ search behavior (UB model), where we inject relevance between queries and users’ search behavior into a basic probabilistic model. For the relevance between queries, we consider their semantical similarity and co-occurrence which indicates the behavior information from other users in web search. Regarding the current user’s preference to a query, we combine the user’s short-term and long-term search behavior in a linear fashion and deal with the data sparse problem with Bayesian probabilistic matrix factorization (BPMF). In particular, we also investigate the impact of different personalization strategies (the combination of the user’s short-term and long-term search behavior) on the performance of query suggestion reranking. We quantify the improvement of our proposed UB model against a state-of-the-art baseline using the public AOL query logs and show that it beats the baseline in terms of metrics used in query suggestion reranking. The experimental results show that: (i) for personalized ranking, users’ behavioral information helps to improve query suggestion effectiveness; and (ii) given a query, merging information inferred from the short-term and long-term search behavior of a particular user can result in a better performance than both plain approaches.

Hadoop-GIS: A High Performance Spatial Data Warehousing System over MapReduce.

PubMed

Aji, Ablimit; Wang, Fusheng; Vo, Hoang; Lee, Rubao; Liu, Qiaoling; Zhang, Xiaodong; Saltz, Joel

2013-08-01

Support of high performance queries on large volumes of spatial data becomes increasingly important in many application domains, including geospatial problems in numerous fields, location based services, and emerging scientific applications that are increasingly data- and compute-intensive. The emergence of massive scale spatial data is due to the proliferation of cost effective and ubiquitous positioning technologies, development of high resolution imaging technologies, and contribution from a large number of community users. There are two major challenges for managing and querying massive spatial data to support spatial queries: the explosion of spatial data, and the high computational complexity of spatial queries. In this paper, we present Hadoop-GIS - a scalable and high performance spatial data warehousing system for running large scale spatial queries on Hadoop. Hadoop-GIS supports multiple types of spatial queries on MapReduce through spatial partitioning, customizable spatial query engine RESQUE, implicit parallel spatial query execution on MapReduce, and effective methods for amending query results through handling boundary objects. Hadoop-GIS utilizes global partition indexing and customizable on demand local spatial indexing to achieve efficient query processing. Hadoop-GIS is integrated into Hive to support declarative spatial queries with an integrated architecture. Our experiments have demonstrated the high efficiency of Hadoop-GIS on query response and high scalability to run on commodity clusters. Our comparative experiments have showed that performance of Hadoop-GIS is on par with parallel SDBMS and outperforms SDBMS for compute-intensive queries. Hadoop-GIS is available as a set of library for processing spatial queries, and as an integrated software package in Hive.

Hadoop-GIS: A High Performance Spatial Data Warehousing System over MapReduce

PubMed Central

Aji, Ablimit; Wang, Fusheng; Vo, Hoang; Lee, Rubao; Liu, Qiaoling; Zhang, Xiaodong; Saltz, Joel

2013-01-01

Support of high performance queries on large volumes of spatial data becomes increasingly important in many application domains, including geospatial problems in numerous fields, location based services, and emerging scientific applications that are increasingly data- and compute-intensive. The emergence of massive scale spatial data is due to the proliferation of cost effective and ubiquitous positioning technologies, development of high resolution imaging technologies, and contribution from a large number of community users. There are two major challenges for managing and querying massive spatial data to support spatial queries: the explosion of spatial data, and the high computational complexity of spatial queries. In this paper, we present Hadoop-GIS – a scalable and high performance spatial data warehousing system for running large scale spatial queries on Hadoop. Hadoop-GIS supports multiple types of spatial queries on MapReduce through spatial partitioning, customizable spatial query engine RESQUE, implicit parallel spatial query execution on MapReduce, and effective methods for amending query results through handling boundary objects. Hadoop-GIS utilizes global partition indexing and customizable on demand local spatial indexing to achieve efficient query processing. Hadoop-GIS is integrated into Hive to support declarative spatial queries with an integrated architecture. Our experiments have demonstrated the high efficiency of Hadoop-GIS on query response and high scalability to run on commodity clusters. Our comparative experiments have showed that performance of Hadoop-GIS is on par with parallel SDBMS and outperforms SDBMS for compute-intensive queries. Hadoop-GIS is available as a set of library for processing spatial queries, and as an integrated software package in Hive. PMID:24187650

Arkansas and Louisiana Aeromagnetic and Gravity Maps and Data - A Website for Distribution of Data

USGS Publications Warehouse

Bankey, Viki; Daniels, David L.

2008-01-01

This report contains digital data, image files, and text files describing data formats for aeromagnetic and gravity data used to compile the State aeromagnetic and gravity maps of Arkansas and Louisiana. The digital files include grids, images, ArcInfo, and Geosoft compatible files. In some of the data folders, ASCII files with the extension 'txt' describe the format and contents of the data files. Read the 'txt' files before using the data files.

Lidar Observations of the Optical Properties and 3-Dimensional Structure of Cirrus Clouds

NASA Technical Reports Server (NTRS)

Eloranta, E. W.

1996-01-01

The scientific research conducted under this grant have been reported in a series of journal articles, dissertations, and conference proceedings. This report consists of a compilation of these publications in the following areas: development and operation of a High Spectral Resolution Lidar, cloud physics and cloud formation, mesoscale observations of cloud phenomena, ground-based and satellite cloud cover observations, impact of volcanic aerosols on cloud formation, visible and infrared radiative relationships as measured by satellites and lidar, and scattering cross sections.

Estimating Influenza Outbreaks Using Both Search Engine Query Data and Social Media Data in South Korea.

PubMed

Woo, Hyekyung; Cho, Youngtae; Shim, Eunyoung; Lee, Jong-Koo; Lee, Chang-Gun; Kim, Seong Hwan

2016-07-04

As suggested as early as in 2006, logs of queries submitted to search engines seeking information could be a source for detection of emerging influenza epidemics if changes in the volume of search queries are monitored (infodemiology). However, selecting queries that are most likely to be associated with influenza epidemics is a particular challenge when it comes to generating better predictions. In this study, we describe a methodological extension for detecting influenza outbreaks using search query data; we provide a new approach for query selection through the exploration of contextual information gleaned from social media data. Additionally, we evaluate whether it is possible to use these queries for monitoring and predicting influenza epidemics in South Korea. Our study was based on freely available weekly influenza incidence data and query data originating from the search engine on the Korean website Daum between April 3, 2011 and April 5, 2014. To select queries related to influenza epidemics, several approaches were applied: (1) exploring influenza-related words in social media data, (2) identifying the chief concerns related to influenza, and (3) using Web query recommendations. Optimal feature selection by least absolute shrinkage and selection operator (Lasso) and support vector machine for regression (SVR) were used to construct a model predicting influenza epidemics. In total, 146 queries related to influenza were generated through our initial query selection approach. A considerable proportion of optimal features for final models were derived from queries with reference to the social media data. The SVR model performed well: the prediction values were highly correlated with the recent observed influenza-like illness (r=.956; P<.001) and virological incidence rate (r=.963; P<.001). These results demonstrate the feasibility of using search queries to enhance influenza surveillance in South Korea. In addition, an approach for query selection using social media data seems ideal for supporting influenza surveillance based on search query data.

Estimating Influenza Outbreaks Using Both Search Engine Query Data and Social Media Data in South Korea

PubMed Central

Woo, Hyekyung; Shim, Eunyoung; Lee, Jong-Koo; Lee, Chang-Gun; Kim, Seong Hwan

2016-01-01

Background As suggested as early as in 2006, logs of queries submitted to search engines seeking information could be a source for detection of emerging influenza epidemics if changes in the volume of search queries are monitored (infodemiology). However, selecting queries that are most likely to be associated with influenza epidemics is a particular challenge when it comes to generating better predictions. Objective In this study, we describe a methodological extension for detecting influenza outbreaks using search query data; we provide a new approach for query selection through the exploration of contextual information gleaned from social media data. Additionally, we evaluate whether it is possible to use these queries for monitoring and predicting influenza epidemics in South Korea. Methods Our study was based on freely available weekly influenza incidence data and query data originating from the search engine on the Korean website Daum between April 3, 2011 and April 5, 2014. To select queries related to influenza epidemics, several approaches were applied: (1) exploring influenza-related words in social media data, (2) identifying the chief concerns related to influenza, and (3) using Web query recommendations. Optimal feature selection by least absolute shrinkage and selection operator (Lasso) and support vector machine for regression (SVR) were used to construct a model predicting influenza epidemics. Results In total, 146 queries related to influenza were generated through our initial query selection approach. A considerable proportion of optimal features for final models were derived from queries with reference to the social media data. The SVR model performed well: the prediction values were highly correlated with the recent observed influenza-like illness (r=.956; P<.001) and virological incidence rate (r=.963; P<.001). Conclusions These results demonstrate the feasibility of using search queries to enhance influenza surveillance in South Korea. In addition, an approach for query selection using social media data seems ideal for supporting influenza surveillance based on search query data. PMID:27377323

Lost in translation? A multilingual Query Builder improves the quality of PubMed queries: a randomised controlled trial.

PubMed

Schuers, Matthieu; Joulakian, Mher; Kerdelhué, Gaetan; Segas, Léa; Grosjean, Julien; Darmoni, Stéfan J; Griffon, Nicolas

2017-07-03

MEDLINE is the most widely used medical bibliographic database in the world. Most of its citations are in English and this can be an obstacle for some researchers to access the information the database contains. We created a multilingual query builder to facilitate access to the PubMed subset using a language other than English. The aim of our study was to assess the impact of this multilingual query builder on the quality of PubMed queries for non-native English speaking physicians and medical researchers. A randomised controlled study was conducted among French speaking general practice residents. We designed a multi-lingual query builder to facilitate information retrieval, based on available MeSH translations and providing users with both an interface and a controlled vocabulary in their own language. Participating residents were randomly allocated either the French or the English version of the query builder. They were asked to translate 12 short medical questions into MeSH queries. The main outcome was the quality of the query. Two librarians blind to the arm independently evaluated each query, using a modified published classification that differentiated eight types of errors. Twenty residents used the French version of the query builder and 22 used the English version. 492 queries were analysed. There were significantly more perfect queries in the French group vs. the English group (respectively 37.9% vs. 17.9%; p < 0.01). It took significantly more time for the members of the English group than the members of the French group to build each query, respectively 194 sec vs. 128 sec; p < 0.01. This multi-lingual query builder is an effective tool to improve the quality of PubMed queries in particular for researchers whose first language is not English.

Advanced Query and Data Mining Capabilities for MaROS

NASA Technical Reports Server (NTRS)

Wang, Paul; Wallick, Michael N.; Allard, Daniel A.; Gladden, Roy E.; Hy, Franklin H.

2013-01-01

The Mars Relay Operational Service (MaROS) comprises a number of tools to coordinate, plan, and visualize various aspects of the Mars Relay network. These levels include a Web-based user interface, a back-end "ReSTlet" built in Java, and databases that store the data as it is received from the network. As part of MaROS, the innovators have developed and implemented a feature set that operates on several levels of the software architecture. This new feature is an advanced querying capability through either the Web-based user interface, or through a back-end REST interface to access all of the data gathered from the network. This software is not meant to replace the REST interface, but to augment and expand the range of available data. The current REST interface provides specific data that is used by the MaROS Web application to display and visualize the information; however, the returned information from the REST interface has typically been pre-processed to return only a subset of the entire information within the repository, particularly only the information that is of interest to the GUI (graphical user interface). The new, advanced query and data mining capabilities allow users to retrieve the raw data and/or to perform their own data processing. The query language used to access the repository is a restricted subset of the structured query language (SQL) that can be built safely from the Web user interface, or entered as freeform SQL by a user. The results are returned in a CSV (Comma Separated Values) format for easy exporting to third party tools and applications that can be used for data mining or user-defined visualization and interpretation. This is the first time that a service is capable of providing access to all cross-project relay data from a single Web resource. Because MaROS contains the data for a variety of missions from the Mars network, which span both NASA and ESA, the software also establishes an access control list (ACL) on each data record in the database repository to enforce user access permissions through a multilayered approach.

Visual analytics for semantic queries of TerraSAR-X image content

NASA Astrophysics Data System (ADS)

Espinoza-Molina, Daniela; Alonso, Kevin; Datcu, Mihai

2015-10-01

With the continuous image product acquisition of satellite missions, the size of the image archives is considerably increasing every day as well as the variety and complexity of their content, surpassing the end-user capacity to analyse and exploit them. Advances in the image retrieval field have contributed to the development of tools for interactive exploration and extraction of the images from huge archives using different parameters like metadata, key-words, and basic image descriptors. Even though we count on more powerful tools for automated image retrieval and data analysis, we still face the problem of understanding and analyzing the results. Thus, a systematic computational analysis of these results is required in order to provide to the end-user a summary of the archive content in comprehensible terms. In this context, visual analytics combines automated analysis with interactive visualizations analysis techniques for an effective understanding, reasoning and decision making on the basis of very large and complex datasets. Moreover, currently several researches are focused on associating the content of the images with semantic definitions for describing the data in a format to be easily understood by the end-user. In this paper, we present our approach for computing visual analytics and semantically querying the TerraSAR-X archive. Our approach is mainly composed of four steps: 1) the generation of a data model that explains the information contained in a TerraSAR-X product. The model is formed by primitive descriptors and metadata entries, 2) the storage of this model in a database system, 3) the semantic definition of the image content based on machine learning algorithms and relevance feedback, and 4) querying the image archive using semantic descriptors as query parameters and computing the statistical analysis of the query results. The experimental results shows that with the help of visual analytics and semantic definitions we are able to explain the image content using semantic terms and the relations between them answering questions such as what is the percentage of urban area in a region? or what is the distribution of water bodies in a city?

Technical Writing: Past, Present, and Future.

ERIC Educational Resources Information Center

Mathes, J. C., Comp.; Pinelli, Thomas E., Comp.

This compilation of papers addresses the history, present status, and trends of technical and related writing. The first of the eight papers surveys the present environment of the technical report and assesses the effectiveness of the technical report format of the National Aeronautics and Space Administration (NASA) in transmitting information.…

BOOK REVIEW (ABSTRACT FORMAT) "WATER FOR URBAN AREAS: CHALLENGES AND PERSPECTIVES"

EPA Science Inventory

This book is a compilation of papers from the Sixth Global Environmental Forum, convened by the United Nations University in Tokyo, Japan in June 1997 on "Water for Urban Areas in the 21st Century." This book has a broad perspective of urban water including drinking, wastewater ...

Resources for Creative Preschool Teaching.

ERIC Educational Resources Information Center

Flemming, Bonnie, Ed.; And Others

A resource book intended as a teaching aid for preschool teachers, this compilation includes those ideas that have been used with success with children three through five years of age. The curriculum material is presented in outline format under the following headings: Subject of Interest; Basic Understandings; Additional Facts the Teacher Should…

Within the School and the Community--A Speaker's Bureau.

ERIC Educational Resources Information Center

McClintock, Joy H.

Student interest prompted the formation of a Speaker's Bureau in Seminole Senior High School, Seminole, Florida. First, students compiled a list of community contacts, including civic clubs, churches, retirement villages, newspaper offices, and the County School Administration media center. A letter of introduction was composed and speaking…

Pedagogical System of Future Teachers' Professional Thinking Culture Formation

ERIC Educational Resources Information Center

Abildina, Saltanat K.; Sarsekeyeva, Zhanar Y.; Aidarbekova, Kulzhan A.; Asetova, Zhannur B.; Adanov, Kuanysbek B.

2016-01-01

Research objective is to theoretically justify and to develop a pedagogical system of development of future teachers' professional thinking culture. In the research there are used a set of theoretical methods: systematic analysis of the philosophical, psychological and pedagogical literature on the researched topic; compilation and classification…

Federal Programs of Assistance to American Indians.

ERIC Educational Resources Information Center

Jones, Richard S.

Comprehensive descriptions of all federal programs which specifically benefit American Indians are compiled in this document which utilizes information contributed by government agencies and departments in 1974. The format of each program includes: (1) the name, nature, and purpose of the program; (2) eligibility requirements; (3) how to apply…

5 CFR 294.107 - Places to obtain records.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Retirement; life and health insurance. Associate Director for Personnel Systems and Oversight Personnel...) Creating records. If a person seeks information from OPM in a format that does not currently exist, OPM will not ordinarily compile the information for the purpose of creating a record to respond to the...

A novel method for efficient archiving and retrieval of biomedical images using MPEG-7

NASA Astrophysics Data System (ADS)

Meyer, Joerg; Pahwa, Ash

2004-10-01

Digital archiving and efficient retrieval of radiological scans have become critical steps in contemporary medical diagnostics. Since more and more images and image sequences (single scans or video) from various modalities (CT/MRI/PET/digital X-ray) are now available in digital formats (e.g., DICOM-3), hospitals and radiology clinics need to implement efficient protocols capable of managing the enormous amounts of data generated daily in a typical clinical routine. We present a method that appears to be a viable way to eliminate the tedious step of manually annotating image and video material for database indexing. MPEG-7 is a new framework that standardizes the way images are characterized in terms of color, shape, and other abstract, content-related criteria. A set of standardized descriptors that are automatically generated from an image is used to compare an image to other images in a database, and to compute the distance between two images for a given application domain. Text-based database queries can be replaced with image-based queries using MPEG-7. Consequently, image queries can be conducted without any prior knowledge of the keys that were used as indices in the database. Since the decoding and matching steps are not part of the MPEG-7 standard, this method also enables searches that were not planned by the time the keys were generated.

FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide.

PubMed

van Baal, Sjozef; Kaimakis, Polynikis; Phommarinh, Manyphong; Koumbi, Daphne; Cuppens, Harry; Riccardino, Francesca; Macek, Milan; Scriver, Charles R; Patrinos, George P

2007-01-01

Frequency of INherited Disorders database (FINDbase) (http://www.findbase.org) is a relational database, derived from the ETHNOS software, recording frequencies of causative mutations leading to inherited disorders worldwide. Database records include the population and ethnic group, the disorder name and the related gene, accompanied by links to any corresponding locus-specific mutation database, to the respective Online Mendelian Inheritance in Man entries and the mutation together with its frequency in that population. The initial information is derived from the published literature, locus-specific databases and genetic disease consortia. FINDbase offers a user-friendly query interface, providing instant access to the list and frequencies of the different mutations. Query outputs can be either in a table or graphical format, accompanied by reference(s) on the data source. Registered users from three different groups, namely administrator, national coordinator and curator, are responsible for database curation and/or data entry/correction online via a password-protected interface. Databaseaccess is free of charge and there are no registration requirements for data querying. FINDbase provides a simple, web-based system for population-based mutation data collection and retrieval and can serve not only as a valuable online tool for molecular genetic testing of inherited disorders but also as a non-profit model for sustainable database funding, in the form of a 'database-journal'.

Space Station Technology, 1983

NASA Technical Reports Server (NTRS)

Wright, R. L. (Editor); Mays, C. R. (Editor)

1984-01-01

This publication is a compilation of the panel summaries presented in the following areas: systems/operations technology; crew and life support; EVA; crew and life support: ECLSS; attitude, control, and stabilization; human capabilities; auxillary propulsion; fluid management; communications; structures and mechanisms; data management; power; and thermal control. The objective of the workshop was to aid the Space Station Technology Steering Committee in defining and implementing a technology development program to support the establishment of a permanent human presence in space. This compilation will provide the participants and their organizations with the information presented at this workshop in a referenceable format. This information will establish a stepping stone for users of space station technology to develop new technology and plan future tasks.

Compilation of Henry's law constants (version 4.0) for water as solvent

NASA Astrophysics Data System (ADS)

Sander, R.

2015-04-01

Many atmospheric chemicals occur in the gas phase as well as in liquid cloud droplets and aerosol particles. Therefore, it is necessary to understand the distribution between the phases. According to Henry's law, the equilibrium ratio between the abundances in the gas phase and in the aqueous phase is constant for a dilute solution. Henry's law constants of trace gases of potential importance in environmental chemistry have been collected and converted into a uniform format. The compilation contains 17 350 values of Henry's law constants for 4632 species, collected from 689 references. It is also available at http://www.henrys-law.org.

Compilation of Henry's law constants, version 3.99

NASA Astrophysics Data System (ADS)

Sander, R.

2014-11-01

Many atmospheric chemicals occur in the gas phase as well as in liquid cloud droplets and aerosol particles. Therefore, it is necessary to understand the distribution between the phases. According to Henry's law, the equilibrium ratio between the abundances in the gas phase and in the aqueous phase is constant for a dilute solution. Henry's law constants of trace gases of potential importance in environmental chemistry have been collected and converted into a uniform format. The compilation contains 14775 values of Henry's law constants for 3214 species, collected from 639 references. It is also available on the internet at http://www.henrys-law.org.

World petroleum assessment 2000; compiled PowerPoint slides

USGS Publications Warehouse

Ahlbrandt, Thomas S.

2001-01-01

The slides in this compilation have been produced for a number of presentations on the World Petroleum Assessment 20000. Many of the figures are taken directly form the publication "U.S. Geological Survey World Petroleum Assessment 2000" - Description and Results: USGS Digital Data Series DDS-60, 2000. Some of the slides are modifications of figures from DDS-60, some are new descriptive slides, and a few are new slides. Several of the slides appear to be duplicates, but in fact are slight modifications for format or content from the same image. Forty-one people participated in this effort as part of the World Energy Assessment Team. The full list of contributors is given ion DDS-60. 

Mining Longitudinal Web Queries: Trends and Patterns.

ERIC Educational Resources Information Center

Wang, Peiling; Berry, Michael W.; Yang, Yiheng

2003-01-01

Analyzed user queries submitted to an academic Web site during a four-year period, using a relational database, to examine users' query behavior, to identify problems they encounter, and to develop techniques for optimizing query analysis and mining. Linguistic analyses focus on query structures, lexicon, and word associations using statistical…

Optimizing a Query by Transformation and Expansion.

PubMed

Glocker, Katrin; Knurr, Alexander; Dieter, Julia; Dominick, Friederike; Forche, Melanie; Koch, Christian; Pascoe Pérez, Analie; Roth, Benjamin; Ückert, Frank

2017-01-01

In the biomedical sector not only the amount of information produced and uploaded into the web is enormous, but also the number of sources where these data can be found. Clinicians and researchers spend huge amounts of time on trying to access this information and to filter the most important answers to a given question. As the formulation of these queries is crucial, automated query expansion is an effective tool to optimize a query and receive the best possible results. In this paper we introduce the concept of a workflow for an optimization of queries in the medical and biological sector by using a series of tools for expansion and transformation of the query. After the definition of attributes by the user, the query string is compared to previous queries in order to add semantic co-occurring terms to the query. Additionally, the query is enlarged by an inclusion of synonyms. The translation into database specific ontologies ensures the optimal query formulation for the chosen database(s). As this process can be performed in various databases at once, the results are ranked and normalized in order to achieve a comparable list of answers for a question.

WATCHMAN: A Data Warehouse Intelligent Cache Manager

NASA Technical Reports Server (NTRS)

Scheuermann, Peter; Shim, Junho; Vingralek, Radek

1996-01-01

Data warehouses store large volumes of data which are used frequently by decision support applications. Such applications involve complex queries. Query performance in such an environment is critical because decision support applications often require interactive query response time. Because data warehouses are updated infrequently, it becomes possible to improve query performance by caching sets retrieved by queries in addition to query execution plans. In this paper we report on the design of an intelligent cache manager for sets retrieved by queries called WATCHMAN, which is particularly well suited for data warehousing environment. Our cache manager employs two novel, complementary algorithms for cache replacement and for cache admission. WATCHMAN aims at minimizing query response time and its cache replacement policy swaps out entire retrieved sets of queries instead of individual pages. The cache replacement and admission algorithms make use of a profit metric, which considers for each retrieved set its average rate of reference, its size, and execution cost of the associated query. We report on a performance evaluation based on the TPC-D and Set Query benchmarks. These experiments show that WATCHMAN achieves a substantial performance improvement in a decision support environment when compared to a traditional LRU replacement algorithm.

Inflammatory Cells and Proteases in Abdominal Aortic Aneurysm and its Complications.

PubMed

Haiying, Jiang; Sasaki, Takeshi; Jin, Enze; Kuzuya, Masafumi; Cheng, Xianwu

2018-05-30

Abdominal aortic aneurysm (AAA), a common disease among elderly individuals, involves the progressive dilatation of the abdominal aorta as a consequence of degeneration. The mechanisms of AAA formation, development and rupture are largely unknown. Surgical repair is the only available method of treatment since the lack of knowledge regarding the pathogenesis of AAA has hindered the development of suitable medical treatments, particularly the development of drugs. In this review, we describe the inflammatory cells and proteases that may be involved in the formation and development of AAA. This knowledge can contribute to the development of new drugs for AAA. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Compilation of VS30 Data for the United States

USGS Publications Warehouse

Yong, Alan; Thompson, Eric M.; Wald, David J.; Knudsen, Keith L.; Odum, Jack K.; Stephenson, William J.; Haefner, Scott

2016-01-01

VS30, the time-averaged shear-wave velocity (VS) to a depth of 30 meters, is a key index adopted by the earthquake engineering community to account for seismic site conditions. VS30 is typically based on geophysical measurements of VS derived from invasive and noninvasive techniques at sites of interest. Owing to cost considerations, as well as logistical and environmental concerns, VS30 data are sparse or not readily available for most areas. Where data are available, VS30 values are often assembled in assorted formats that are accessible from disparate and (or) impermanent Web sites. To help remedy this situation, we compiled VS30 measurements obtained by studies funded by the U.S. Geological Survey (USGS) and other governmental agencies. Thus far, we have compiled VS30 values for 2,997 sites in the United States, along with metadata for each measurement from government-sponsored reports, Web sites, and scientific and engineering journals. Most of the data in our VS30 compilation originated from publications directly reporting the work of field investigators. A small subset (less than 20 percent) of VS30 values was previously compiled by the USGS and other research institutions. Whenever possible, VS30 originating from these earlier compilations were crosschecked against published reports. Both downhole and surface-based VS30 estimates are represented in our VS30 compilation. Most of the VS30 data are for sites in the western contiguous United States (2,141 sites), whereas 786 VS30 values are for sites in the Central and Eastern United States; 70 values are for sites in other parts of the United States, including Alaska (15 sites), Hawaii (30 sites), and Puerto Rico (25 sites). An interactive map is hosted on the primary USGS Web site for accessing VS30 data (http://earthquake.usgs.gov/research/vs30/).

A high-performance spatial database based approach for pathology imaging algorithm evaluation

PubMed Central

Wang, Fusheng; Kong, Jun; Gao, Jingjing; Cooper, Lee A.D.; Kurc, Tahsin; Zhou, Zhengwen; Adler, David; Vergara-Niedermayr, Cristobal; Katigbak, Bryan; Brat, Daniel J.; Saltz, Joel H.

2013-01-01

Background: Algorithm evaluation provides a means to characterize variability across image analysis algorithms, validate algorithms by comparison with human annotations, combine results from multiple algorithms for performance improvement, and facilitate algorithm sensitivity studies. The sizes of images and image analysis results in pathology image analysis pose significant challenges in algorithm evaluation. We present an efficient parallel spatial database approach to model, normalize, manage, and query large volumes of analytical image result data. This provides an efficient platform for algorithm evaluation. Our experiments with a set of brain tumor images demonstrate the application, scalability, and effectiveness of the platform. Context: The paper describes an approach and platform for evaluation of pathology image analysis algorithms. The platform facilitates algorithm evaluation through a high-performance database built on the Pathology Analytic Imaging Standards (PAIS) data model. Aims: (1) Develop a framework to support algorithm evaluation by modeling and managing analytical results and human annotations from pathology images; (2) Create a robust data normalization tool for converting, validating, and fixing spatial data from algorithm or human annotations; (3) Develop a set of queries to support data sampling and result comparisons; (4) Achieve high performance computation capacity via a parallel data management infrastructure, parallel data loading and spatial indexing optimizations in this infrastructure. Materials and Methods: We have considered two scenarios for algorithm evaluation: (1) algorithm comparison where multiple result sets from different methods are compared and consolidated; and (2) algorithm validation where algorithm results are compared with human annotations. We have developed a spatial normalization toolkit to validate and normalize spatial boundaries produced by image analysis algorithms or human annotations. The validated data were formatted based on the PAIS data model and loaded into a spatial database. To support efficient data loading, we have implemented a parallel data loading tool that takes advantage of multi-core CPUs to accelerate data injection. The spatial database manages both geometric shapes and image features or classifications, and enables spatial sampling, result comparison, and result aggregation through expressive structured query language (SQL) queries with spatial extensions. To provide scalable and efficient query support, we have employed a shared nothing parallel database architecture, which distributes data homogenously across multiple database partitions to take advantage of parallel computation power and implements spatial indexing to achieve high I/O throughput. Results: Our work proposes a high performance, parallel spatial database platform for algorithm validation and comparison. This platform was evaluated by storing, managing, and comparing analysis results from a set of brain tumor whole slide images. The tools we develop are open source and available to download. Conclusions: Pathology image algorithm validation and comparison are essential to iterative algorithm development and refinement. One critical component is the support for queries involving spatial predicates and comparisons. In our work, we develop an efficient data model and parallel database approach to model, normalize, manage and query large volumes of analytical image result data. Our experiments demonstrate that the data partitioning strategy and the grid-based indexing result in good data distribution across database nodes and reduce I/O overhead in spatial join queries through parallel retrieval of relevant data and quick subsetting of datasets. The set of tools in the framework provide a full pipeline to normalize, load, manage and query analytical results for algorithm evaluation. PMID:23599905

Geologic map of the greater Denver area, Front Range urban corridor, Colorado

USGS Publications Warehouse

Trimble, Donald E.; Machette, Michael N.

1979-01-01

This digital map shows the areal extent of surficial deposits and rock stratigraphic units (formations) as compiled by Trimble and Machette from 1973 to 1977 and published in 1979 under the Front Range Urban Corridor Geology Program. Trimble and Machette compiled their geologic map from published geologic maps and unpublished geologic mapping having varied map unit schemes. A convenient feature of the compiled map is its uniform classification of geologic units that mostly matches those of companion maps to the north (USGS I-855-G) and to the south (USGS I-857-F). Published as a color paper map, the Trimble and Machette map was intended for land-use planning in the Front Range Urban Corridor. This map recently (1997-1999) was digitized under the USGS Front Range Infrastructure Resources Project. In general, the mountainous areas in the western part of the map exhibit various igneous and metamorphic bedrock units of Precambrian age, major faults, and fault brecciation zones at the east margin (5-20 km wide) of the Front Range. The eastern and central parts of the map (Colorado Piedmont) depict a mantle of unconsolidated deposits of Quaternary age and interspersed outcroppings of Cretaceous or Tertiary-Cretaceous sedimentary bedrock. The Quaternary mantle comprises eolian deposits (quartz sand and silt), alluvium (gravel, sand, and silt of variable composition), colluvium, and a few landslides. At the mountain front, north-trending, dipping Paleozoic and Mesozoic sandstone, shale, and limestone bedrock formations form hogbacks and intervening valleys.

Digital soil mapping for the support of delineation of Areas Facing Natural Constraints defined by common European biophysical criteria

NASA Astrophysics Data System (ADS)

Pásztor, László; Bakacsi, Zsófia; Laborczi, Annamária; Takács, Katalin; Szatmári, Gábor; Tóth, Tibor; Szabó, József

2016-04-01

One of the main objectives of the EU's Common Agricultural Policy is to encourage maintaining agricultural production in Areas Facing Natural Constraints (ANC) in order to sustain agricultural production and use natural resources, in such a way to secure both stable production and income to farmers and to protect the environment. ANC assignment has both ecological and severe economical aspects. Recently the delimitation of ANCs is suggested to be carried out by using common biophysical diagnostic criteria on low soil productivity and poor climate conditions all over Europe. The criterion system was elaborated and has been repeatedly upgraded by JRC. The operational implementation is under member state competence. This process requires application of available soil databases and proper thematic and spatial inference methods. In our paper we present the inferences applied for the latest identification and delineation of areas with low soil productivity in Hungary according to JRC biophysical criteria related to soil: limited soil drainage, texture and stoniness (coarse texture, heavy clay, vertic properties), shallow rooting depth, chemical properties (salinity, sodicity, low pH). The compilation of target specific maps were based on the available legacy and recently collected data. In the present work three different data sources were used. The most relevant available data were queried from the datasets for each mapped criterion for either direct application or for the compilation a suitable, synthetic (non-measured) parameter. In some cases the values of the target variable originated from only one, in other cases from more databases. The reference dataset used in the mapping process was set up after substantial statistical analysis and filtering. It consisted of the values of the target variable attributed to the finally selected georeferenced locations. For spatial inference regression kriging was applied. Accuracy assessment was carried out by Leave One Out Cross Validation (LOOCV). In some cases the DSM product directly provided the delineation result by simple querying, in other cases further interpretation of the map was necessary. As the result of our work not only spatial fulfilment of the European biophysical criteria was assessed and provided for decision makers, but unique digital soil map products were elaborated regionalizing specific soil features, which were never mapped before, even nationally with 1 ha spatial resolution. Acknowledgement: Our work was supported by the "European Fund for Agricultural and Rural Development: Europe investing in rural areas" with the support of the European Union and Hungary and by the Hungarian National Scientific Research Foundation (OTKA, Grant No. K105167).

Ontology based log content extraction engine for a posteriori security control.

PubMed

Azkia, Hanieh; Cuppens-Boulahia, Nora; Cuppens, Frédéric; Coatrieux, Gouenou

2012-01-01

In a posteriori access control, users are accountable for actions they performed and must provide evidence, when required by some legal authorities for instance, to prove that these actions were legitimate. Generally, log files contain the needed data to achieve this goal. This logged data can be recorded in several formats; we consider here IHE-ATNA (Integrating the healthcare enterprise-Audit Trail and Node Authentication) as log format. The difficulty lies in extracting useful information regardless of the log format. A posteriori access control frameworks often include a log filtering engine that provides this extraction function. In this paper we define and enforce this function by building an IHE-ATNA based ontology model, which we query using SPARQL, and show how the a posteriori security controls are made effective and easier based on this function.

PAQ: Persistent Adaptive Query Middleware for Dynamic Environments

NASA Astrophysics Data System (ADS)

Rajamani, Vasanth; Julien, Christine; Payton, Jamie; Roman, Gruia-Catalin

Pervasive computing applications often entail continuous monitoring tasks, issuing persistent queries that return continuously updated views of the operational environment. We present PAQ, a middleware that supports applications' needs by approximating a persistent query as a sequence of one-time queries. PAQ introduces an integration strategy abstraction that allows composition of one-time query responses into streams representing sophisticated spatio-temporal phenomena of interest. A distinguishing feature of our middleware is the realization that the suitability of a persistent query's result is a function of the application's tolerance for accuracy weighed against the associated overhead costs. In PAQ, programmers can specify an inquiry strategy that dictates how information is gathered. Since network dynamics impact the suitability of a particular inquiry strategy, PAQ associates an introspection strategy with a persistent query, that evaluates the quality of the query's results. The result of introspection can trigger application-defined adaptation strategies that alter the nature of the query. PAQ's simple API makes developing adaptive querying systems easily realizable. We present the key abstractions, describe their implementations, and demonstrate the middleware's usefulness through application examples and evaluation.

The CMS DBS query language

NASA Astrophysics Data System (ADS)

Kuznetsov, Valentin; Riley, Daniel; Afaq, Anzar; Sekhri, Vijay; Guo, Yuyi; Lueking, Lee

2010-04-01

The CMS experiment has implemented a flexible and powerful system enabling users to find data within the CMS physics data catalog. The Dataset Bookkeeping Service (DBS) comprises a database and the services used to store and access metadata related to CMS physics data. To this, we have added a generalized query system in addition to the existing web and programmatic interfaces to the DBS. This query system is based on a query language that hides the complexity of the underlying database structure by discovering the join conditions between database tables. This provides a way of querying the system that is simple and straightforward for CMS data managers and physicists to use without requiring knowledge of the database tables or keys. The DBS Query Language uses the ANTLR tool to build the input query parser and tokenizer, followed by a query builder that uses a graph representation of the DBS schema to construct the SQL query sent to underlying database. We will describe the design of the query system, provide details of the language components and overview of how this component fits into the overall data discovery system architecture.

Spatial aggregation query in dynamic geosensor networks

NASA Astrophysics Data System (ADS)

Yi, Baolin; Feng, Dayang; Xiao, Shisong; Zhao, Erdun

2007-11-01

Wireless sensor networks have been widely used for civilian and military applications, such as environmental monitoring and vehicle tracking. In many of these applications, the researches mainly aim at building sensor network based systems to leverage the sensed data to applications. However, the existing works seldom exploited spatial aggregation query considering the dynamic characteristics of sensor networks. In this paper, we investigate how to process spatial aggregation query over dynamic geosensor networks where both the sink node and sensor nodes are mobile and propose several novel improvements on enabling techniques. The mobility of sensors makes the existing routing protocol based on information of fixed framework or the neighborhood infeasible. We present an improved location-based stateless implicit geographic forwarding (IGF) protocol for routing a query toward the area specified by query window, a diameter-based window aggregation query (DWAQ) algorithm for query propagation and data aggregation in the query window, finally considering the location changing of the sink node, we present two schemes to forward the result to the sink node. Simulation results show that the proposed algorithms can improve query latency and query accuracy.

Ada (Trade Name)/SQL (Structured Query Language) Binding Specification

DTIC Science & Technology

1988-06-01

TYPES iS package ADA-SOL Is type DWPLOYEEyNAME Is new STRING ( 1 .. 30 ); type BOSSNAME is new EMPLOYEENAME; type EMPLOYEE SALARY is digits 7 range 0.00...minimum number of significant decimal digits . All real numbers between the lower and upper bounds, inclusive, belong to the subtype, and are...and the elements of strings. Format <character> -:- < digit > I <letter> ! <special character> < digit > ::- 0111213141516171819 <letter> ::- <upper case

Efficient genotype compression and analysis of large genetic variation datasets

PubMed Central

Layer, Ryan M.; Kindlon, Neil; Karczewski, Konrad J.; Quinlan, Aaron R.

2015-01-01

Genotype Query Tools (GQT) is a new indexing strategy that expedites analyses of genome variation datasets in VCF format based on sample genotypes, phenotypes and relationships. GQT’s compressed genotype index minimizes decompression for analysis, and performance relative to existing methods improves with cohort size. We show substantial (up to 443 fold) performance gains over existing methods and demonstrate GQT’s utility for exploring massive datasets involving thousands to millions of genomes. PMID:26550772

BioMart Central Portal: an open database network for the biological community

PubMed Central

Guberman, Jonathan M.; Ai, J.; Arnaiz, O.; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J.; Di Génova, A.; Forbes, Simon; Fujisawa, T.; Gadaleta, E.; Goodstein, D. M.; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S.; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R.; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J.; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S.; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B.; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J.; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D. T.; Wong-Erasmus, Marie; Yao, L.; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities. Database URL: http://central.biomart.org. PMID:21930507

The Selection and Placement Method of Materialized Views on Big Data Platform of Equipment Condition Assessment

NASA Astrophysics Data System (ADS)

Ma, Yan; Yao, Jinxia; Gu, Chao; Chen, Yufeng; Yang, Yi; Zou, Lida

2017-05-01

With the formation of electric big data environment, more and more big data analyses emerge. In the complicated data analysis on equipment condition assessment, there exist many join operations, which are time-consuming. In order to save time, the approach of materialized view is usually used. It places part of common and critical join results on external storage and avoids the frequent join operation. In the paper we propose the methods of selecting and placing materialized views to reduce the query time of electric transmission and transformation equipment, and make the profits of service providers maximal. In selection method we design a computation way for the value of non-leaf node based on MVPP structure chart. In placement method we use relevance weights to place the selected materialized views, which help reduce the network transmission time. Our experiments show that the proposed selection and placement methods have a high throughput and good optimization ability of query time for electric transmission and transformation equipment.

RANDOMNESS of Numbers DEFINITION(QUERY:WHAT? V HOW?) ONLY Via MAXWELL-BOLTZMANN CLASSICAL-Statistics(MBCS) Hot-Plasma VS. Digits-Clumping Log-Law NON-Randomness Inversion ONLY BOSE-EINSTEIN QUANTUM-Statistics(BEQS) .

NASA Astrophysics Data System (ADS)

Siegel, Z.; Siegel, Edward Carl-Ludwig

2011-03-01

RANDOMNESS of Numbers cognitive-semantics DEFINITION VIA Cognition QUERY: WHAT???, NOT HOW?) VS. computer-``science" mindLESS number-crunching (Harrel-Sipser-...) algorithmics Goldreich "PSEUDO-randomness"[Not.AMS(02)] mea-culpa is ONLY via MAXWELL-BOLTZMANN CLASSICAL-STATISTICS(NOT FDQS!!!) "hot-plasma" REPULSION VERSUS Newcomb(1881)-Weyl(1914;1916)-Benford(1938) "NeWBe" logarithmic-law digit-CLUMPING/ CLUSTERING NON-Randomness simple Siegel[AMS Joint.Mtg.(02)-Abs. # 973-60-124] algebraic-inversion to THE QUANTUM and ONLY BEQS preferentially SEQUENTIALLY lower-DIGITS CLUMPING/CLUSTERING with d = 0 BEC, is ONLY VIA Siegel-Baez FUZZYICS=CATEGORYICS (SON OF TRIZ)/"Category-Semantics"(C-S), latter intersection/union of Lawvere(1964)-Siegel(1964)] category-theory (matrix: MORPHISMS V FUNCTORS) "+" cognitive-semantics'' (matrix: ANTONYMS V SYNONYMS) yields Siegel-Baez FUZZYICS=CATEGORYICS/C-S tabular list-format matrix truth-table analytics: MBCS RANDOMNESS TRUTH/EMET!!!

A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers

PubMed Central

Putnam, Christopher D.; Srivatsan, Anjana; Nene, Rahul V.; Martinez, Sandra L.; Clotfelter, Sarah P.; Bell, Sara N.; Somach, Steven B.; E.S. de Souza, Jorge; Fonseca, André F.; de Souza, Sandro J.; Kolodner, Richard D.

2016-01-01

Gross chromosomal rearrangements (GCRs) play an important role in human diseases, including cancer. The identity of all Genome Instability Suppressing (GIS) genes is not currently known. Here multiple Saccharomyces cerevisiae GCR assays and query mutations were crossed into arrays of mutants to identify progeny with increased GCR rates. One hundred eighty two GIS genes were identified that suppressed GCR formation. Another 438 cooperatively acting GIS genes were identified that were not GIS genes, but suppressed the increased genome instability caused by individual query mutations. Analysis of TCGA data using the human genes predicted to act in GIS pathways revealed that a minimum of 93% of ovarian and 66% of colorectal cancer cases had defects affecting one or more predicted GIS gene. These defects included loss-of-function mutations, copy-number changes associated with reduced expression, and silencing. In contrast, acute myeloid leukaemia cases did not appear to have defects affecting the predicted GIS genes. PMID:27071721

Comparative analysis of data base management systems

NASA Technical Reports Server (NTRS)

Smith, R.

1983-01-01

A study to determine if the Remote File Inquiry (RFI) system would handle the future requirements of the user community is discussed. RFI is a locally written and locally maintained on-line query/update package. The current and future on-line requirements of the user community were studied. Additional consideration was given to the types of data structuring the users required. The survey indicated the features of greatest benefit were: sort, subtotals, totals, record selection, storage of queries, global updating and the ability to page break. The major deficiencies were: one level of hierarchy, excessive response time, software unreliability, difficult to add, delete and modify records, complicated error messages and the lack of ability to perform interfield comparisons. Missing features users required were: formatted screens, interfield comparions, interfield arithmetic, multiple file access, security and data integrity. The survey team recommended Kennedy Space Center move forward to state-of-the-art software, a Data Base Management System which is thoroughly tested and easy to implement and use.

How to improve your PubMed/MEDLINE searches: 2. display settings, complex search queries and topic searching.

PubMed

Fatehi, Farhad; Gray, Leonard C; Wootton, Richard

2014-01-01

The way that PubMed results are displayed can be changed using the Display Settings drop-down menu in the result screen. There are three groups of options: Format, Items per page and Sort by, which allow a good deal of control. The results from several searches can be temporarily stored on the Clipboard. Records of interest can be selected on the results page using check boxes and can then be combined, for example to form a reference list. The Related Citations is a valuable feature of PubMed that can provide a set of similar articles when you have identified a record of interest among the results. You can easily search for RCTs or reviews using the appropriate filters or field tags. If you are interested in clinical articles, rather than basic science or health service research, then the Clinical Queries tool on the PubMed home page can be used to retrieve them.

BioMart Central Portal: an open database network for the biological community.

PubMed

Guberman, Jonathan M; Ai, J; Arnaiz, O; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J; Di Génova, A; Forbes, Simon; Fujisawa, T; Gadaleta, E; Goodstein, D M; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D T; Wong-Erasmus, Marie; Yao, L; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.

Analysis of queries sent to PubMed at the point of care: Observation of search behaviour in a medical teaching hospital

PubMed Central

Hoogendam, Arjen; Stalenhoef, Anton FH; Robbé, Pieter F de Vries; Overbeke, A John PM

2008-01-01

Background The use of PubMed to answer daily medical care questions is limited because it is challenging to retrieve a small set of relevant articles and time is restricted. Knowing what aspects of queries are likely to retrieve relevant articles can increase the effectiveness of PubMed searches. The objectives of our study were to identify queries that are likely to retrieve relevant articles by relating PubMed search techniques and tools to the number of articles retrieved and the selection of articles for further reading. Methods This was a prospective observational study of queries regarding patient-related problems sent to PubMed by residents and internists in internal medicine working in an Academic Medical Centre. We analyzed queries, search results, query tools (Mesh, Limits, wildcards, operators), selection of abstract and full-text for further reading, using a portal that mimics PubMed. Results PubMed was used to solve 1121 patient-related problems, resulting in 3205 distinct queries. Abstracts were viewed in 999 (31%) of these queries, and in 126 (39%) of 321 queries using query tools. The average term count per query was 2.5. Abstracts were selected in more than 40% of queries using four or five terms, increasing to 63% if the use of four or five terms yielded 2–161 articles. Conclusion Queries sent to PubMed by physicians at our hospital during daily medical care contain fewer than three terms. Queries using four to five terms, retrieving less than 161 article titles, are most likely to result in abstract viewing. PubMed search tools are used infrequently by our population and are less effective than the use of four or five terms. Methods to facilitate the formulation of precise queries, using more relevant terms, should be the focus of education and research. PMID:18816391

Health-Care Referrals from Direct-to-Consumer Genetic Testing

PubMed Central

Giovanni, Monica A.; Fickie, Matthew R.; Lehmann, Lisa S.; Green, Robert C.; Meckley, Lisa M.; Veenstra, David

2010-01-01

Background: Direct-to-consumer genetic testing (DTC-GT) provides personalized genetic risk information directly to consumers. Little is known about how and why consumers then communicate the results of this testing to health-care professionals. Aim: To query specialists in clinical genetics about their experience with individuals who consulted them after DTC-GT. Methods: Invitations to participate in a questionnaire were sent to three different groups of genetic professionals, totaling 4047 invitations, asking questions about individuals who consulted them after DTC-GT. For each case reported, respondents were asked to describe how the case was referred to them, the patient's rationale for DTC-GT, and the type of DTC-GT performed. Respondents were also queried about the consequences of the consultations in terms of additional testing ordered. The costs associated with each consultation were estimated. A clinical case series was compiled based upon clinician responses. Results: The invitation resulted in 133 responses describing 22 cases of clinical interactions following DTC-GT. Most consultations (59.1%) were self-referred to genetics professionals, but 31.8% were physician referred. Among respondents, 52.3% deemed the DTC-GT to be “clinically useful.” BRCA1/2 testing was considered clinically useful in 85.7% of cases; 35.7% of other tests were considered clinically useful. Subsequent referrals from genetics professionals to specialists and/or additional diagnostic testing were common, generating individual downstream costs estimated to range from $40 to $20,600. Conclusions: This clinical case series suggests that approximately half of clinical geneticists who saw patients after DTC-GT judged that testing was clinically useful, especially the BRCA1/2 testing. Further studies are needed in larger and more diverse populations to better understand the interactions between DTC-GT and the health-care system. PMID:20979566

Health-care referrals from direct-to-consumer genetic testing.

PubMed

Giovanni, Monica A; Fickie, Matthew R; Lehmann, Lisa S; Green, Robert C; Meckley, Lisa M; Veenstra, David; Murray, Michael F

2010-12-01

direct-to-consumer genetic testing (DTC-GT) provides personalized genetic risk information directly to consumers. Little is known about how and why consumers then communicate the results of this testing to health-care professionals. to query specialists in clinical genetics about their experience with individuals who consulted them after DTC-GT. invitations to participate in a questionnaire were sent to three different groups of genetic professionals, totaling 4047 invitations, asking questions about individuals who consulted them after DTC-GT. For each case reported, respondents were asked to describe how the case was referred to them, the patient's rationale for DTC-GT, and the type of DTC-GT performed. Respondents were also queried about the consequences of the consultations in terms of additional testing ordered. The costs associated with each consultation were estimated. A clinical case series was compiled based upon clinician responses. the invitation resulted in 133 responses describing 22 cases of clinical interactions following DTC-GT. Most consultations (59.1%) were self-referred to genetics professionals, but 31.8% were physician referred. Among respondents, 52.3% deemed the DTC-GT to be "clinically useful." BRCA1/2 testing was considered clinically useful in 85.7% of cases; 35.7% of other tests were considered clinically useful. Subsequent referrals from genetics professionals to specialists and/or additional diagnostic testing were common, generating individual downstream costs estimated to range from $40 to $20,600. this clinical case series suggests that approximately half of clinical geneticists who saw patients after DTC-GT judged that testing was clinically useful, especially the BRCA1/2 testing. Further studies are needed in larger and more diverse populations to better understand the interactions between DTC-GT and the health-care system.

Bayesian belief network modelling of chlorine disinfection for human pathogenic viruses in municipal wastewater.

PubMed

Carvajal, Guido; Roser, David J; Sisson, Scott A; Keegan, Alexandra; Khan, Stuart J

2017-02-01

Chlorine disinfection of biologically treated wastewater is practiced in many locations prior to environmental discharge or beneficial reuse. The effectiveness of chlorine disinfection processes may be influenced by several factors, such as pH, temperature, ionic strength, organic carbon concentration, and suspended solids. We investigated the use of Bayesian multilayer perceptron (BMLP) models as efficient and practical tools for compiling and analysing free chlorine and monochloramine virus disinfection performance as a multivariate problem. Corresponding to their relative susceptibility, Adenovirus 2 was used to assess disinfection by monochloramine and Coxsackievirus B5 was used for free chlorine. A BMLP model was constructed to relate key disinfection conditions (CT, pH, turbidity) to observed Log Reduction Values (LRVs) for these viruses at constant temperature. The models proved to be valuable for incorporating uncertainty in the chlor(am)ination performance estimation and interpolating between operating conditions. Various types of queries could be performed with this model including the identification of target CT for a particular combination of LRV, pH and turbidity. Similarly, it was possible to derive achievable LRVs for combinations of CT, pH and turbidity. These queries yielded probability density functions for the target variable reflecting the uncertainty in the model parameters and variability of the input variables. The disinfection efficacy was greatly impacted by pH and to a lesser extent by turbidity for both types of disinfections. Non-linear relationships were observed between pH and target CT, and turbidity and target CT, with compound effects on target CT also evidenced. This work demonstrated that the use of BMLP models had considerable ability to improve the resolution and understanding of the multivariate relationships between operational parameters and disinfection outcomes for wastewater treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Copper-silver deposits of the Revett Formation, Montana and Idaho: origin and resource potential

USGS Publications Warehouse

Frost, Thomas P.; Zientek, Michael L.

2006-01-01

The Revett Formation of northern Idaho and western Montana contains major stratabound copper-silver deposits near Troy, Rock Creek, and Rock Lake, Montana. To help the U.S. Forest Service (USFS) meet its goal of integrating geoscience information into the land-planning process, U.S. Geological Survey (USGS) scientists recently completed a compilation of regional stratigraphy and mineralogy of the Revett Formation and a mineral resource assessment of Revett-type copper-silver deposits. The USGS assessment indicates that a large area of USFS-administered land in northwestern Montana and northern Idaho may contain significant undiscovered Revett-type copper-silver deposits.

LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions.

PubMed

Chen, Jinbo; Scholz, Uwe; Zhou, Ruonan; Lange, Matthias

2018-03-01

In order to access and filter content of life-science databases, full text search is a widely applied query interface. But its high flexibility and intuitiveness is paid for with potentially imprecise and incomplete query results. To reduce this drawback, query assistance systems suggest those combinations of keywords with the highest potential to match most of the relevant data records. Widespread approaches are syntactic query corrections that avoid misspelling and support expansion of words by suffixes and prefixes. Synonym expansion approaches apply thesauri, ontologies, and query logs. All need laborious curation and maintenance. Furthermore, access to query logs is in general restricted. Approaches that infer related queries by their query profile like research field, geographic location, co-authorship, affiliation etc. require user's registration and its public accessibility that contradict privacy concerns. To overcome these drawbacks, we implemented LAILAPS-QSM, a machine learning approach that reconstruct possible linguistic contexts of a given keyword query. The context is referred from the text records that are stored in the databases that are going to be queried or extracted for a general purpose query suggestion from PubMed abstracts and UniProt data. The supplied tool suite enables the pre-processing of these text records and the further computation of customized distributed word vectors. The latter are used to suggest alternative keyword queries. An evaluated of the query suggestion quality was done for plant science use cases. Locally present experts enable a cost-efficient quality assessment in the categories trait, biological entity, taxonomy, affiliation, and metabolic function which has been performed using ontology term similarities. LAILAPS-QSM mean information content similarity for 15 representative queries is 0.70, whereas 34% have a score above 0.80. In comparison, the information content similarity for human expert made query suggestions is 0.90. The software is either available as tool set to build and train dedicated query suggestion services or as already trained general purpose RESTful web service. The service uses open interfaces to be seamless embeddable into database frontends. The JAVA implementation uses highly optimized data structures and streamlined code to provide fast and scalable response for web service calls. The source code of LAILAPS-QSM is available under GNU General Public License version 2 in Bitbucket GIT repository: https://bitbucket.org/ipk_bit_team/bioescorte-suggestion.

Facilitating Cohort Discovery by Enhancing Ontology Exploration, Query Management and Query Sharing for Large Clinical Data Repositories.

PubMed

Tao, Shiqiang; Cui, Licong; Wu, Xi; Zhang, Guo-Qiang

2017-01-01

To help researchers better access clinical data, we developed a prototype query engine called DataSphere for exploring large-scale integrated clinical data repositories. DataSphere expedites data importing using a NoSQL data management system and dynamically renders its user interface for concept-based querying tasks. DataSphere provides an interactive query-building interface together with query translation and optimization strategies, which enable users to build and execute queries effectively and efficiently. We successfully loaded a dataset of one million patients for University of Kentucky (UK) Healthcare into DataSphere with more than 300 million clinical data records. We evaluated DataSphere by comparing it with an instance of i2b2 deployed at UK Healthcare, demonstrating that DataSphere provides enhanced user experience for both query building and execution.

Facilitating Cohort Discovery by Enhancing Ontology Exploration, Query Management and Query Sharing for Large Clinical Data Repositories

PubMed Central

Tao, Shiqiang; Cui, Licong; Wu, Xi; Zhang, Guo-Qiang

2017-01-01

To help researchers better access clinical data, we developed a prototype query engine called DataSphere for exploring large-scale integrated clinical data repositories. DataSphere expedites data importing using a NoSQL data management system and dynamically renders its user interface for concept-based querying tasks. DataSphere provides an interactive query-building interface together with query translation and optimization strategies, which enable users to build and execute queries effectively and efficiently. We successfully loaded a dataset of one million patients for University of Kentucky (UK) Healthcare into DataSphere with more than 300 million clinical data records. We evaluated DataSphere by comparing it with an instance of i2b2 deployed at UK Healthcare, demonstrating that DataSphere provides enhanced user experience for both query building and execution. PMID:29854239

Improve Performance of Data Warehouse by Query Cache

NASA Astrophysics Data System (ADS)

Gour, Vishal; Sarangdevot, S. S.; Sharma, Anand; Choudhary, Vinod

2010-11-01

The primary goal of data warehouse is to free the information locked up in the operational database so that decision makers and business analyst can make queries, analysis and planning regardless of the data changes in operational database. As the number of queries is large, therefore, in certain cases there is reasonable probability that same query submitted by the one or multiple users at different times. Each time when query is executed, all the data of warehouse is analyzed to generate the result of that query. In this paper we will study how using query cache improves performance of Data Warehouse and try to find the common problems faced. These kinds of problems are faced by Data Warehouse administrators which are minimizes response time and improves the efficiency of query in data warehouse overall, particularly when data warehouse is updated at regular interval.

Complex analyses on clinical information systems using restricted natural language querying to resolve time-event dependencies.

PubMed

Safari, Leila; Patrick, Jon D

2018-06-01

This paper reports on a generic framework to provide clinicians with the ability to conduct complex analyses on elaborate research topics using cascaded queries to resolve internal time-event dependencies in the research questions, as an extension to the proposed Clinical Data Analytics Language (CliniDAL). A cascaded query model is proposed to resolve internal time-event dependencies in the queries which can have up to five levels of criteria starting with a query to define subjects to be admitted into a study, followed by a query to define the time span of the experiment. Three more cascaded queries can be required to define control groups, control variables and output variables which all together simulate a real scientific experiment. According to the complexity of the research questions, the cascaded query model has the flexibility of merging some lower level queries for simple research questions or adding a nested query to each level to compose more complex queries. Three different scenarios (one of them contains two studies) are described and used for evaluation of the proposed solution. CliniDAL's complex analyses solution enables answering complex queries with time-event dependencies at most in a few hours which manually would take many days. An evaluation of results of the research studies based on the comparison between CliniDAL and SQL solutions reveals high usability and efficiency of CliniDAL's solution. Copyright © 2018 Elsevier Inc. All rights reserved.

Evaluation of Sub Query Performance in SQL Server

NASA Astrophysics Data System (ADS)

Oktavia, Tanty; Sujarwo, Surya

2014-03-01

The paper explores several sub query methods used in a query and their impact on the query performance. The study uses experimental approach to evaluate the performance of each sub query methods combined with indexing strategy. The sub query methods consist of in, exists, relational operator and relational operator combined with top operator. The experimental shows that using relational operator combined with indexing strategy in sub query has greater performance compared with using same method without indexing strategy and also other methods. In summary, for application that emphasized on the performance of retrieving data from database, it better to use relational operator combined with indexing strategy. This study is done on Microsoft SQL Server 2012.

HITRANonline: a New Structure and Interface for HITRAN Line Lists and Cross Sections

NASA Astrophysics Data System (ADS)

Hill, Christian; Rothman, Laurence S.; Gordon, Iouli E.; Kochanov, Roman V.; Wcislo, Piotr; Wilzewski, Jonas

2015-06-01

We present HITRANonline, an online interface to the internationally-recognised HITRAN molecular spectroscopic database[1], and describe the structure of its relational database backend[2]. As the amount and complexity of spectroscopic data on molecules used in atmospheric modelling has increased, the existing 160-character, text-based format has become inadequate for its description. For example, line shapes such as the Hartmann-Tran profile[3] require up to six parameters for their full description (each with uncertainties and references), data is available on line-broadening by species other than ``air'' and ``self'' and more than the current maximum of 10 isotopologues of some molecules (for example, CO_2) can be important for accurate radiative-transfer modelling. The new relational database structure overcomes all of these limitations as well as allowing for better data provenance through ``timestamping'' of transitions and a direct link between items of data and their literature sources. To take full advantage of this new database structure, the online interface HITRANonline, available at www.hitran.org, provides a user-friendly way to make queries of HITRAN data with the option of returning it in a customizable format with user-defined fields and precisions. Binary formats such as HDF-5 are also supported. In addition to the data, each query also produces its own bibliography (in HTML and BibTeX formats), ``README'' documentation and interactive graph for easy visualization. L. S. Rothman et al., JSQRT 130, 4-50 (2013). C. Hill, I. E. Gordon, L. S. Rothman, J. Tennyson, JQSRT130, 51-61 (2013). N. H. Ngo, D. Lisak, H. Tran, J.-M. Hartmann, JQSRT 129, 89--100, (2013); erratum: JQSRT 134, 105 (2014). This work has been supported by NASA Aura Science Team Grant NNX14AI55G and NASA Planetary Atmospheres Grant NNX13AI59G.

Secure Skyline Queries on Cloud Platform.

PubMed

Liu, Jinfei; Yang, Juncheng; Xiong, Li; Pei, Jian

2017-04-01

Outsourcing data and computation to cloud server provides a cost-effective way to support large scale data storage and query processing. However, due to security and privacy concerns, sensitive data (e.g., medical records) need to be protected from the cloud server and other unauthorized users. One approach is to outsource encrypted data to the cloud server and have the cloud server perform query processing on the encrypted data only. It remains a challenging task to support various queries over encrypted data in a secure and efficient way such that the cloud server does not gain any knowledge about the data, query, and query result. In this paper, we study the problem of secure skyline queries over encrypted data. The skyline query is particularly important for multi-criteria decision making but also presents significant challenges due to its complex computations. We propose a fully secure skyline query protocol on data encrypted using semantically-secure encryption. As a key subroutine, we present a new secure dominance protocol, which can be also used as a building block for other queries. Finally, we provide both serial and parallelized implementations and empirically study the protocols in terms of efficiency and scalability under different parameter settings, verifying the feasibility of our proposed solutions.

Distributed query plan generation using multiobjective genetic algorithm.

PubMed

Panicker, Shina; Kumar, T V Vijay

2014-01-01

A distributed query processing strategy, which is a key performance determinant in accessing distributed databases, aims to minimize the total query processing cost. One way to achieve this is by generating efficient distributed query plans that involve fewer sites for processing a query. In the case of distributed relational databases, the number of possible query plans increases exponentially with respect to the number of relations accessed by the query and the number of sites where these relations reside. Consequently, computing optimal distributed query plans becomes a complex problem. This distributed query plan generation (DQPG) problem has already been addressed using single objective genetic algorithm, where the objective is to minimize the total query processing cost comprising the local processing cost (LPC) and the site-to-site communication cost (CC). In this paper, this DQPG problem is formulated and solved as a biobjective optimization problem with the two objectives being minimize total LPC and minimize total CC. These objectives are simultaneously optimized using a multiobjective genetic algorithm NSGA-II. Experimental comparison of the proposed NSGA-II based DQPG algorithm with the single objective genetic algorithm shows that the former performs comparatively better and converges quickly towards optimal solutions for an observed crossover and mutation probability.

Distributed Query Plan Generation Using Multiobjective Genetic Algorithm

PubMed Central

Panicker, Shina; Vijay Kumar, T. V.

2014-01-01

A distributed query processing strategy, which is a key performance determinant in accessing distributed databases, aims to minimize the total query processing cost. One way to achieve this is by generating efficient distributed query plans that involve fewer sites for processing a query. In the case of distributed relational databases, the number of possible query plans increases exponentially with respect to the number of relations accessed by the query and the number of sites where these relations reside. Consequently, computing optimal distributed query plans becomes a complex problem. This distributed query plan generation (DQPG) problem has already been addressed using single objective genetic algorithm, where the objective is to minimize the total query processing cost comprising the local processing cost (LPC) and the site-to-site communication cost (CC). In this paper, this DQPG problem is formulated and solved as a biobjective optimization problem with the two objectives being minimize total LPC and minimize total CC. These objectives are simultaneously optimized using a multiobjective genetic algorithm NSGA-II. Experimental comparison of the proposed NSGA-II based DQPG algorithm with the single objective genetic algorithm shows that the former performs comparatively better and converges quickly towards optimal solutions for an observed crossover and mutation probability. PMID:24963513

Towards Hybrid Online On-Demand Querying of Realtime Data with Stateful Complex Event Processing

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

Zhou, Qunzhi; Simmhan, Yogesh; Prasanna, Viktor K.

Emerging Big Data applications in areas like e-commerce and energy industry require both online and on-demand queries to be performed over vast and fast data arriving as streams. These present novel challenges to Big Data management systems. Complex Event Processing (CEP) is recognized as a high performance online query scheme which in particular deals with the velocity aspect of the 3-V’s of Big Data. However, traditional CEP systems do not consider data variety and lack the capability to embed ad hoc queries over the volume of data streams. In this paper, we propose H2O, a stateful complex event processing framework,more » to support hybrid online and on-demand queries over realtime data. We propose a semantically enriched event and query model to address data variety. A formal query algebra is developed to precisely capture the stateful and containment semantics of online and on-demand queries. We describe techniques to achieve the interactive query processing over realtime data featured by efficient online querying, dynamic stream data persistence and on-demand access. The system architecture is presented and the current implementation status reported.« less

Demonstration of Hadoop-GIS: A Spatial Data Warehousing System Over MapReduce.

PubMed

Aji, Ablimit; Sun, Xiling; Vo, Hoang; Liu, Qioaling; Lee, Rubao; Zhang, Xiaodong; Saltz, Joel; Wang, Fusheng

2013-11-01

The proliferation of GPS-enabled devices, and the rapid improvement of scientific instruments have resulted in massive amounts of spatial data in the last decade. Support of high performance spatial queries on large volumes data has become increasingly important in numerous fields, which requires a scalable and efficient spatial data warehousing solution as existing approaches exhibit scalability limitations and efficiency bottlenecks for large scale spatial applications. In this demonstration, we present Hadoop-GIS - a scalable and high performance spatial query system over MapReduce. Hadoop-GIS provides an efficient spatial query engine to process spatial queries, data and space based partitioning, and query pipelines that parallelize queries implicitly on MapReduce. Hadoop-GIS also provides an expressive, SQL-like spatial query language for workload specification. We will demonstrate how spatial queries are expressed in spatially extended SQL queries, and submitted through a command line/web interface for execution. Parallel to our system demonstration, we explain the system architecture and details on how queries are translated to MapReduce operators, optimized, and executed on Hadoop. In addition, we will showcase how the system can be used to support two representative real world use cases: large scale pathology analytical imaging, and geo-spatial data warehousing.

Basic growth relationships in thinned and unthinned longleaf pine plantations

Treesearch

V. Clark Baldwin; Daniel J. Leduc; K. O. Peterson; Bernard R. Parresol

1998-01-01

Compilation, editing, and formatting of seven long-term longleaf pine (Pinus palustris Mill.) growth and yield studies has "been completed"and development of a growth and yield prediction system for longleaf pine plantations is underway. The studies are located in Central Louisiana, East Texas, Southern Mississippi, Southern Alabama, and Northern Florida...

Directions in Marriage and Family Therapy, 1994.

ERIC Educational Resources Information Center

Cermele, Debra E., Ed.

1994-01-01

In an effort to help practitioners deal with the great volume of current literature in the field of marriage and family therapy, this compilation attempts to present clinically relevant material in a user-friendly format. Topics selected for inclusion are believed to be up-to-date, informative, and clinically meaningful--as well as theoretically…

Directions in Marriage and Family Therapy: Volume 1.

ERIC Educational Resources Information Center

Directions in Marriage and Family Therapy, 1993

1993-01-01

In an effort to help practitioners deal with the great volume of current literature in the field of marriage and family therapy, this compilation attempts to present clinically relevant material in a user-friendly format. Topics selected for inclusion are believed to be up-to-date, informative, and clinically meaningful--as well as theoretically…

Amino Acid Distribution Rules Predict Protein Fold: Protein Grammar for Beta-Strand Sandwich-Like Structures

PubMed Central

Kister, Alexander

2015-01-01

We present an alternative approach to protein 3D folding prediction based on determination of rules that specify distribution of “favorable” residues, that are mainly responsible for a given fold formation, and “unfavorable” residues, that are incompatible with that fold, in polypeptide sequences. The process of determining favorable and unfavorable residues is iterative. The starting assumptions are based on the general principles of protein structure formation as well as structural features peculiar to a protein fold under investigation. The initial assumptions are tested one-by-one for a set of all known proteins with a given structure. The assumption is accepted as a “rule of amino acid distribution” for the protein fold if it holds true for all, or near all, structures. If the assumption is not accepted as a rule, it can be modified to better fit the data and then tested again in the next step of the iterative search algorithm, or rejected. We determined the set of amino acid distribution rules for a large group of beta sandwich-like proteins characterized by a specific arrangement of strands in two beta sheets. It was shown that this set of rules is highly sensitive (~90%) and very specific (~99%) for identifying sequences of proteins with specified beta sandwich fold structure. The advantage of the proposed approach is that it does not require that query proteins have a high degree of homology to proteins with known structure. So long as the query protein satisfies residue distribution rules, it can be confidently assigned to its respective protein fold. Another advantage of our approach is that it allows for a better understanding of which residues play an essential role in protein fold formation. It may, therefore, facilitate rational protein engineering design. PMID:25625198

The IRIS Federator: Accessing Seismological Data Across Data Centers

NASA Astrophysics Data System (ADS)

Trabant, C. M.; Van Fossen, M.; Ahern, T. K.; Weekly, R. T.

2015-12-01

In 2013 the International Federation of Digital Seismograph Networks (FDSN) approved a specification for web service interfaces for accessing seismological station metadata, time series and event parameters. Since then, a number of seismological data centers have implemented FDSN service interfaces, with more implementations in development. We have developed a new system called the IRIS Federator which leverages this standardization and provides the scientific community with a service for easy discovery and access of seismological data across FDSN data centers. These centers are located throughout the world and this work represents one model of a system for data collection across geographic and political boundaries.The main components of the IRIS Federator are a catalog of time series metadata holdings at each data center and a web service interface for searching the catalog. The service interface is designed to support client­-side federated data access, a model in which the client (software run by the user) queries the catalog and then collects the data from each identified center. By default the results are returned in a format suitable for direct submission to those web services, but could also be formatted in a simple text format for general data discovery purposes. The interface will remove any duplication of time series channels between data centers according to a set of business rules by default, however a user may request results with all duplicate time series entries included. We will demonstrate how client­-side federation is being incorporated into some of the DMC's data access tools. We anticipate further enhancement of the IRIS Federator to improve data discovery in various scenarios and to improve usefulness to communities beyond seismology.Data centers with FDSN web services: http://www.fdsn.org/webservices/The IRIS Federator query interface: http://service.iris.edu/irisws/fedcatalog/1/

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

PubMed

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

2000-01-01

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

A prototype molecular interactive collaborative environment (MICE).

PubMed

Bourne, P; Gribskov, M; Johnson, G; Moreland, J; Wavra, S; Weissig, H

1998-01-01

Illustrations of macromolecular structure in the scientific literature contain a high level of semantic content through which the authors convey, among other features, the biological function of that macromolecule. We refer to these illustrations as molecular scenes. Such scenes, if available electronically, are not readily accessible for further interactive interrogation. The basic PDB format does not retain features of the scene; formats like PostScript retain the scene but are not interactive; and the many formats used by individual graphics programs, while capable of reproducing the scene, are neither interchangeable nor can they be stored in a database and queried for features of the scene. MICE defines a Molecular Scene Description Language (MSDL) which allows scenes to be stored in a relational database (a molecular scene gallery) and queried. Scenes retrieved from the gallery are rendered in Virtual Reality Modeling Language (VRML) and currently displayed in WebView, a VRML browser modified to support the Virtual Reality Behavior System (VRBS) protocol. VRBS provides communication between multiple client browsers, each capable of manipulating the scene. This level of collaboration works well over standard Internet connections and holds promise for collaborative research at a distance and distance learning. Further, via VRBS, the VRML world can be used as a visual cue to trigger an application such as a remote MEME search. MICE is very much work in progress. Current work seeks to replace WebView with Netscape, Cosmoplayer, a standard VRML plug-in, and a Java-based console. The console consists of a generic kernel suitable for multiple collaborative applications and additional application-specific controls. Further details of the MICE project are available at http:/(/)mice.sdsc.edu.

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

PubMed Central

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

2000-01-01

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

Space environment data storage and access: lessons learned and recommendations for the future

NASA Astrophysics Data System (ADS)

Evans, Hugh; Heynderickx, Daniel

2012-07-01

With the ever increasing volume of space environment data available at present and planned for the near future, the demands on data storage and access methods are increasing as well. In addition, continued access to historical, archived data remains crucial. On the basis of many years of experience, the authors identify the following issues as important for continued and efficient handling of datasets now and in the future: The huge data volumes currently or very soon avaiable from a number of space missions will limi direct Internet download access to even relatively short epoch ranges of data. Therefore, data providers should establish or extend standardised data (post-) processing services so that only data query results should be downloaded. Although a single standardised data format will in all likelihood remain utopia, data providers should at least include extensive metadata with their data products, according to established standards and practices (e.g. ISTP, SPASE). Standardisation of (sets of) metadata greatly facilitates data mining and querying. The use of SQL database storage should be considered instead of, or in parallel with, classic storage of data files. The use of SQL does away with having to handle file parsing and processing, while at the same time standard access protocols can be used to (remotely) connect to such data repositories. Many data holdings are still lacking in extensive descriptions of data provenance (e.g. instrument description), content and format. Unfortunately, detailed data information is usually rejected by scientific and technical journals. Re-processing of historical archived datasets into modern formats, making them easily available and usable, is urgently required, as knowledge is being lost. A global data directory has still not been achieved; policy makers should enforce stricter rules for "broadcasting" dataset information.

Geologic database for digital geology of California, Nevada, and Utah: an application of the North American Data Model

USGS Publications Warehouse

Bedford, David R.; Ludington, Steve; Nutt, Constance M.; Stone, Paul A.; Miller, David M.; Miller, Robert J.; Wagner, David L.; Saucedo, George J.

2003-01-01

The USGS is creating an integrated national database for digital state geologic maps that includes stratigraphic, age, and lithologic information. The majority of the conterminous 48 states have digital geologic base maps available, often at scales of 1:500,000. This product is a prototype, and is intended to demonstrate the types of derivative maps that will be possible with the national integrated database. This database permits the creation of a number of types of maps via simple or sophisticated queries, maps that may be useful in a number of areas, including mineral-resource assessment, environmental assessment, and regional tectonic evolution. This database is distributed with three main parts: a Microsoft Access 2000 database containing geologic map attribute data, an Arc/Info (Environmental Systems Research Institute, Redlands, California) Export format file containing points representing designation of stratigraphic regions for the Geologic Map of Utah, and an ArcView 3.2 (Environmental Systems Research Institute, Redlands, California) project containing scripts and dialogs for performing a series of generalization and mineral resource queries. IMPORTANT NOTE: Spatial data for the respective stage geologic maps is not distributed with this report. The digital state geologic maps for the states involved in this report are separate products, and two of them are produced by individual state agencies, which may be legally and/or financially responsible for this data. However, the spatial datasets for maps discussed in this report are available to the public. Questions regarding the distribution, sale, and use of individual state geologic maps should be sent to the respective state agency. We do provide suggestions for obtaining and formatting the spatial data to make it compatible with data in this report. See section ‘Obtaining and Formatting Spatial Data’ in the PDF version of the report.

Compiling the space shuttle wind tunnel data base: An exercise in technical and managerial innovators

NASA Technical Reports Server (NTRS)

Kemp, N. D.

1983-01-01

Engineers evaluating Space Shuttle flight data and performance results are using a massive data base of wind tunnel test data. A wind tunnel test data base of the magnitude attained is a major accomplishment. The Apollo program spawned an automated wind tunnel data analysis system called SADSAC developed by the Chrysler Space Division. An improved version of this system renamed DATAMAN was used by Chrysler to document analyzed wind tunnel data and data bank the test data in standardized formats. These analysis documents, associated computer graphics and standard formatted data were disseminated nationwide to the Shuttle technical community. These outputs became the basis for substantiating and certifying the flight worthiness of the Space Shuttle and for improving future designs. As an aid to future programs this paper documents the lessons learned in compiling the massive wind tunnel test data base for developing the Space Shuttle. In particular, innovative managerial and technical concepts evolved in the course of conceiving and developing this successful DATAMAN system and the methods and organization for applying the system are presented.

Significant Published Articles for Pharmacy Nutrition Support Practice in 2014 and 2015.

PubMed

Dickerson, Roland N; Kumpf, Vanessa J; Blackmer, Allison B; Bingham, Angela L; Tucker, Anne M; Ybarra, Joseph V; Kraft, Michael D; Canada, Todd W

2016-07-01

To assist the pharmacy clinician engaged in nutrition support in staying current with the most pertinent literature. Several experienced board-certified clinical pharmacists engaged in nutrition support therapy compiled a list of articles published in 2014 and 2015 that they considered to be important to their practice. Only those articles available in print format were considered for potential inclusion. Articles available only in preprint electronic format were not evaluated. The citation list was compiled into a single spreadsheet where the author participants were asked to ascertain whether they considered the paper important to nutrition support pharmacy practice. A culled list of publications was then identified whereby the majority of author participants (at least 5 out of 8) considered the paper to be important. A total of 108 articles were identified; 36 of which were considered to be of high importance. An important guideline article published in early 2016, but not ranked, was also included. The top-ranked articles from the primary literature were reviewed. It is recommended that the informed pharmacist, who is engaged in nutrition support therapy, be familiar with the majority of these articles.

Using search engine query data to track pharmaceutical utilization: a study of statins.

PubMed

Schuster, Nathaniel M; Rogers, Mary A M; McMahon, Laurence F

2010-08-01

To examine temporal and geographic associations between Google queries for health information and healthcare utilization benchmarks. Retrospective longitudinal study. Using Google Trends and Google Insights for Search data, the search terms Lipitor (atorvastatin calcium; Pfizer, Ann Arbor, MI) and simvastatin were evaluated for change over time and for association with Lipitor revenues. The relationship between query data and community-based resource use per Medicare beneficiary was assessed for 35 US metropolitan areas. Google queries for Lipitor significantly decreased from January 2004 through June 2009 and queries for simvastatin significantly increased (P <.001 for both), particularly after Lipitor came off patent (P <.001 for change in slope). The mean number of Google queries for Lipitor correlated (r = 0.98) with the percentage change in Lipitor global revenues from 2004 to 2008 (P <.001). Query preference for Lipitor over simvastatin was positively associated (r = 0.40) with a community's use of Medicare services. For every 1% increase in utilization of Medicare services in a community, there was a 0.2-unit increase in the ratio of Lipitor queries to simvastatin queries in that community (P = .02). Specific search engine queries for medical information correlate with pharmaceutical revenue and with overall healthcare utilization in a community. This suggests that search query data can track community-wide characteristics in healthcare utilization and have the potential for informing payers and policy makers regarding trends in utilization.

CSRQ: Communication-Efficient Secure Range Queries in Two-Tiered Sensor Networks

PubMed Central

Dai, Hua; Ye, Qingqun; Yang, Geng; Xu, Jia; He, Ruiliang

2016-01-01

In recent years, we have seen many applications of secure query in two-tiered wireless sensor networks. Storage nodes are responsible for storing data from nearby sensor nodes and answering queries from Sink. It is critical to protect data security from a compromised storage node. In this paper, the Communication-efficient Secure Range Query (CSRQ)—a privacy and integrity preserving range query protocol—is proposed to prevent attackers from gaining information of both data collected by sensor nodes and queries issued by Sink. To preserve privacy and integrity, in addition to employing the encoding mechanisms, a novel data structure called encrypted constraint chain is proposed, which embeds the information of integrity verification. Sink can use this encrypted constraint chain to verify the query result. The performance evaluation shows that CSRQ has lower communication cost than the current range query protocols. PMID:26907293

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.

Improved Data Access From the Northern California Earthquake Data Center

NASA Astrophysics Data System (ADS)

Neuhauser, D.; Oppenheimer, D.; Zuzlewski, S.; Klein, F.; Jensen, E.; Gee, L.; Murray, M.; Romanowicz, B.

2002-12-01

The NCEDC is a joint project of the UC Berkeley Seismological Laboratory and the USGS Menlo Park to provide a long-term archive and distribution center for geophysical data for northern California. Most data are available via the Web at http://quake.geo.berkeley.edu and research accounts are available for access to specialized datasets. Current efforts continue to expand the available datasets, enhance distribution methods, and to provide rapid access to all datasets. The NCEDC archives continuous and event-based seismic and geophysical time-series data from the BDSN, the USGS NCSN, the UNR Seismic Network, the Parkfield HRSN, and the Calpine/Unocal Geysers network. In collaboration with the USGS, the NCEDC has archived a total of 887 channels from 139 sites of the "USGS low-frequency" geophysical network (UL), including data from strainmeters, creep meters, magnetometers, water well levels, and tiltmeters. There are 336 active continuous data channels that are updated at the NCEDC on a daily basis. Geodetic data from the BARD network of over 40 continuously recording GPS sites are archived at the NCEDC in both raw and RINEX format. The NCEDC is the primary archive for survey-mode GPS and other geodetic data collected in northern California by the USGS, universities, and other agencies. All of the BARD data and GPS data archived from USGS Menlo Park surveys are now available through the GPS Seamless Archive Centers (GSAC), and by FTP directly from the NCEDC. Virtually all time-series data at the NCEDC are now available in SEED with complete instrument responses. Assembling, verifying, and maintaining the response information for these networks is a huge task, and is accomplished through the collaborative efforts of the NCEDC and the contributing agencies. Until recently, the NCSN waveform data were available only through research accounts and special request methods due to incomplete instrument responses. In the last year, the USGS compiled the necessary descriptions for for both historic and current NCSN instrumentation. The NCEDC and USGS jointly developed a procedure to create and maintain the hardware attributes and instrument responses at the NCEDC for the 3500 NCSN channels. As a result, the NCSN waveform data can now be distributed in SEED format. The NCEDC provides access to waveform data through Web forms, email requests, and programming interfaces. The SeismiQuery Web interface provides information about data holdings. NetDC allows users to retrieve inventory information, instrument responses, and waveforms in SEED format. STP provides both a Web and programming interface to retrieve data in SEED or other user-friendly formats. Through the newly formed California Integrated Seismic Network, we are working with the SCEDC to provide unified access to California earthquake data.

Improving accuracy for identifying related PubMed queries by an integrated approach.

PubMed

Lu, Zhiyong; Wilbur, W John

2009-10-01

PubMed is the most widely used tool for searching biomedical literature online. As with many other online search tools, a user often types a series of multiple related queries before retrieving satisfactory results to fulfill a single information need. Meanwhile, it is also a common phenomenon to see a user type queries on unrelated topics in a single session. In order to study PubMed users' search strategies, it is necessary to be able to automatically separate unrelated queries and group together related queries. Here, we report a novel approach combining both lexical and contextual analyses for segmenting PubMed query sessions and identifying related queries and compare its performance with the previous approach based solely on concept mapping. We experimented with our integrated approach on sample data consisting of 1539 pairs of consecutive user queries in 351 user sessions. The prediction results of 1396 pairs agreed with the gold-standard annotations, achieving an overall accuracy of 90.7%. This demonstrates that our approach is significantly better than the previously published method. By applying this approach to a one day query log of PubMed, we found that a significant proportion of information needs involved more than one PubMed query, and that most of the consecutive queries for the same information need are lexically related. Finally, the proposed PubMed distance is shown to be an accurate and meaningful measure for determining the contextual similarity between biological terms. The integrated approach can play a critical role in handling real-world PubMed query log data as is demonstrated in our experiments.

Improving accuracy for identifying related PubMed queries by an integrated approach

PubMed Central

Lu, Zhiyong; Wilbur, W. John

2009-01-01

PubMed is the most widely used tool for searching biomedical literature online. As with many other online search tools, a user often types a series of multiple related queries before retrieving satisfactory results to fulfill a single information need. Meanwhile, it is also a common phenomenon to see a user type queries on unrelated topics in a single session. In order to study PubMed users’ search strategies, it is necessary to be able to automatically separate unrelated queries and group together related queries. Here, we report a novel approach combining both lexical and contextual analyses for segmenting PubMed query sessions and identifying related queries and compare its performance with the previous approach based solely on concept mapping. We experimented with our integrated approach on sample data consisting of 1,539 pairs of consecutive user queries in 351 user sessions. The prediction results of 1,396 pairs agreed with the gold-standard annotations, achieving an overall accuracy of 90.7%. This demonstrates that our approach is significantly better than the previously published method. By applying this approach to a one day query log of PubMed, we found that a significant proportion of information needs involved more than one PubMed query, and that most of the consecutive queries for the same information need are lexically related. Finally, the proposed PubMed distance is shown to be an accurate and meaningful measure for determining the contextual similarity between biological terms. The integrated approach can play a critical role in handling real-world PubMed query log data as is demonstrated in our experiments. PMID:19162232

Multi-Bit Quantum Private Query

NASA Astrophysics Data System (ADS)

Shi, Wei-Xu; Liu, Xing-Tong; Wang, Jian; Tang, Chao-Jing

2015-09-01

Most of the existing Quantum Private Queries (QPQ) protocols provide only single-bit queries service, thus have to be repeated several times when more bits are retrieved. Wei et al.'s scheme for block queries requires a high-dimension quantum key distribution system to sustain, which is still restricted in the laboratory. Here, based on Markus Jakobi et al.'s single-bit QPQ protocol, we propose a multi-bit quantum private query protocol, in which the user can get access to several bits within one single query. We also extend the proposed protocol to block queries, using a binary matrix to guard database security. Analysis in this paper shows that our protocol has better communication complexity, implementability and can achieve a considerable level of security.

Evaluation of Content-Matched Range Monitoring Queries over Moving Objects in Mobile Computing Environments.

PubMed

Jung, HaRim; Song, MoonBae; Youn, Hee Yong; Kim, Ung Mo

2015-09-18

A content-matched (CM) rangemonitoring query overmoving objects continually retrieves the moving objects (i) whose non-spatial attribute values are matched to given non-spatial query values; and (ii) that are currently located within a given spatial query range. In this paper, we propose a new query indexing structure, called the group-aware query region tree (GQR-tree) for efficient evaluation of CMrange monitoring queries. The primary role of the GQR-tree is to help the server leverage the computational capabilities of moving objects in order to improve the system performance in terms of the wireless communication cost and server workload. Through a series of comprehensive simulations, we verify the superiority of the GQR-tree method over the existing methods.

Estimating Missing Features to Improve Multimedia Information Retrieval

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

Bagherjeiran, A; Love, N S; Kamath, C

Retrieval in a multimedia database usually involves combining information from different modalities of data, such as text and images. However, all modalities of the data may not be available to form the query. The retrieval results from such a partial query are often less than satisfactory. In this paper, we present an approach to complete a partial query by estimating the missing features in the query. Our experiments with a database of images and their associated captions show that, with an initial text-only query, our completion method has similar performance to a full query with both image and text features.more » In addition, when we use relevance feedback, our approach outperforms the results obtained using a full query.« less

a Spatiotemporal Aggregation Query Method Using Multi-Thread Parallel Technique Based on Regional Division

NASA Astrophysics Data System (ADS)

Liao, S.; Chen, L.; Li, J.; Xiong, W.; Wu, Q.

2015-07-01

Existing spatiotemporal database supports spatiotemporal aggregation query over massive moving objects datasets. Due to the large amounts of data and single-thread processing method, the query speed cannot meet the application requirements. On the other hand, the query efficiency is more sensitive to spatial variation then temporal variation. In this paper, we proposed a spatiotemporal aggregation query method using multi-thread parallel technique based on regional divison and implemented it on the server. Concretely, we divided the spatiotemporal domain into several spatiotemporal cubes, computed spatiotemporal aggregation on all cubes using the technique of multi-thread parallel processing, and then integrated the query results. By testing and analyzing on the real datasets, this method has improved the query speed significantly.

Constructing Uniform Resource Locators (URLs) for Searching the Marine Realms Information Bank

USGS Publications Warehouse

Linck, Guthrie A.; Allwardt, Alan O.; Lightsom, Frances L.

2009-01-01

The Marine Realms Information Bank (MRIB) is a digital library that provides access to free online scientific information about the oceans and coastal regions. To search its collection, MRIB uses a Common Gateway Interface (CGI) program, which allows automated search requests using Uniform Resource Locators (URLs). This document provides an overview of how to construct URLs to execute MRIB queries. The parameters listed allow detailed control of which records are retrieved, how they are returned, and how their display is formatted.

TADPLOT program, version 2.0: User's guide

NASA Technical Reports Server (NTRS)

Hammond, Dana P.

1991-01-01

The TADPLOT Program, Version 2.0 is described. The TADPLOT program is a software package coordinated by a single, easy-to-use interface, enabling the researcher to access several standard file formats, selectively collect specific subsets of data, and create full-featured publication and viewgraph quality plots. The user-interface was designed to be independent from any file format, yet provide capabilities to accommodate highly specialized data queries. Integrated with an applications software network, data can be assessed, collected, and viewed quickly and easily. Since the commands are data independent, subsequent modifications to the file format will be transparent, while additional file formats can be integrated with minimal impact on the user-interface. The graphical capabilities are independent of the method of data collection; thus, the data specification and subsequent plotting can be modified and upgraded as separate functional components. The graphics kernel selected adheres to the full functional specifications of the CORE standard. Both interface and postprocessing capabilities are fully integrated into TADPLOT.

Montana geoenvironmental explorer

USGS Publications Warehouse

Lee, Greg K.

2001-01-01

This report is the result of a multidisciplinary effort to assess relative potential for acidic, metal-rich drainage in the State of Montana; evaluate alternative GIS-based modeling strategies; and provide the statewide digital spatial data produced and compiled for the project. The CD is usable on various computer systems (Windows 95, 98, NT, and 2000; MacOS 7.1 or later; many versions of UNIX and Linux; and OS/2). This report and maps are in PDF format, and the data have been provided in various GIS formats. Software for viewing the report and data is included.

DSPSR: Digital Signal Processing Software for Pulsar Astronomy

NASA Astrophysics Data System (ADS)

van Straten, W.; Bailes, M.

2010-10-01

DSPSR, written primarily in C++, is an open-source, object-oriented, digital signal processing software library and application suite for use in radio pulsar astronomy. The library implements an extensive range of modular algorithms for use in coherent dedispersion, filterbank formation, pulse folding, and other tasks. The software is installed and compiled using the standard GNU configure and make system, and is able to read astronomical data in 18 different file formats, including FITS, S2, CPSR, CPSR2, PuMa, PuMa2, WAPP, ASP, and Mark5.

Comprehensive database of wellbore temperatures and drilling mud weight pressures by depth for Judge Digby field, Louisiana

USGS Publications Warehouse

Burke, Lauri

2010-01-01

This document serves as the repository for the unprocessed data used in the investigation of temperature and overpressure relations within the deep Tuscaloosa Formation in Judge Digby field. It is a compilation of all the publicly accessible wellbore temperature and pressure data for Judge Digby field, a prolific natural gas field producing from the Upper Cretaceous lower part of the Tuscaloosa Formation in the Gulf Coast region. This natural gas field is in Pointe Coupee Parish in the southern part of onshore Louisiana.

Pick_sw: a program for interactive picking of S-wave data, version 2.00

USGS Publications Warehouse

Ellefsen, Karl J.

2002-01-01

Program pick_sw is used to interactively pick travel times from S-wave data. It is assumed that the data are collected using 2 shots of opposite polarity at each shot location. The traces must be in either the SEG-2 format or the SU format. The program is written in the IDL and C programming languages, and the program is executed under the Windows operating system. (The program may also execute under other operating systems like UNIX if the C language functions are re-compiled).

TS-SRP/PACK - COMPUTER PROGRAMS TO CHARACTERIZE ALLOYS AND PREDICT CYCLIC LIFE USING THE TOTAL STRAIN VERSION OF STRAINRANGE PARTITIONING

NASA Technical Reports Server (NTRS)

Saltsman, J. F.

1994-01-01

TS-SRP/PACK is a set of computer programs for characterizing and predicting fatigue and creep-fatigue resistance of metallic materials in the high-temperature, long-life regime for isothermal and nonisothermal fatigue. The programs use the total strain version of the Strainrange Partitioning (TS-SRP). The user should be thoroughly familiar with the TS-SRP method before attempting to use any of these programs. The document for this program includes a theory manual as well as a detailed user's manual with a tutorial to guide the user in the proper use of TS-SRP. An extensive database has also been developed in a parallel effort. This database is an excellent source of high-temperature, creep-fatigue test data and can be used with other life-prediction methods as well. Five programs are included in TS-SRP/PACK along with the alloy database. The TABLE program is used to print the datasets, which are in NAMELIST format, in a reader friendly format. INDATA is used to create new datasets or add to existing ones. The FAIL program is used to characterize the failure behavior of an alloy as given by the constants in the strainrange-life relations used by the total strain version of SRP (TS-SRP) and the inelastic strainrange-based version of SRP. The program FLOW is used to characterize the flow behavior (the constitutive response) of an alloy as given by the constants in the flow equations used by TS-SRP. Finally, LIFE is used to predict the life of a specified cycle, using the constants characterizing failure and flow behavior determined by FAIL and FLOW. LIFE is written in interpretive BASIC to avoid compiling and linking every time the equation constants are changed. Four out of five programs in this package are written in FORTRAN 77 for IBM PC series and compatible computers running MS-DOS and are designed to read data using the NAMELIST format statement. The fifth is written in BASIC version 3.0 for IBM PC series and compatible computers running MS-DOS version 3.10. The executables require at least 239K of memory and DOS 3.1 or higher. To compile the source, a Lahey FORTRAN compiler is required. Source code modifications will be necessary if the compiler to be used does not support NAMELIST input. Probably the easiest revision to make is to use a list-directed READ statement. The standard distribution medium for this program is a set of two 5.25 inch 360K MS-DOS format diskettes. The contents of the diskettes are compressed using the PKWARE archiving tools. The utility to unarchive the files, PKUNZIP.EXE, is included. TS-SRP/PACK was developed in 1992.

A Framework for WWW Query Processing

NASA Technical Reports Server (NTRS)

Wu, Binghui Helen; Wharton, Stephen (Technical Monitor)

2000-01-01

Query processing is the most common operation in a DBMS. Sophisticated query processing has been mainly targeted at a single enterprise environment providing centralized control over data and metadata. Submitting queries by anonymous users on the web is different in such a way that load balancing or DBMS' accessing control becomes the key issue. This paper provides a solution by introducing a framework for WWW query processing. The success of this framework lies in the utilization of query optimization techniques and the ontological approach. This methodology has proved to be cost effective at the NASA Goddard Space Flight Center Distributed Active Archive Center (GDAAC).

QBIC project: querying images by content, using color, texture, and shape

NASA Astrophysics Data System (ADS)

Niblack, Carlton W.; Barber, Ron; Equitz, Will; Flickner, Myron D.; Glasman, Eduardo H.; Petkovic, Dragutin; Yanker, Peter; Faloutsos, Christos; Taubin, Gabriel

1993-04-01

In the query by image content (QBIC) project we are studying methods to query large on-line image databases using the images' content as the basis of the queries. Examples of the content we use include color, texture, and shape of image objects and regions. Potential applications include medical (`Give me other images that contain a tumor with a texture like this one'), photo-journalism (`Give me images that have blue at the top and red at the bottom'), and many others in art, fashion, cataloging, retailing, and industry. Key issues include derivation and computation of attributes of images and objects that provide useful query functionality, retrieval methods based on similarity as opposed to exact match, query by image example or user drawn image, the user interfaces, query refinement and navigation, high dimensional database indexing, and automatic and semi-automatic database population. We currently have a prototype system written in X/Motif and C running on an RS/6000 that allows a variety of queries, and a test database of over 1000 images and 1000 objects populated from commercially available photo clip art images. In this paper we present the main algorithms for color texture, shape and sketch query that we use, show example query results, and discuss future directions.

a Novel Approach of Indexing and Retrieving Spatial Polygons for Efficient Spatial Region Queries

NASA Astrophysics Data System (ADS)

Zhao, J. H.; Wang, X. Z.; Wang, F. Y.; Shen, Z. H.; Zhou, Y. C.; Wang, Y. L.

2017-10-01

Spatial region queries are more and more widely used in web-based applications. Mechanisms to provide efficient query processing over geospatial data are essential. However, due to the massive geospatial data volume, heavy geometric computation, and high access concurrency, it is difficult to get response in real time. Spatial indexes are usually used in this situation. In this paper, based on k-d tree, we introduce a distributed KD-Tree (DKD-Tree) suitbable for polygon data, and a two-step query algorithm. The spatial index construction is recursive and iterative, and the query is an in memory process. Both the index and query methods can be processed in parallel, and are implemented based on HDFS, Spark and Redis. Experiments on a large volume of Remote Sensing images metadata have been carried out, and the advantages of our method are investigated by comparing with spatial region queries executed on PostgreSQL and PostGIS. Results show that our approach not only greatly improves the efficiency of spatial region query, but also has good scalability, Moreover, the two-step spatial range query algorithm can also save cluster resources to support a large number of concurrent queries. Therefore, this method is very useful when building large geographic information systems.

Secure Skyline Queries on Cloud Platform

PubMed Central

Liu, Jinfei; Yang, Juncheng; Xiong, Li; Pei, Jian

2017-01-01

Outsourcing data and computation to cloud server provides a cost-effective way to support large scale data storage and query processing. However, due to security and privacy concerns, sensitive data (e.g., medical records) need to be protected from the cloud server and other unauthorized users. One approach is to outsource encrypted data to the cloud server and have the cloud server perform query processing on the encrypted data only. It remains a challenging task to support various queries over encrypted data in a secure and efficient way such that the cloud server does not gain any knowledge about the data, query, and query result. In this paper, we study the problem of secure skyline queries over encrypted data. The skyline query is particularly important for multi-criteria decision making but also presents significant challenges due to its complex computations. We propose a fully secure skyline query protocol on data encrypted using semantically-secure encryption. As a key subroutine, we present a new secure dominance protocol, which can be also used as a building block for other queries. Finally, we provide both serial and parallelized implementations and empirically study the protocols in terms of efficiency and scalability under different parameter settings, verifying the feasibility of our proposed solutions. PMID:28883710

Heuristic query optimization for query multiple table and multiple clausa on mobile finance application

NASA Astrophysics Data System (ADS)

Indrayana, I. N. E.; P, N. M. Wirasyanti D.; Sudiartha, I. KG

2018-01-01

Mobile application allow many users to access data from the application without being limited to space, space and time. Over time the data population of this application will increase. Data access time will cause problems if the data record has reached tens of thousands to millions of records.The objective of this research is to maintain the performance of data execution for large data records. One effort to maintain data access time performance is to apply query optimization method. The optimization used in this research is query heuristic optimization method. The built application is a mobile-based financial application using MySQL database with stored procedure therein. This application is used by more than one business entity in one database, thus enabling rapid data growth. In this stored procedure there is an optimized query using heuristic method. Query optimization is performed on a “Select” query that involves more than one table with multiple clausa. Evaluation is done by calculating the average access time using optimized and unoptimized queries. Access time calculation is also performed on the increase of population data in the database. The evaluation results shown the time of data execution with query heuristic optimization relatively faster than data execution time without using query optimization.

Demonstration of Hadoop-GIS: A Spatial Data Warehousing System Over MapReduce

PubMed Central

Aji, Ablimit; Sun, Xiling; Vo, Hoang; Liu, Qioaling; Lee, Rubao; Zhang, Xiaodong; Saltz, Joel; Wang, Fusheng

2016-01-01

The proliferation of GPS-enabled devices, and the rapid improvement of scientific instruments have resulted in massive amounts of spatial data in the last decade. Support of high performance spatial queries on large volumes data has become increasingly important in numerous fields, which requires a scalable and efficient spatial data warehousing solution as existing approaches exhibit scalability limitations and efficiency bottlenecks for large scale spatial applications. In this demonstration, we present Hadoop-GIS – a scalable and high performance spatial query system over MapReduce. Hadoop-GIS provides an efficient spatial query engine to process spatial queries, data and space based partitioning, and query pipelines that parallelize queries implicitly on MapReduce. Hadoop-GIS also provides an expressive, SQL-like spatial query language for workload specification. We will demonstrate how spatial queries are expressed in spatially extended SQL queries, and submitted through a command line/web interface for execution. Parallel to our system demonstration, we explain the system architecture and details on how queries are translated to MapReduce operators, optimized, and executed on Hadoop. In addition, we will showcase how the system can be used to support two representative real world use cases: large scale pathology analytical imaging, and geo-spatial data warehousing. PMID:27617325

Testing models for the formation of the equatorial ridge on Iapetus via crater counting

NASA Astrophysics Data System (ADS)

Damptz, Amanda L.; Dombard, Andrew J.; Kirchoff, Michelle R.

2018-03-01

Iapetus's equatorial ridge, visible in global views of the moon, is unique in the Solar System. The formation of this feature is likely attributed to a key event in the evolution of Iapetus, and various models have been proposed as the source of the ridge. By surveying imagery from the Cassini and Voyager missions, this study aims to compile a database of the impact crater population on and around Iapetus's equatorial ridge, assess the relative age of the ridge from differences in cratering between on ridge and off ridge, and test the various models of ridge formation. This work presents a database that contains 7748 craters ranging from 0.83 km to 591 km in diameter. The database includes the study area in which the crater is located, the latitude and longitude of the crater, the major and minor axis lengths, and the azimuthal angle of orientation of the major axis. Analysis of crater orientation over the entire study area reveals that there is no preference for long-axis orientation, particularly in the area with the highest resolution. Comparison of the crater size-frequency distributions show that the crater distribution on the ridge appears to be depleted in craters larger than 16 km with an abruptly enhanced crater population less than 16 km in diameter up to saturation. One possible interpretation is that the ridge is a relatively younger surface with an enhanced small impactor population. Finally, the compiled results are used to examine each ridge formation hypothesis. Based on these results, a model of ridge formation via a tidally disrupted sub-satellite appears most consistent with our interpretation of a younger ridge with an enhanced small impactor population.

NCBI GEO: mining tens of millions of expression profiles--database and tools update.

PubMed

Barrett, Tanya; Troup, Dennis B; Wilhite, Stephen E; Ledoux, Pierre; Rudnev, Dmitry; Evangelista, Carlos; Kim, Irene F; Soboleva, Alexandra; Tomashevsky, Maxim; Edgar, Ron

2007-01-01

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment (MIAME)-compliant infrastructure that captures fully annotated raw and processed data. Several data deposit options and formats are supported, including web forms, spreadsheets, XML and Simple Omnibus Format in Text (SOFT). In addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in GEO. This paper provides a summary of the GEO database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. GEO is accessible at http://www.ncbi.nlm.nih.gov/geo/

The dangers of being trigger-happy

NASA Astrophysics Data System (ADS)

Dale, J. E.; Haworth, T. J.; Bressert, E.

2015-06-01

We examine the evidence offered for triggered star formation against the backdrop provided by recent numerical simulations of feedback from massive stars at or below giant molecular cloud sizescales. We compile a catalogue of 67 observational papers, mostly published over the last decade, and examine the signposts most commonly used to infer the presence of triggered star formation. We then determine how well these signposts perform in a recent suite of hydrodynamic simulations of star formation including feedback from O-type stars performed by Dale et al. We find that none of the observational markers improve the chances of correctly identifying a given star as triggered by more than factors of 2 at most. This limits the fidelity of these techniques in interpreting star formation histories. We therefore urge caution in interpreting observations of star formation near feedback-driven structures in terms of triggering.

Pathology data integration with eXtensible Markup Language.

PubMed

Berman, Jules J

2005-02-01

It is impossible to overstate the importance of XML (eXtensible Markup Language) as a data organization tool. With XML, pathologists can annotate all of their data (clinical and anatomic) in a format that can transform every pathology report into a database, without compromising narrative structure. The purpose of this manuscript is to provide an overview of XML for pathologists. Examples will demonstrate how pathologists can use XML to annotate individual data elements and to structure reports in a common format that can be merged with other XML files or queried using standard XML tools. This manuscript gives pathologists a glimpse into how XML allows pathology data to be linked to other types of biomedical data and reduces our dependence on centralized proprietary databases.

Comparing ICD9-encoded diagnoses and NLP-processed discharge summaries for clinical trials pre-screening: a case study.

PubMed

Li, Li; Chase, Herbert S; Patel, Chintan O; Friedman, Carol; Weng, Chunhua

2008-11-06

The prevalence of electronic medical record (EMR) systems has made mass-screening for clinical trials viable through secondary uses of clinical data, which often exist in both structured and free text formats. The tradeoffs of using information in either data format for clinical trials screening are understudied. This paper compares the results of clinical trial eligibility queries over ICD9-encoded diagnoses and NLP-processed textual discharge summaries. The strengths and weaknesses of both data sources are summarized along the following dimensions: information completeness, expressiveness, code granularity, and accuracy of temporal information. We conclude that NLP-processed patient reports supplement important information for eligibility screening and should be used in combination with structured data.

Rapid Deployment of a RESTful Service for Oceanographic Research Cruises

NASA Astrophysics Data System (ADS)

Fu, Linyun; Arko, Robert; Leadbetter, Adam

2014-05-01

The Ocean Data Interoperability Platform (ODIP) seeks to increase data sharing across scientific domains and international boundaries, by providing a forum to harmonize diverse regional data systems. ODIP participants from the US include the Rolling Deck to Repository (R2R) program, whose mission is to capture, catalog, and describe the underway/environmental sensor data from US oceanographic research vessels and submit the data to public long-term archives. R2R publishes information online as Linked Open Data, making it widely available using Semantic Web standards. Each vessel, sensor, cruise, dataset, person, organization, funding award, log, report, etc, has a Uniform Resource Identifier (URI). Complex queries that federate results from other data providers are supported, using the SPARQL query language. To facilitate interoperability, R2R uses controlled vocabularies developed collaboratively by the science community (eg. SeaDataNet device categories) and published online by the NERC Vocabulary Server (NVS). In response to user feedback, we are developing a standard programming interface (API) and Web portal for R2R's Linked Open Data. The API provides a set of simple REST-type URLs that are translated on-the-fly into SPARQL queries, and supports common output formats (eg. JSON). We will demonstrate an implementation based on the Epimorphics Linked Data API (ELDA) open-source Java package. Our experience shows that constructing a simple portal with limited schema elements in this way can significantly reduce development time and maintenance complexity.

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

Evaluation of Content-Matched Range Monitoring Queries over Moving Objects in Mobile Computing Environments

PubMed Central

Jung, HaRim; Song, MoonBae; Youn, Hee Yong; Kim, Ung Mo

2015-01-01

A content-matched (CM) range monitoring query over moving objects continually retrieves the moving objects (i) whose non-spatial attribute values are matched to given non-spatial query values; and (ii) that are currently located within a given spatial query range. In this paper, we propose a new query indexing structure, called the group-aware query region tree (GQR-tree) for efficient evaluation of CM range monitoring queries. The primary role of the GQR-tree is to help the server leverage the computational capabilities of moving objects in order to improve the system performance in terms of the wireless communication cost and server workload. Through a series of comprehensive simulations, we verify the superiority of the GQR-tree method over the existing methods. PMID:26393613

Systems and methods for an extensible business application framework

NASA Technical Reports Server (NTRS)

Bell, David G. (Inventor); Crawford, Michael (Inventor)

2012-01-01

Method and systems for editing data from a query result include requesting a query result using a unique collection identifier for a collection of individual files and a unique identifier for a configuration file that specifies a data structure for the query result. A query result is generated that contains a plurality of fields as specified by the configuration file, by combining each of the individual files associated with a unique identifier for a collection of individual files. The query result data is displayed with a plurality of labels as specified in the configuration file. Edits can be performed by querying a collection of individual files using the configuration file, editing a portion of the query result, and transmitting only the edited information for storage back into a data repository.

Specifics on a XML Data Format for Scientific Data

NASA Astrophysics Data System (ADS)

Shaya, E.; Thomas, B.; Cheung, C.

An XML-based data format for interchange and archiving of scientific data would benefit in many ways from the features standardized in XML. Foremost of these features is the world-wide acceptance and adoption of XML. Applications, such as browsers, XQL and XSQL advanced query, XML editing, or CSS or XSLT transformation, that are coming out of industry and academia can be easily adopted and provide startling new benefits and features. We have designed a prototype of a core format for holding, in a very general way, parameters, tables, scalar and vector fields, atlases, animations and complex combinations of these. This eXtensible Data Format (XDF) makes use of XML functionalities such as: self-validation of document structure, default values for attributes, XLink hyperlinks, entity replacements, internal referencing, inheritance, and XSLT transformation. An API is available to aid in detailed assembly, extraction, and manipulation. Conversion tools to and from FITS and other existing data formats are under development. In the future, we hope to provide object oriented interfaces to C++, Java, Python, IDL, Mathematica, Maple, and various databases. http://xml.gsfc.nasa.gov/XDF

Analysis of Information Needs of Users of MEDLINEplus, 2002 – 2003

PubMed Central

Scott-Wright, Alicia; Crowell, Jon; Zeng, Qing; Bates, David W.; Greenes, Robert

2006-01-01

We analyzed query logs from use of MEDLINEplus to answer the questions: Are consumers’ health information needs stable over time? and To what extent do users’ queries change over time? To determine log stability, we assessed an Overlap Rate (OR) defined as the number of unique queries common to two adjacent months divided by the total number of unique queries in those months. All exactly matching queries were considered as one unique query. We measured ORs for the top 10 and 100 unique queries of a month and compared these to ORs for the following month. Over ten months, users submitted 12,234,737 queries; only 2,179,571 (17.8%) were unique and these had a mean word count of 2.73 (S.D., 0.24); 121 of 137 (88.3%) unique queries each comprised of exactly matching search term(s) used at least 5000 times were of only one word. We could predict with 95% confidence that the monthly OR for the top 100 unique queries would lie between 67% – 87% when compared with the top 100 from the previous month. The mean month-to-month OR for top 10 queries was 62% (S.D., 20%) indicating significant variability; the lowest OR of 33% between the top 10 in Mar. compared to Apr. was likely due to “new” interest in information about SARS pneumonia in Apr. 2003. Consumers’ health information needs are relatively stable and the 100 most common unique queries are about 77% the same from month to month. Website sponsors should provide a broad range of information about a relatively stable number of topics. Analyses of log similarity may identify media-induced, cyclical, or seasonal changes in areas of consumer interest. PMID:17238431

Big Data and Dysmenorrhea: What Questions Do Women and Men Ask About Menstrual Pain?

PubMed

Chen, Chen X; Groves, Doyle; Miller, Wendy R; Carpenter, Janet S

2018-04-30

Menstrual pain is highly prevalent among women of reproductive age. As the general public increasingly obtains health information online, Big Data from online platforms provide novel sources to understand the public's perspectives and information needs about menstrual pain. The study's purpose was to describe salient queries about dysmenorrhea using Big Data from a question and answer platform. We performed text-mining of 1.9 billion queries from ChaCha, a United States-based question and answer platform. Dysmenorrhea-related queries were identified by using keyword searching. Each relevant query was split into token words (i.e., meaningful words or phrases) and stop words (i.e., not meaningful functional words). Word Adjacency Graph (WAG) modeling was used to detect clusters of queries and visualize the range of dysmenorrhea-related topics. We constructed two WAG models respectively from queries by women of reproductive age and bymen. Salient themes were identified through inspecting clusters of WAG models. We identified two subsets of queries: Subset 1 contained 507,327 queries from women aged 13-50 years. Subset 2 contained 113,888 queries from men aged 13 or above. WAG modeling revealed topic clusters for each subset. Between female and male subsets, topic clusters overlapped on dysmenorrhea symptoms and management. Among female queries, there were distinctive topics on approaching menstrual pain at school and menstrual pain-related conditions; while among male queries, there was a distinctive cluster of queries on menstrual pain from male's perspectives. Big Data mining of the ChaCha ® question and answer service revealed a series of information needs among women and men on menstrual pain. Findings may be useful in structuring the content and informing the delivery platform for educational interventions.

Chandra Source Catalog: User Interfaces

NASA Astrophysics Data System (ADS)

Bonaventura, Nina; Evans, I. N.; Harbo, P. N.; Rots, A. H.; Tibbetts, M. S.; Van Stone, D. W.; Zografou, P.; Anderson, C. S.; Chen, J. C.; Davis, J. E.; Doe, S. M.; Evans, J. D.; Fabbiano, G.; Galle, E.; Gibbs, D. G.; Glotfelty, K. J.; Grier, J. D.; Hain, R.; Hall, D. M.; He, X.; Houck, J. C.; Karovska, M.; Lauer, J.; McCollough, M. L.; McDowell, J. C.; Miller, J. B.; Mitschang, A. W.; Morgan, D. L.; Nichols, J. S.; Nowak, M. A.; Plummer, D. A.; Primini, F. A.; Refsdal, B. L.; Siemiginowska, A. L.; Sundheim, B. A.; Winkelman, S. L.

2010-03-01

The CSCview data mining interface is available for browsing the Chandra Source Catalog (CSC) and downloading tables of quality-assured source properties and data products. Once the desired source properties and search criteria are entered into the CSCview query form, the resulting source matches are returned in a table along with the values of the requested source properties for each source. (The catalog can be searched on any source property, not just position.) At this point, the table of search results may be saved to a text file, and the available data products for each source may be downloaded. CSCview save files are output in RDB-like and VOTable format. The available CSC data products include event files, spectra, lightcurves, and images, all of which are processed with the CIAO software. CSC data may also be accessed non-interactively with Unix command-line tools such as cURL and Wget, using ADQL 2.0 query syntax. In fact, CSCview features a separate ADQL query form for those who wish to specify this type of query within the GUI. Several interfaces are available for learning if a source is included in the catalog (in addition to CSCview): 1) the CSC interface to Sky in Google Earth shows the footprint of each Chandra observation on the sky, along with the CSC footprint for comparison (CSC source properties are also accessible when a source within a Chandra field-of-view is clicked); 2) the CSC Limiting Sensitivity online tool indicates if a source at an input celestial location was too faint for detection; 3) an IVOA Simple Cone Search interface locates all CSC sources within a specified radius of an R.A. and Dec.; and 4) the CSC-SDSS cross-match service returns the list of sources common to the CSC and SDSS, either all such sources or a subset based on search criteria.

QCS : a system for querying, clustering, and summarizing documents.

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

Dunlavy, Daniel M.

2006-08-01

Information retrieval systems consist of many complicated components. Research and development of such systems is often hampered by the difficulty in evaluating how each particular component would behave across multiple systems. We present a novel hybrid information retrieval system--the Query, Cluster, Summarize (QCS) system--which is portable, modular, and permits experimentation with different instantiations of each of the constituent text analysis components. Most importantly, the combination of the three types of components in the QCS design improves retrievals by providing users more focused information organized by topic. We demonstrate the improved performance by a series of experiments using standard test setsmore » from the Document Understanding Conferences (DUC) along with the best known automatic metric for summarization system evaluation, ROUGE. Although the DUC data and evaluations were originally designed to test multidocument summarization, we developed a framework to extend it to the task of evaluation for each of the three components: query, clustering, and summarization. Under this framework, we then demonstrate that the QCS system (end-to-end) achieves performance as good as or better than the best summarization engines. Given a query, QCS retrieves relevant documents, separates the retrieved documents into topic clusters, and creates a single summary for each cluster. In the current implementation, Latent Semantic Indexing is used for retrieval, generalized spherical k-means is used for the document clustering, and a method coupling sentence ''trimming'', and a hidden Markov model, followed by a pivoted QR decomposition, is used to create a single extract summary for each cluster. The user interface is designed to provide access to detailed information in a compact and useful format. Our system demonstrates the feasibility of assembling an effective IR system from existing software libraries, the usefulness of the modularity of the design, and the value of this particular combination of modules.« less

QCS: a system for querying, clustering and summarizing documents.

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

Dunlavy, Daniel M.; Schlesinger, Judith D.; O'Leary, Dianne P.

2006-10-01

Information retrieval systems consist of many complicated components. Research and development of such systems is often hampered by the difficulty in evaluating how each particular component would behave across multiple systems. We present a novel hybrid information retrieval system--the Query, Cluster, Summarize (QCS) system--which is portable, modular, and permits experimentation with different instantiations of each of the constituent text analysis components. Most importantly, the combination of the three types of components in the QCS design improves retrievals by providing users more focused information organized by topic. We demonstrate the improved performance by a series of experiments using standard test setsmore » from the Document Understanding Conferences (DUC) along with the best known automatic metric for summarization system evaluation, ROUGE. Although the DUC data and evaluations were originally designed to test multidocument summarization, we developed a framework to extend it to the task of evaluation for each of the three components: query, clustering, and summarization. Under this framework, we then demonstrate that the QCS system (end-to-end) achieves performance as good as or better than the best summarization engines. Given a query, QCS retrieves relevant documents, separates the retrieved documents into topic clusters, and creates a single summary for each cluster. In the current implementation, Latent Semantic Indexing is used for retrieval, generalized spherical k-means is used for the document clustering, and a method coupling sentence 'trimming', and a hidden Markov model, followed by a pivoted QR decomposition, is used to create a single extract summary for each cluster. The user interface is designed to provide access to detailed information in a compact and useful format. Our system demonstrates the feasibility of assembling an effective IR system from existing software libraries, the usefulness of the modularity of the design, and the value of this particular combination of modules.« less

Method and apparatus for data decoding and processing

DOEpatents

Hunter, Timothy M.; Levy, Arthur J.

1992-01-01

A system and technique is disclosed for automatically controlling the decoding and digitizaiton of an analog tape. The system includes the use of a tape data format which includes a plurality of digital codes recorded on the analog tape in a predetermined proximity to a period of recorded analog data. The codes associated with each period of analog data include digital identification codes prior to the analog data, a start of data code coincident with the analog data recording, and an end of data code subsequent to the associated period of recorded analog data. The formatted tape is decoded in a processing and digitization system which includes an analog tape player coupled to a digitizer to transmit analog information from the recorded tape over at least one channel to the digitizer. At the same time, the tape player is coupled to a decoder and interface system which detects and decodes the digital codes on the tape corresponding to each period of recorded analog data and controls tape movement and digitizer initiation in response to preprogramed modes. A host computer is also coupled to the decoder and interface system and the digitizer and programmed to initiate specific modes of data decoding through the decoder and interface system including the automatic compilation and storage of digital identification information and digitized data for the period of recorded analog data corresponding to the digital identification data, compilation and storage of selected digitized data representing periods of recorded analog data, and compilation of digital identification information related to each of the periods of recorded analog data.

A spatial database of bedding attitudes to accompany Geologic map of the greater Denver area, Front Range Urban Corridor, Colorado

USGS Publications Warehouse

Trimble, Donald E.; Machette, Michael N.; Brandt, Theodore R.; Moore, David W.; Murray, Kyle E.

2003-01-01

This digital map shows bedding attitude symbols display over the geographic extent of surficial deposits and rock stratigraphic units (formations) as compiled by Trimble and Machette 1973-1977 and published in 1979 (U.S. Geological Survey Map I-856-H) under the Front Range Urban Corridor Geology Program. Trimble and Machette compiled their geologic map from published geologic maps and unpublished geologic mapping having varied map unit schemes. A convenient feature of the compiled map is its uniform classification of geologic units that mostly matches those of companion maps to the north (USGS I-855-G) and to the south (USGS I-857-F). Published as a color paper map, the Trimble and Machette map was intended for land-use planning in the Front Range Urban Corridor. This map recently (1997-1999), was digitized under the USGS Front Range Infrastructure Resources Project (see cross-reference). In general, the mountainous areas in the west part of the map exhibit various igneous and metamorphic bedrock units of Precambrian age, major faults, and fault brecciation zones at the east margin (5-20 km wide) of the Front Range. The eastern and central parts of the map (Colorado Piedmont) depict a mantle of unconsolidated deposits of Quaternary age and interspersed outcroppings of Cretaceous or Tertiary-Cretaceous sedimentary bedrock. The Quaternary mantle is comprised of eolian deposits (quartz sand and silt), alluvium (gravel, sand, and silt of variable composition), colluvium, and few landslides. At the mountain front, north-trending, dipping Paleozoic and Mesozoic sandstone, shale, and limestone bedrock formations form hogbacks and intervening valleys.

Multiple Query Evaluation Based on an Enhanced Genetic Algorithm.

ERIC Educational Resources Information Center

Tamine, Lynda; Chrisment, Claude; Boughanem, Mohand

2003-01-01

Explains the use of genetic algorithms to combine results from multiple query evaluations to improve relevance in information retrieval. Discusses niching techniques, relevance feedback techniques, and evolution heuristics, and compares retrieval results obtained by both genetic multiple query evaluation and classical single query evaluation…

Relational Algebra and SQL: Better Together

ERIC Educational Resources Information Center

McMaster, Kirby; Sambasivam, Samuel; Hadfield, Steven; Wolthuis, Stuart

2013-01-01

In this paper, we describe how database instructors can teach Relational Algebra and Structured Query Language together through programming. Students write query programs consisting of sequences of Relational Algebra operations vs. Structured Query Language SELECT statements. The query programs can then be run interactively, allowing students to…

A Firefly Algorithm-based Approach for Pseudo-Relevance Feedback: Application to Medical Database.

PubMed

Khennak, Ilyes; Drias, Habiba

2016-11-01

The difficulty of disambiguating the sense of the incomplete and imprecise keywords that are extensively used in the search queries has caused the failure of search systems to retrieve the desired information. One of the most powerful and promising method to overcome this shortcoming and improve the performance of search engines is Query Expansion, whereby the user's original query is augmented by new keywords that best characterize the user's information needs and produce more useful query. In this paper, a new Firefly Algorithm-based approach is proposed to enhance the retrieval effectiveness of query expansion while maintaining low computational complexity. In contrast to the existing literature, the proposed approach uses a Firefly Algorithm to find the best expanded query among a set of expanded query candidates. Moreover, this new approach allows the determination of the length of the expanded query empirically. Experimental results on MEDLINE, the on-line medical information database, show that our proposed approach is more effective and efficient compared to the state-of-the-art.

RiPPAS: A Ring-Based Privacy-Preserving Aggregation Scheme in Wireless Sensor Networks

PubMed Central

Zhang, Kejia; Han, Qilong; Cai, Zhipeng; Yin, Guisheng

2017-01-01

Recently, data privacy in wireless sensor networks (WSNs) has been paid increased attention. The characteristics of WSNs determine that users’ queries are mainly aggregation queries. In this paper, the problem of processing aggregation queries in WSNs with data privacy preservation is investigated. A Ring-based Privacy-Preserving Aggregation Scheme (RiPPAS) is proposed. RiPPAS adopts ring structure to perform aggregation. It uses pseudonym mechanism for anonymous communication and uses homomorphic encryption technique to add noise to the data easily to be disclosed. RiPPAS can handle both sum() queries and min()/max() queries, while the existing privacy-preserving aggregation methods can only deal with sum() queries. For processing sum() queries, compared with the existing methods, RiPPAS has advantages in the aspects of privacy preservation and communication efficiency, which can be proved by theoretical analysis and simulation results. For processing min()/max() queries, RiPPAS provides effective privacy preservation and has low communication overhead. PMID:28178197

A compilation of spatial digital databases for selected U.S. Geological Survey nonfuel mineral resource assessments for parts of Idaho and Montana

USGS Publications Warehouse

Carlson, Mary H.; Zientek, Michael L.; Causey, J. Douglas; Kayser, Helen Z.; Spanski, Gregory T.; Wilson, Anna B.; Van Gosen, Bradley S.; Trautwein, Charles M.

2007-01-01

This report compiles selected results from 13 U.S. Geological Survey (USGS) mineral resource assessment studies conducted in Idaho and Montana into consistent spatial databases that can be used in a geographic information system. The 183 spatial databases represent areas of mineral potential delineated in these studies and include attributes on mineral deposit type, level of mineral potential, certainty, and a reference. The assessments were conducted for five 1? x 2? quadrangles (Butte, Challis, Choteau, Dillon, and Wallace), several U.S. Forest Service (USFS) National Forests (including Challis, Custer, Gallatin, Helena, and Payette), and one Bureau of Land Management (BLM) Resource Area (Dillon). The data contained in the spatial databases are based on published information: no new interpretations are made. This digital compilation is part of an ongoing effort to provide mineral resource information formatted for use in spatial analysis. In particular, this is one of several reports prepared to address USFS needs for science information as forest management plans are revised in the Northern Rocky Mountains.

Report of the Data Base Subcommittee to the National Commission on New Technological Uses of Copyrighted Works.

ERIC Educational Resources Information Center

National Commission on New Technological Uses of Copyrighted Works, Washington, DC.

The agreement of the National Commission on New Technological Uses of Copyrighted Works (CONTU) with the legislative intent of the new copyright law, which accords copyright protection for computer data bases equivalent with the protection accorded compilations in traditional hard-copy format, includes several problem areas: (1) What copyright…

Achieving Equity in Education Programs for Disabled Women and Girls. A Model Workshop Manual.

ERIC Educational Resources Information Center

Kratovil, Jane; And Others

The model workshop manual is intended for use with state and local special education and sex equity staff. The manual contains a model workshop format, information on problems faced by disabled students, and suggested workshop activities. A sample workshop agenda, accompanying materials and resources developed, compiled, and field-tested at two…

Specialized Word Lists--Survey of the Literature--Research Perspective

ERIC Educational Resources Information Center

Palinkaševic, Radmila

2017-01-01

Word lists present an essential tool in vocabulary teaching. Compilation of specific word lists for various fields is one of the most prominent branches of research in this field at the moment. New methodological changes in word list formation have been proposed because of the appearance of the New-GSL (Brezina & Gablasova, 2013) and AVL…

Teaching at Its Best: A Research-Based Resource for College Instructors. Second Edition.

ERIC Educational Resources Information Center

Nilson, Linda B.

This handbook is meant to be a toolbox, a compilation of hundreds of practical teaching techniques, formats, classroom activities, and exercises. This edition is revised and expanded to cover more about topics relevant to today's classroom, such as technology and the Internet. The 31 chapters are grouped into these sections: (1) "Sound…

Memoir Upon the Formation of a Deaf Variety of the Human Race.

ERIC Educational Resources Information Center

Bell, Alexander Graham

A compilation of data on the hereditary aspects of deafness presented at a conference in 1883 by Alexander Graham Bell, the document contains records of familial occurences of deafness and marriage statistics. Tables indicate that within schools for the deaf many students had the same family name; it was considered highly probable that a…

America's Black Population: 1970 to 1982. A Statistical View. Special Publication PIO/POP-83-1.

ERIC Educational Resources Information Center

Matney, William C.; Johnson, Dwight L.

This pamphlet is the first in a series designed to provide a compilation of selected demographic, social, economic, and other statistical data relating to selected populations. Topics covered here (in both discussion and table/graph format) include Black population growth and distribution, residence, income gain, poverty rate increase, labor force…

Compendium of Statistical and Financial Information: Ontario Universities, 1998-99.

ERIC Educational Resources Information Center

Council of Ontario Universities, Toronto.

This compendium presents data on various aspects of the Ontario University system. Compiled by the Council of Finance Officers - Universities of Ontario (COFO-UO), it is intended as a companion to the Financial Report of Ontario Universities and as an aid to financial planning and policy. Data are presented in graphical and tabular formats.…

Fact Sheets from the ERIC Clearinghouse on Handicapped and Gifted Children, 1980.

ERIC Educational Resources Information Center

ERIC Clearinghouse on Handicapped and Gifted Children, Reston, VA.

The document is a compilation of 15 fact sheets developed during 1980 by the ERIC Clearinghouse on Handicapped and Gifted Children. Fact sheets are single sheets which provide basic information in a question-answer format and include additional resources and references. The fact sheets have the following titles: "Sex Education for Retarded…

Dynamic Querying of Mass-Storage RDF Data with Rule-Based Entailment Regimes

NASA Astrophysics Data System (ADS)

Ianni, Giovambattista; Krennwallner, Thomas; Martello, Alessandra; Polleres, Axel

RDF Schema (RDFS) as a lightweight ontology language is gaining popularity and, consequently, tools for scalable RDFS inference and querying are needed. SPARQL has become recently a W3C standard for querying RDF data, but it mostly provides means for querying simple RDF graphs only, whereas querying with respect to RDFS or other entailment regimes is left outside the current specification. In this paper, we show that SPARQL faces certain unwanted ramifications when querying ontologies in conjunction with RDF datasets that comprise multiple named graphs, and we provide an extension for SPARQL that remedies these effects. Moreover, since RDFS inference has a close relationship with logic rules, we generalize our approach to select a custom ruleset for specifying inferences to be taken into account in a SPARQL query. We show that our extensions are technically feasible by providing benchmark results for RDFS querying in our prototype system GiaBATA, which uses Datalog coupled with a persistent Relational Database as a back-end for implementing SPARQL with dynamic rule-based inference. By employing different optimization techniques like magic set rewriting our system remains competitive with state-of-the-art RDFS querying systems.

Mining the SDSS SkyServer SQL queries log

NASA Astrophysics Data System (ADS)

Hirota, Vitor M.; Santos, Rafael; Raddick, Jordan; Thakar, Ani

2016-05-01

SkyServer, the Internet portal for the Sloan Digital Sky Survey (SDSS) astronomic catalog, provides a set of tools that allows data access for astronomers and scientific education. One of SkyServer data access interfaces allows users to enter ad-hoc SQL statements to query the catalog. SkyServer also presents some template queries that can be used as basis for more complex queries. This interface has logged over 330 million queries submitted since 2001. It is expected that analysis of this data can be used to investigate usage patterns, identify potential new classes of queries, find similar queries, etc. and to shed some light on how users interact with the Sloan Digital Sky Survey data and how scientists have adopted the new paradigm of e-Science, which could in turn lead to enhancements on the user interfaces and experience in general. In this paper we review some approaches to SQL query mining, apply the traditional techniques used in the literature and present lessons learned, namely, that the general text mining approach for feature extraction and clustering does not seem to be adequate for this type of data, and, most importantly, we find that this type of analysis can result in very different queries being clustered together.

Applying Query Structuring in Cross-language Retrieval.

ERIC Educational Resources Information Center

Pirkola, Ari; Puolamaki, Deniz; Jarvelin, Kalervo

2003-01-01

Explores ways to apply query structuring in cross-language information retrieval. Tested were: English queries translated into Finnish using an electronic dictionary, and run in a Finnish newspaper databases; effects of compound-based structuring using a proximity operator for translation equivalents of query language compound components; and a…

Querying and Ranking XML Documents.

ERIC Educational Resources Information Center

Schlieder, Torsten; Meuss, Holger

2002-01-01

Discussion of XML, information retrieval, precision, and recall focuses on a retrieval technique that adopts the similarity measure of the vector space model, incorporates the document structure, and supports structured queries. Topics include a query model based on tree matching; structured queries and term-based ranking; and term frequency and…

Advanced Query Formulation in Deductive Databases.

ERIC Educational Resources Information Center

Niemi, Timo; Jarvelin, Kalervo

1992-01-01

Discusses deductive databases and database management systems (DBMS) and introduces a framework for advanced query formulation for end users. Recursive processing is described, a sample extensional database is presented, query types are explained, and criteria for advanced query formulation from the end user's viewpoint are examined. (31…

A Semantic Graph Query Language

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

Kaplan, I L

2006-10-16

Semantic graphs can be used to organize large amounts of information from a number of sources into one unified structure. A semantic query language provides a foundation for extracting information from the semantic graph. The graph query language described here provides a simple, powerful method for querying semantic graphs.

Using Common Table Expressions to Build a Scalable Boolean Query Generator for Clinical Data Warehouses

PubMed Central

Harris, Daniel R.; Henderson, Darren W.; Kavuluru, Ramakanth; Stromberg, Arnold J.; Johnson, Todd R.

2015-01-01

We present a custom, Boolean query generator utilizing common-table expressions (CTEs) that is capable of scaling with big datasets. The generator maps user-defined Boolean queries, such as those interactively created in clinical-research and general-purpose healthcare tools, into SQL. We demonstrate the effectiveness of this generator by integrating our work into the Informatics for Integrating Biology and the Bedside (i2b2) query tool and show that it is capable of scaling. Our custom generator replaces and outperforms the default query generator found within the Clinical Research Chart (CRC) cell of i2b2. In our experiments, sixteen different types of i2b2 queries were identified by varying four constraints: date, frequency, exclusion criteria, and whether selected concepts occurred in the same encounter. We generated non-trivial, random Boolean queries based on these 16 types; the corresponding SQL queries produced by both generators were compared by execution times. The CTE-based solution significantly outperformed the default query generator and provided a much more consistent response time across all query types (M=2.03, SD=6.64 vs. M=75.82, SD=238.88 seconds). Without costly hardware upgrades, we provide a scalable solution based on CTEs with very promising empirical results centered on performance gains. The evaluation methodology used for this provides a means of profiling clinical data warehouse performance. PMID:25192572

RCQ-GA: RDF Chain Query Optimization Using Genetic Algorithms

NASA Astrophysics Data System (ADS)

Hogenboom, Alexander; Milea, Viorel; Frasincar, Flavius; Kaymak, Uzay

The application of Semantic Web technologies in an Electronic Commerce environment implies a need for good support tools. Fast query engines are needed for efficient querying of large amounts of data, usually represented using RDF. We focus on optimizing a special class of SPARQL queries, the so-called RDF chain queries. For this purpose, we devise a genetic algorithm called RCQ-GA that determines the order in which joins need to be performed for an efficient evaluation of RDF chain queries. The approach is benchmarked against a two-phase optimization algorithm, previously proposed in literature. The more complex a query is, the more RCQ-GA outperforms the benchmark in solution quality, execution time needed, and consistency of solution quality. When the algorithms are constrained by a time limit, the overall performance of RCQ-GA compared to the benchmark further improves.

Query Language for Location-Based Services: A Model Checking Approach

NASA Astrophysics Data System (ADS)

Hoareau, Christian; Satoh, Ichiro

We present a model checking approach to the rationale, implementation, and applications of a query language for location-based services. Such query mechanisms are necessary so that users, objects, and/or services can effectively benefit from the location-awareness of their surrounding environment. The underlying data model is founded on a symbolic model of space organized in a tree structure. Once extended to a semantic model for modal logic, we regard location query processing as a model checking problem, and thus define location queries as hybrid logicbased formulas. Our approach is unique to existing research because it explores the connection between location models and query processing in ubiquitous computing systems, relies on a sound theoretical basis, and provides modal logic-based query mechanisms for expressive searches over a decentralized data structure. A prototype implementation is also presented and will be discussed.

Towards Building a High Performance Spatial Query System for Large Scale Medical Imaging Data.

PubMed

Aji, Ablimit; Wang, Fusheng; Saltz, Joel H

2012-11-06

Support of high performance queries on large volumes of scientific spatial data is becoming increasingly important in many applications. This growth is driven by not only geospatial problems in numerous fields, but also emerging scientific applications that are increasingly data- and compute-intensive. For example, digital pathology imaging has become an emerging field during the past decade, where examination of high resolution images of human tissue specimens enables more effective diagnosis, prediction and treatment of diseases. Systematic analysis of large-scale pathology images generates tremendous amounts of spatially derived quantifications of micro-anatomic objects, such as nuclei, blood vessels, and tissue regions. Analytical pathology imaging provides high potential to support image based computer aided diagnosis. One major requirement for this is effective querying of such enormous amount of data with fast response, which is faced with two major challenges: the "big data" challenge and the high computation complexity. In this paper, we present our work towards building a high performance spatial query system for querying massive spatial data on MapReduce. Our framework takes an on demand index building approach for processing spatial queries and a partition-merge approach for building parallel spatial query pipelines, which fits nicely with the computing model of MapReduce. We demonstrate our framework on supporting multi-way spatial joins for algorithm evaluation and nearest neighbor queries for microanatomic objects. To reduce query response time, we propose cost based query optimization to mitigate the effect of data skew. Our experiments show that the framework can efficiently support complex analytical spatial queries on MapReduce.

Towards Building a High Performance Spatial Query System for Large Scale Medical Imaging Data

PubMed Central

Aji, Ablimit; Wang, Fusheng; Saltz, Joel H.

2013-01-01

Support of high performance queries on large volumes of scientific spatial data is becoming increasingly important in many applications. This growth is driven by not only geospatial problems in numerous fields, but also emerging scientific applications that are increasingly data- and compute-intensive. For example, digital pathology imaging has become an emerging field during the past decade, where examination of high resolution images of human tissue specimens enables more effective diagnosis, prediction and treatment of diseases. Systematic analysis of large-scale pathology images generates tremendous amounts of spatially derived quantifications of micro-anatomic objects, such as nuclei, blood vessels, and tissue regions. Analytical pathology imaging provides high potential to support image based computer aided diagnosis. One major requirement for this is effective querying of such enormous amount of data with fast response, which is faced with two major challenges: the “big data” challenge and the high computation complexity. In this paper, we present our work towards building a high performance spatial query system for querying massive spatial data on MapReduce. Our framework takes an on demand index building approach for processing spatial queries and a partition-merge approach for building parallel spatial query pipelines, which fits nicely with the computing model of MapReduce. We demonstrate our framework on supporting multi-way spatial joins for algorithm evaluation and nearest neighbor queries for microanatomic objects. To reduce query response time, we propose cost based query optimization to mitigate the effect of data skew. Our experiments show that the framework can efficiently support complex analytical spatial queries on MapReduce. PMID:24501719

User involvement in the implementation of clinical guidelines for common mental health disorders: a review and compilation of strategies and resources.

PubMed

Moreno, Eliana M; Moriana, Juan Antonio

2016-08-09

There is now broad consensus regarding the importance of involving users in the process of implementing guidelines. Few studies, however, have addressed this issue, let alone the implementation of guidelines for common mental health disorders. The aim of this study is to compile and describe implementation strategies and resources related to common clinical mental health disorders targeted at service users. The literature was reviewed and resources for the implementation of clinical guidelines were compiled using the PRISMA model. A mixed qualitative and quantitative analysis was performed based on a series of categories developed ad hoc. A total of 263 items were included in the preliminary analysis and 64 implementation resources aimed at users were analysed in depth. A wide variety of types, sources and formats were identified, including guides (40%), websites (29%), videos and leaflets, as well as instruments for the implementation of strategies regarding information and education (64%), self-care, or users' assessment of service quality. The results reveal the need to establish clear criteria for assessing the quality of implementation materials in general and standardising systems to classify user-targeted strategies. The compilation and description of key elements of strategies and resources for users can be of interest in designing materials and specific actions for this target audience, as well as improving the implementation of clinical guidelines.

Query Expansion and Query Translation as Logical Inference.

ERIC Educational Resources Information Center

Nie, Jian-Yun

2003-01-01

Examines query expansion during query translation in cross language information retrieval and develops a general framework for inferential information retrieval in two particular contexts: using fuzzy logic and probability theory. Obtains evaluation formulas that are shown to strongly correspond to those used in other information retrieval models.…

End-User Use of Data Base Query Language: Pros and Cons.

ERIC Educational Resources Information Center

Nicholes, Walter

1988-01-01

Man-machine interface, the concept of a computer "query," a review of database technology, and a description of the use of query languages at Brigham Young University are discussed. The pros and cons of end-user use of database query languages are explored. (Author/MLW)

Information Retrieval Using UMLS-based Structured Queries

PubMed Central

Fagan, Lawrence M.; Berrios, Daniel C.; Chan, Albert; Cucina, Russell; Datta, Anupam; Shah, Maulik; Surendran, Sujith

2001-01-01

During the last three years, we have developed and described components of ELBook, a semantically based information-retrieval system [1-4]. Using these components, domain experts can specify a query model, indexers can use the query model to index documents, and end-users can search these documents for instances of indexed queries.

A Relational Algebra Query Language for Programming Relational Databases

ERIC Educational Resources Information Center

McMaster, Kirby; Sambasivam, Samuel; Anderson, Nicole

2011-01-01

In this paper, we describe a Relational Algebra Query Language (RAQL) and Relational Algebra Query (RAQ) software product we have developed that allows database instructors to teach relational algebra through programming. Instead of defining query operations using mathematical notation (the approach commonly taken in database textbooks), students…

Capturing Accurate and Useful Information on Medication-Related Telenursing Triage Calls.

PubMed

Lake, R; Li, L; Baysari, M; Byrne, M; Robinson, M; Westbrook, J I

2016-01-01

Registered nurses providing telenursing triage and advice services record information on the medication related calls they handle. However the quality and consistency of these data were rarely examined. Our aim was to examine medication related calls made to the healthdirect advice service in November 2014, to assess their basic characteristics and how the data entry format influenced information collected and data consistency. Registered nurses selected the patient question type from a range of categories, and entered the medications involved in a free text field. Medication names were manually extracted from the free text fields. We also compared the selected patient question type with the free text description of the call, in order to gauge data consistency. Results showed that nurses provided patients with advice on medication-related queries in a timely matter (the median call duration of 9 minutes). From 1835 calls, we were able to identify and classify 2156 medications into 384 generic names. However, in 204 cases (11.2% of calls) no medication name was entered. A further 308 (15.0%) of the medication names entered were not identifiable. When we compared the selected patient question with the free text description of calls, we found that these were consistent in 63.27% of cases. Telenursing and triage advice services provide a valuable resource to the public with quick and easily accessible advice. To support nurses provide quality services and record accurate information about the queries, appropriate data entry format and design would be beneficial.

An Ensemble Approach for Expanding Queries

DTIC Science & Technology

2012-11-01

0.39 pain^0.39 Hospital 15094 0.82 hospital^0.82 Miscarriage 45 3.35 miscarriage ^3.35 Radiotherapy 53 3.28 radiotherapy^3.28 Hypoaldosteronism 3...negated query is the expansion of the original query with negation terms preceding each word. For example, the negated version of “ miscarriage ^3.35...includes “no miscarriage ”^3.35 and “not miscarriage ”^3.35. If a document is the result of both original query and negated query, its score is

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.

CruiseViewer: SIOExplorer Graphical Interface to Metadata and Archives.

NASA Astrophysics Data System (ADS)

Sutton, D. W.; Helly, J. J.; Miller, S. P.; Chase, A.; Clark, D.

2002-12-01

We are introducing "CruiseViewer" as a prototype graphical interface for the SIOExplorer digital library project, part of the overall NSF National Science Digital Library (NSDL) effort. When complete, CruiseViewer will provide access to nearly 800 cruises, as well as 100 years of documents and images from the archives of the Scripps Institution of Oceanography (SIO). The project emphasizes data object accessibility, a rich metadata format, efficient uploading methods and interoperability with other digital libraries. The primary function of CruiseViewer is to provide a human interface to the metadata database and to storage systems filled with archival data. The system schema is based on the concept of an "arbitrary digital object" (ADO). Arbitrary in that if the object can be stored on a computer system then SIOExplore can manage it. Common examples are a multibeam swath bathymetry file, a .pdf cruise report, or a tar file containing all the processing scripts used on a cruise. We require a metadata file for every ADO in an ascii "metadata interchange format" (MIF), which has proven to be highly useful for operability and extensibility. Bulk ADO storage is managed using the Storage Resource Broker, SRB, data handling middleware developed at the San Diego Supercomputer Center that centralizes management and access to distributed storage devices. MIF metadata are harvested from several sources and housed in a relational (Oracle) database. For CruiseViewer, cgi scripts resident on an Apache server are the primary communication and service request handling tools. Along with the CruiseViewer java application, users can query, access and download objects via a separate method that operates through standard web browsers, http://sioexplorer.ucsd.edu. Both provide the functionability to query and view object metadata, and select and download ADOs. For the CruiseViewer application Java 2D is used to add a geo-referencing feature that allows users to select basemap images and have vector shapes representing query results mapped over the basemap in the image panel. The two methods together address a wide range of user access needs and will allow for widespread use of SIOExplorer.

A Software Prototype For Accessing Large Climate Simulation Data Through Digital Globe Interface

NASA Astrophysics Data System (ADS)

Chaudhuri, A.; Sorokine, A.

2010-12-01

The IPCC suite of global Earth system models produced terabytes of data for the CMIP3/AR4 archive and is expected to reach the petabyte scale by CMIP5/AR5. Dynamic downscaling of global models based on regional climate models can potentially lead to even larger data volumes. The model simulations for global or regional climate models like CCSM3 or WRF are typically run on supercomputers like the ORNL/DOE Jaguar and the results are stored on high performance storage systems. Access to these results from a user workstation is impeded by a number of factors such as enormous data size, limited bandwidth of standard office networks, data formats which are not fully supported by applications. So, a user-friendly interface for accessing and visualizing these results over standard Internet connection is required to facilitate collaborative work among geographically dispersed groups of scientists. To address this problem, we have developed a virtual globe based application which enables the scientists to query, visualize and analyze the results without the need of large data transfers to desktops and department-level servers. We have used open-source NASA WorldWind as a virtual globe platform and extended it with modules capable of visualizing model outputs stored in NetCDF format, while the data resides on the high-performance system. Based on the query placed by the scientist, our system initiates data processing routines on the high performance storage system to subset the data and reduce its size and then transfer it back to scientist's workstation through secure shell tunnel. The whole operation is kept totally transparent to the scientist and for the most part is controlled from a point-and-click GUI. The virtual globe also serves as a common platform for geospatial data, allowing smooth integration of the model simulation results with geographic data from other sources such as various web services or user-specific data in local files, if required. Also the system has the capability of building and updating a metadata catalog on the high performance storage that presents a simplified summary of the stored variables, hiding the low-level details such as physical location, size or format of the files from the user. Since data are often contributed to the system from multiple sources, the metadata catalog provides the user with a bird's eye view of the recent status of the database. As a next step, we plan on parallelizing the metadata updating and query-driven data selection routines to reduce the query response time. At current stage, the system can be immediately useful in making climate model simulation results available to a greater number of researchers who need simple and intuitive visualization of the simulation data or want to perform some analysis on it. The system's utility can reach beyond this particular application since it is generic enough to be ported to other high performance systems and to enable easy access to other types of geographic data.

A novel adaptive Cuckoo search for optimal query plan generation.

PubMed

Gomathi, Ramalingam; Sharmila, Dhandapani

2014-01-01

The emergence of multiple web pages day by day leads to the development of the semantic web technology. A World Wide Web Consortium (W3C) standard for storing semantic web data is the resource description framework (RDF). To enhance the efficiency in the execution time for querying large RDF graphs, the evolving metaheuristic algorithms become an alternate to the traditional query optimization methods. This paper focuses on the problem of query optimization of semantic web data. An efficient algorithm called adaptive Cuckoo search (ACS) for querying and generating optimal query plan for large RDF graphs is designed in this research. Experiments were conducted on different datasets with varying number of predicates. The experimental results have exposed that the proposed approach has provided significant results in terms of query execution time. The extent to which the algorithm is efficient is tested and the results are documented.

Query-Based Outlier Detection in Heterogeneous Information Networks.

PubMed

Kuck, Jonathan; Zhuang, Honglei; Yan, Xifeng; Cam, Hasan; Han, Jiawei

2015-03-01

Outlier or anomaly detection in large data sets is a fundamental task in data science, with broad applications. However, in real data sets with high-dimensional space, most outliers are hidden in certain dimensional combinations and are relative to a user's search space and interest. It is often more effective to give power to users and allow them to specify outlier queries flexibly, and the system will then process such mining queries efficiently. In this study, we introduce the concept of query-based outlier in heterogeneous information networks, design a query language to facilitate users to specify such queries flexibly, define a good outlier measure in heterogeneous networks, and study how to process outlier queries efficiently in large data sets. Our experiments on real data sets show that following such a methodology, interesting outliers can be defined and uncovered flexibly and effectively in large heterogeneous networks.

Query-Based Outlier Detection in Heterogeneous Information Networks

PubMed Central

Kuck, Jonathan; Zhuang, Honglei; Yan, Xifeng; Cam, Hasan; Han, Jiawei

2015-01-01

Outlier or anomaly detection in large data sets is a fundamental task in data science, with broad applications. However, in real data sets with high-dimensional space, most outliers are hidden in certain dimensional combinations and are relative to a user’s search space and interest. It is often more effective to give power to users and allow them to specify outlier queries flexibly, and the system will then process such mining queries efficiently. In this study, we introduce the concept of query-based outlier in heterogeneous information networks, design a query language to facilitate users to specify such queries flexibly, define a good outlier measure in heterogeneous networks, and study how to process outlier queries efficiently in large data sets. Our experiments on real data sets show that following such a methodology, interesting outliers can be defined and uncovered flexibly and effectively in large heterogeneous networks. PMID:27064397

Querying and Extracting Timeline Information from Road Traffic Sensor Data

PubMed Central

Imawan, Ardi; Indikawati, Fitri Indra; Kwon, Joonho; Rao, Praveen

2016-01-01

The escalation of traffic congestion in urban cities has urged many countries to use intelligent transportation system (ITS) centers to collect historical traffic sensor data from multiple heterogeneous sources. By analyzing historical traffic data, we can obtain valuable insights into traffic behavior. Many existing applications have been proposed with limited analysis results because of the inability to cope with several types of analytical queries. In this paper, we propose the QET (querying and extracting timeline information) system—a novel analytical query processing method based on a timeline model for road traffic sensor data. To address query performance, we build a TQ-index (timeline query-index) that exploits spatio-temporal features of timeline modeling. We also propose an intuitive timeline visualization method to display congestion events obtained from specified query parameters. In addition, we demonstrate the benefit of our system through a performance evaluation using a Busan ITS dataset and a Seattle freeway dataset. PMID:27563900

ChemProt-2.0: visual navigation in a disease chemical biology database

PubMed Central

Kim Kjærulff, Sonny; Wich, Louis; Kringelum, Jens; Jacobsen, Ulrik P.; Kouskoumvekaki, Irene; Audouze, Karine; Lund, Ole; Brunak, Søren; Oprea, Tudor I.; Taboureau, Olivier

2013-01-01

ChemProt-2.0 (http://www.cbs.dtu.dk/services/ChemProt-2.0) is a public available compilation of multiple chemical–protein annotation resources integrated with diseases and clinical outcomes information. The database has been updated to >1.15 million compounds with 5.32 millions bioactivity measurements for 15 290 proteins. Each protein is linked to quality-scored human protein–protein interactions data based on more than half a million interactions, for studying diseases and biological outcomes (diseases, pathways and GO terms) through protein complexes. In ChemProt-2.0, therapeutic effects as well as adverse drug reactions have been integrated allowing for suggesting proteins associated to clinical outcomes. New chemical structure fingerprints were computed based on the similarity ensemble approach. Protein sequence similarity search was also integrated to evaluate the promiscuity of proteins, which can help in the prediction of off-target effects. Finally, the database was integrated into a visual interface that enables navigation of the pharmacological space for small molecules. Filtering options were included in order to facilitate and to guide dynamic search of specific queries. PMID:23185041

Ligand.Info small-molecule Meta-Database.

PubMed

von Grotthuss, Marcin; Koczyk, Grzegorz; Pas, Jakub; Wyrwicz, Lucjan S; Rychlewski, Leszek

2004-12-01

Ligand.Info is a compilation of various publicly available databases of small molecules. The total size of the Meta-Database is over 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded from the http://Ligand.Info web page. The database can also be screened using a Java-based tool. The tool can interactively cluster sets of molecules on the user side and automatically download similar molecules from the server. The application requires the Java Runtime Environment 1.4 or higher, which can be automatically downloaded from Sun Microsystems or Apple Computer and installed during the first use of Ligand.Info on desktop systems, which support Java (Ms Windows, Mac OS, Solaris, and Linux). The Ligand.Info Meta-Database can be used for virtual high-throughput screening of new potential drugs. Presented examples showed that using a known antiviral drug as query the system was able to find others antiviral drugs and inhibitors.

A geospatial database model for the management of remote sensing datasets at multiple spectral, spatial, and temporal scales

NASA Astrophysics Data System (ADS)

Ifimov, Gabriela; Pigeau, Grace; Arroyo-Mora, J. Pablo; Soffer, Raymond; Leblanc, George

2017-10-01

In this study the development and implementation of a geospatial database model for the management of multiscale datasets encompassing airborne imagery and associated metadata is presented. To develop the multi-source geospatial database we have used a Relational Database Management System (RDBMS) on a Structure Query Language (SQL) server which was then integrated into ArcGIS and implemented as a geodatabase. The acquired datasets were compiled, standardized, and integrated into the RDBMS, where logical associations between different types of information were linked (e.g. location, date, and instrument). Airborne data, at different processing levels (digital numbers through geocorrected reflectance), were implemented in the geospatial database where the datasets are linked spatially and temporally. An example dataset consisting of airborne hyperspectral imagery, collected for inter and intra-annual vegetation characterization and detection of potential hydrocarbon seepage events over pipeline areas, is presented. Our work provides a model for the management of airborne imagery, which is a challenging aspect of data management in remote sensing, especially when large volumes of data are collected.

Establishment and Assessment of Plasma Disruption and Warning Databases from EAST

NASA Astrophysics Data System (ADS)

Wang, Bo; Robert, Granetz; Xiao, Bingjia; Li, Jiangang; Yang, Fei; Li, Junjun; Chen, Dalong

2016-12-01

Disruption database and disruption warning database of the EAST tokamak had been established by a disruption research group. The disruption database, based on Structured Query Language (SQL), comprises 41 disruption parameters, which include current quench characteristics, EFIT equilibrium characteristics, kinetic parameters, halo currents, and vertical motion. Presently most disruption databases are based on plasma experiments of non-superconducting tokamak devices. The purposes of the EAST database are to find disruption characteristics and disruption statistics to the fully superconducting tokamak EAST, to elucidate the physics underlying tokamak disruptions, to explore the influence of disruption on superconducting magnets and to extrapolate toward future burning plasma devices. In order to quantitatively assess the usefulness of various plasma parameters for predicting disruptions, a similar SQL database to Alcator C-Mod for EAST has been created by compiling values for a number of proposed disruption-relevant parameters sampled from all plasma discharges in the 2015 campaign. The detailed statistic results and analysis of two databases on the EAST tokamak are presented. supported by the National Magnetic Confinement Fusion Science Program of China (No. 2014GB103000)

Integrating personalized medical test contents with XML and XSL-FO.

PubMed

Toddenroth, Dennis; Dugas, Martin; Frankewitsch, Thomas

2011-03-01

In 2004 the adoption of a modular curriculum at the medical faculty in Muenster led to the introduction of centralized examinations based on multiple-choice questions (MCQs). We report on how organizational challenges of realizing faculty-wide personalized tests were addressed by implementation of a specialized software module to automatically generate test sheets from individual test registrations and MCQ contents. Key steps of the presented method for preparing personalized test sheets are (1) the compilation of relevant item contents and graphical media from a relational database with database queries, (2) the creation of Extensible Markup Language (XML) intermediates, and (3) the transformation into paginated documents. The software module by use of an open source print formatter consistently produced high-quality test sheets, while the blending of vectorized textual contents and pixel graphics resulted in efficient output file sizes. Concomitantly the module permitted an individual randomization of item sequences to prevent illicit collusion. The automatic generation of personalized MCQ test sheets is feasible using freely available open source software libraries, and can be efficiently deployed on a faculty-wide scale.

Advanced CLIPS capabilities

NASA Technical Reports Server (NTRS)

Riley, Gary

1991-01-01

The C Language Integrated Production System (CLIPS) is a forward chaining rule based language developed by NASA. CLIPS was designed specifically to provide high portability, low cost, and easy integration with external systems. The current release of CLIPS, version 4.3, is being used by over 2500 users throughout the public and private community. The primary addition to the next release of CLIPS, version 5.0, will be the CLIPS Object Oriented Language (COOL). The major capabilities of COOL are: class definition with multiple inheritance and no restrictions on the number, types, or cardinality of slots; message passing which allows procedural code bundled with an object to be executed; and query functions which allow groups of instances to be examined and manipulated. In addition to COOL, numerous other enhancements were added to CLIPS including: generic functions (which allow different pieces of procedural code to be executed depending upon the types or classes of the arguments); integer and double precision data type support; multiple conflict resolution strategies; global variables; logical dependencies; type checking on facts; full ANSI compiler support; and incremental reset for rules.

Policy Compliance of Queries for Private Information Retrieval

DTIC Science & Technology

2010-11-01

SPARQL, unfortunately, is not in RDF and so we had to develop tools to translate SPARQL queries into RDF to be used by our policy compliance prototype...policy-assurance/sparql2n3.py) that accepts SPARQL queries and returns the translated query in our simplified ontology. An example of a translated

Fragger: a protein fragment picker for structural queries.

PubMed

Berenger, Francois; Simoncini, David; Voet, Arnout; Shrestha, Rojan; Zhang, Kam Y J

2017-01-01

Protein modeling and design activities often require querying the Protein Data Bank (PDB) with a structural fragment, possibly containing gaps. For some applications, it is preferable to work on a specific subset of the PDB or with unpublished structures. These requirements, along with specific user needs, motivated the creation of a new software to manage and query 3D protein fragments. Fragger is a protein fragment picker that allows protein fragment databases to be created and queried. All fragment lengths are supported and any set of PDB files can be used to create a database. Fragger can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. The query fragment can have structural gaps and the allowed amino acid sequences matching a query can be constrained via a regular expression of one-letter amino acid codes. Fragger also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput. Fragger should be useful for protein design, loop grafting and related structural bioinformatics tasks.

Query by forms: User-oriented relational database retrieving system and its application in analysis of experiment data

NASA Astrophysics Data System (ADS)

Skotniczny, Zbigniew

1989-12-01

The Query by Forms (QbF) system is a user-oriented interactive tool for querying large relational database with minimal queries difinition cost. The system was worked out under the assumption that user's time and effort for defining needed queries is the most severe bottleneck. The system may be applied in any Rdb/VMS databases system and is recommended for specific information systems of any project where end-user queries cannot be foreseen. The tool is dedicated to specialist of an application domain who have to analyze data maintained in database from any needed point of view, who do not need to know commercial databases languages. The paper presents the system developed as a compromise between its functionality and usability. User-system communication via a menu-driven "tree-like" structure of screen-forms which produces a query difinition and execution is discussed in detail. Output of query results (printed reports and graphics) is also discussed. Finally the paper shows one application of QbF to a HERA-project.

Hybrid ontology for semantic information retrieval model using keyword matching indexing system.

PubMed

Uthayan, K R; Mala, G S Anandha

2015-01-01

Ontology is the process of growth and elucidation of concepts of an information domain being common for a group of users. Establishing ontology into information retrieval is a normal method to develop searching effects of relevant information users require. Keywords matching process with historical or information domain is significant in recent calculations for assisting the best match for specific input queries. This research presents a better querying mechanism for information retrieval which integrates the ontology queries with keyword search. The ontology-based query is changed into a primary order to predicate logic uncertainty which is used for routing the query to the appropriate servers. Matching algorithms characterize warm area of researches in computer science and artificial intelligence. In text matching, it is more dependable to study semantics model and query for conditions of semantic matching. This research develops the semantic matching results between input queries and information in ontology field. The contributed algorithm is a hybrid method that is based on matching extracted instances from the queries and information field. The queries and information domain is focused on semantic matching, to discover the best match and to progress the executive process. In conclusion, the hybrid ontology in semantic web is sufficient to retrieve the documents when compared to standard ontology.

Hybrid Ontology for Semantic Information Retrieval Model Using Keyword Matching Indexing System

PubMed Central

Uthayan, K. R.; Anandha Mala, G. S.

2015-01-01

Ontology is the process of growth and elucidation of concepts of an information domain being common for a group of users. Establishing ontology into information retrieval is a normal method to develop searching effects of relevant information users require. Keywords matching process with historical or information domain is significant in recent calculations for assisting the best match for specific input queries. This research presents a better querying mechanism for information retrieval which integrates the ontology queries with keyword search. The ontology-based query is changed into a primary order to predicate logic uncertainty which is used for routing the query to the appropriate servers. Matching algorithms characterize warm area of researches in computer science and artificial intelligence. In text matching, it is more dependable to study semantics model and query for conditions of semantic matching. This research develops the semantic matching results between input queries and information in ontology field. The contributed algorithm is a hybrid method that is based on matching extracted instances from the queries and information field. The queries and information domain is focused on semantic matching, to discover the best match and to progress the executive process. In conclusion, the hybrid ontology in semantic web is sufficient to retrieve the documents when compared to standard ontology. PMID:25922851

Multidimensional indexing structure for use with linear optimization queries

NASA Technical Reports Server (NTRS)

Bergman, Lawrence David (Inventor); Castelli, Vittorio (Inventor); Chang, Yuan-Chi (Inventor); Li, Chung-Sheng (Inventor); Smith, John Richard (Inventor)

2002-01-01

Linear optimization queries, which usually arise in various decision support and resource planning applications, are queries that retrieve top N data records (where N is an integer greater than zero) which satisfy a specific optimization criterion. The optimization criterion is to either maximize or minimize a linear equation. The coefficients of the linear equation are given at query time. Methods and apparatus are disclosed for constructing, maintaining and utilizing a multidimensional indexing structure of database records to improve the execution speed of linear optimization queries. Database records with numerical attributes are organized into a number of layers and each layer represents a geometric structure called convex hull. Such linear optimization queries are processed by searching from the outer-most layer of this multi-layer indexing structure inwards. At least one record per layer will satisfy the query criterion and the number of layers needed to be searched depends on the spatial distribution of records, the query-issued linear coefficients, and N, the number of records to be returned. When N is small compared to the total size of the database, answering the query typically requires searching only a small fraction of all relevant records, resulting in a tremendous speedup as compared to linearly scanning the entire dataset.

The role of economics in the QUERI program: QUERI Series

PubMed Central

Smith, Mark W; Barnett, Paul G

2008-01-01

Background The United States (U.S.) Department of Veterans Affairs (VA) Quality Enhancement Research Initiative (QUERI) has implemented economic analyses in single-site and multi-site clinical trials. To date, no one has reviewed whether the QUERI Centers are taking an optimal approach to doing so. Consistent with the continuous learning culture of the QUERI Program, this paper provides such a reflection. Methods We present a case study of QUERI as an example of how economic considerations can and should be integrated into implementation research within both single and multi-site studies. We review theoretical and applied cost research in implementation studies outside and within VA. We also present a critique of the use of economic research within the QUERI program. Results Economic evaluation is a key element of implementation research. QUERI has contributed many developments in the field of implementation but has only recently begun multi-site implementation trials across multiple regions within the national VA healthcare system. These trials are unusual in their emphasis on developing detailed costs of implementation, as well as in the use of business case analyses (budget impact analyses). Conclusion Economics appears to play an important role in QUERI implementation studies, only after implementation has reached the stage of multi-site trials. Economic analysis could better inform the choice of which clinical best practices to implement and the choice of implementation interventions to employ. QUERI economics also would benefit from research on costing methods and development of widely accepted international standards for implementation economics. PMID:18430199

The role of economics in the QUERI program: QUERI Series.

PubMed

Smith, Mark W; Barnett, Paul G

2008-04-22

The United States (U.S.) Department of Veterans Affairs (VA) Quality Enhancement Research Initiative (QUERI) has implemented economic analyses in single-site and multi-site clinical trials. To date, no one has reviewed whether the QUERI Centers are taking an optimal approach to doing so. Consistent with the continuous learning culture of the QUERI Program, this paper provides such a reflection. We present a case study of QUERI as an example of how economic considerations can and should be integrated into implementation research within both single and multi-site studies. We review theoretical and applied cost research in implementation studies outside and within VA. We also present a critique of the use of economic research within the QUERI program. Economic evaluation is a key element of implementation research. QUERI has contributed many developments in the field of implementation but has only recently begun multi-site implementation trials across multiple regions within the national VA healthcare system. These trials are unusual in their emphasis on developing detailed costs of implementation, as well as in the use of business case analyses (budget impact analyses). Economics appears to play an important role in QUERI implementation studies, only after implementation has reached the stage of multi-site trials. Economic analysis could better inform the choice of which clinical best practices to implement and the choice of implementation interventions to employ. QUERI economics also would benefit from research on costing methods and development of widely accepted international standards for implementation economics.

Processing SPARQL queries with regular expressions in RDF databases

PubMed Central

2011-01-01

Background As the Resource Description Framework (RDF) data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf) or Bio2RDF (bio2rdf.org), SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users’ requests for extracting information from the RDF data as well as the lack of users’ knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. Results In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1) We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2) We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3) We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Conclusions Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns. PMID:21489225

Processing SPARQL queries with regular expressions in RDF databases.

PubMed

Lee, Jinsoo; Pham, Minh-Duc; Lee, Jihwan; Han, Wook-Shin; Cho, Hune; Yu, Hwanjo; Lee, Jeong-Hoon

2011-03-29

As the Resource Description Framework (RDF) data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf) or Bio2RDF (bio2rdf.org), SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users' requests for extracting information from the RDF data as well as the lack of users' knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1) We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2) We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3) We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns.

Exploring performance issues for a clinical database organized using an entity-attribute-value representation.

PubMed

Chen, R S; Nadkarni, P; Marenco, L; Levin, F; Erdos, J; Miller, P L

2000-01-01

The entity-attribute-value representation with classes and relationships (EAV/CR) provides a flexible and simple database schema to store heterogeneous biomedical data. In certain circumstances, however, the EAV/CR model is known to retrieve data less efficiently than conventionally based database schemas. To perform a pilot study that systematically quantifies performance differences for database queries directed at real-world microbiology data modeled with EAV/CR and conventional representations, and to explore the relative merits of different EAV/CR query implementation strategies. Clinical microbiology data obtained over a ten-year period were stored using both database models. Query execution times were compared for four clinically oriented attribute-centered and entity-centered queries operating under varying conditions of database size and system memory. The performance characteristics of three different EAV/CR query strategies were also examined. Performance was similar for entity-centered queries in the two database models. Performance in the EAV/CR model was approximately three to five times less efficient than its conventional counterpart for attribute-centered queries. The differences in query efficiency became slightly greater as database size increased, although they were reduced with the addition of system memory. The authors found that EAV/CR queries formulated using multiple, simple SQL statements executed in batch were more efficient than single, large SQL statements. This paper describes a pilot project to explore issues in and compare query performance for EAV/CR and conventional database representations. Although attribute-centered queries were less efficient in the EAV/CR model, these inefficiencies may be addressable, at least in part, by the use of more powerful hardware or more memory, or both.

Correlation between National Influenza Surveillance Data and Search Queries from Mobile Devices and Desktops in South Korea

PubMed Central

Seo, Dong-Woo; Sohn, Chang Hwan; Kim, Sung-Hoon; Ryoo, Seung Mok; Lee, Yoon-Seon; Lee, Jae Ho; Kim, Won Young; Lim, Kyoung Soo

2016-01-01

Background Digital surveillance using internet search queries can improve both the sensitivity and timeliness of the detection of a health event, such as an influenza outbreak. While it has recently been estimated that the mobile search volume surpasses the desktop search volume and mobile search patterns differ from desktop search patterns, the previous digital surveillance systems did not distinguish mobile and desktop search queries. The purpose of this study was to compare the performance of mobile and desktop search queries in terms of digital influenza surveillance. Methods and Results The study period was from September 6, 2010 through August 30, 2014, which consisted of four epidemiological years. Influenza-like illness (ILI) and virologic surveillance data from the Korea Centers for Disease Control and Prevention were used. A total of 210 combined queries from our previous survey work were used for this study. Mobile and desktop weekly search data were extracted from Naver, which is the largest search engine in Korea. Spearman’s correlation analysis was used to examine the correlation of the mobile and desktop data with ILI and virologic data in Korea. We also performed lag correlation analysis. We observed that the influenza surveillance performance of mobile search queries matched or exceeded that of desktop search queries over time. The mean correlation coefficients of mobile search queries and the number of queries with an r-value of ≥ 0.7 equaled or became greater than those of desktop searches over the four epidemiological years. A lag correlation analysis of up to two weeks showed similar trends. Conclusion Our study shows that mobile search queries for influenza surveillance have equaled or even become greater than desktop search queries over time. In the future development of influenza surveillance using search queries, the recognition of changing trend of mobile search data could be necessary. PMID:27391028

Correlation between National Influenza Surveillance Data and Search Queries from Mobile Devices and Desktops in South Korea.

PubMed

Shin, Soo-Yong; Kim, Taerim; Seo, Dong-Woo; Sohn, Chang Hwan; Kim, Sung-Hoon; Ryoo, Seung Mok; Lee, Yoon-Seon; Lee, Jae Ho; Kim, Won Young; Lim, Kyoung Soo

2016-01-01

Digital surveillance using internet search queries can improve both the sensitivity and timeliness of the detection of a health event, such as an influenza outbreak. While it has recently been estimated that the mobile search volume surpasses the desktop search volume and mobile search patterns differ from desktop search patterns, the previous digital surveillance systems did not distinguish mobile and desktop search queries. The purpose of this study was to compare the performance of mobile and desktop search queries in terms of digital influenza surveillance. The study period was from September 6, 2010 through August 30, 2014, which consisted of four epidemiological years. Influenza-like illness (ILI) and virologic surveillance data from the Korea Centers for Disease Control and Prevention were used. A total of 210 combined queries from our previous survey work were used for this study. Mobile and desktop weekly search data were extracted from Naver, which is the largest search engine in Korea. Spearman's correlation analysis was used to examine the correlation of the mobile and desktop data with ILI and virologic data in Korea. We also performed lag correlation analysis. We observed that the influenza surveillance performance of mobile search queries matched or exceeded that of desktop search queries over time. The mean correlation coefficients of mobile search queries and the number of queries with an r-value of ≥ 0.7 equaled or became greater than those of desktop searches over the four epidemiological years. A lag correlation analysis of up to two weeks showed similar trends. Our study shows that mobile search queries for influenza surveillance have equaled or even become greater than desktop search queries over time. In the future development of influenza surveillance using search queries, the recognition of changing trend of mobile search data could be necessary.

BioSWR – Semantic Web Services Registry for Bioinformatics

PubMed Central

Repchevsky, Dmitry; Gelpi, Josep Ll.

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license. PMID:25233118

BioSWR--semantic web services registry for bioinformatics.

PubMed

Repchevsky, Dmitry; Gelpi, Josep Ll

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license.