Sugeno Fuzzy Integral as a Basis for the Interpretation of Flexible Queries Involving Monotonic Aggregates.

ERIC Educational Resources Information Center

Bosc, P.; Lietard, L.; Pivert, O.

2003-01-01

Considers flexible querying of relational databases. Highlights include SQL languages and basic aggregate operators; Sugeno's fuzzy integral; evaluation examples; and how and under what conditions other aggregate functions could be applied to fuzzy sets in a flexible query. (Author/LRW)

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.

Astronomical Data Processing Using SciQL, an SQL Based Query Language for Array Data

NASA Astrophysics Data System (ADS)

Zhang, Y.; Scheers, B.; Kersten, M.; Ivanova, M.; Nes, N.

2012-09-01

SciQL (pronounced as ‘cycle’) is a novel SQL-based array query language for scientific applications with both tables and arrays as first class citizens. SciQL lowers the entrance fee of adopting relational DBMS (RDBMS) in scientific domains, because it includes functionality often only found in mathematics software packages. In this paper, we demonstrate the usefulness of SciQL for astronomical data processing using examples from the Transient Key Project of the LOFAR radio telescope. In particular, how the LOFAR light-curve database of all detected sources can be constructed, by correlating sources across the spatial, frequency, time and polarisation domains.

NVST Data Archiving System Based On FastBit NoSQL Database

NASA Astrophysics Data System (ADS)

Liu, Ying-bo; Wang, Feng; Ji, Kai-fan; Deng, Hui; Dai, Wei; Liang, Bo

2014-06-01

The New Vacuum Solar Telescope (NVST) is a 1-meter vacuum solar telescope that aims to observe the fine structures of active regions on the Sun. The main tasks of the NVST are high resolution imaging and spectral observations, including the measurements of the solar magnetic field. The NVST has been collecting more than 20 million FITS files since it began routine observations in 2012 and produces a maximum observational records of 120 thousand files in a day. Given the large amount of files, the effective archiving and retrieval of files becomes a critical and urgent problem. In this study, we implement a new data archiving system for the NVST based on the Fastbit Not Only Structured Query Language (NoSQL) database. Comparing to the relational database (i.e., MySQL; My Structured Query Language), the Fastbit database manifests distinctive advantages on indexing and querying performance. In a large scale database of 40 million records, the multi-field combined query response time of Fastbit database is about 15 times faster and fully meets the requirements of the NVST. Our study brings a new idea for massive astronomical data archiving and would contribute to the design of data management systems for other astronomical telescopes.

Introduction to SQL. Ch. 1

NASA Technical Reports Server (NTRS)

McGlynn, T.; Santisteban, M.

2007-01-01

This chapter provides a very brief introduction to the Structured Query Language (SQL) for getting information from relational databases. We make no pretense that this is a complete or comprehensive discussion of SQL. There are many aspects of the language the will be completely ignored in the presentation. The goal here is to provide enough background so that users understand the basic concepts involved in building and using relational databases. We also go through the steps involved in building a particular astronomical database used in some of the other presentations in this volume.

Database Reports Over the Internet

NASA Technical Reports Server (NTRS)

Smith, Dean Lance

2002-01-01

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

A searching and reporting system for relational databases using a graph-based metadata representation.

PubMed

Hewitt, Robin; Gobbi, Alberto; Lee, Man-Ling

2005-01-01

Relational databases are the current standard for storing and retrieving data in the pharmaceutical and biotech industries. However, retrieving data from a relational database requires specialized knowledge of the database schema and of the SQL query language. At Anadys, we have developed an easy-to-use system for searching and reporting data in a relational database to support our drug discovery project teams. This system is fast and flexible and allows users to access all data without having to write SQL queries. This paper presents the hierarchical, graph-based metadata representation and SQL-construction methods that, together, are the basis of this system's capabilities.

Methods to Secure Databases Against Vulnerabilities

DTIC Science & Technology

2015-12-01

for several languages such as C, C++, PHP, Java and Python [16]. MySQL will work well with very large databases. The documentation references...using Eclipse and connected to each database management system using Python and Java drivers provided by MySQL , MongoDB, and Datastax (for Cassandra...tiers in Python and Java . Problem MySQL MongoDB Cassandra 1. Injection a. Tautologies Vulnerable Vulnerable Not Vulnerable b. Illegal query

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

Computer-Aided Clinical Trial Recruitment Based on Domain-Specific Language Translation: A Case Study of Retinopathy of Prematurity

PubMed Central

2017-01-01

Reusing the data from healthcare information systems can effectively facilitate clinical trials (CTs). How to select candidate patients eligible for CT recruitment criteria is a central task. Related work either depends on DBA (database administrator) to convert the recruitment criteria to native SQL queries or involves the data mapping between a standard ontology/information model and individual data source schema. This paper proposes an alternative computer-aided CT recruitment paradigm, based on syntax translation between different DSLs (domain-specific languages). In this paradigm, the CT recruitment criteria are first formally represented as production rules. The referenced rule variables are all from the underlying database schema. Then the production rule is translated to an intermediate query-oriented DSL (e.g., LINQ). Finally, the intermediate DSL is directly mapped to native database queries (e.g., SQL) automated by ORM (object-relational mapping). PMID:29065644

Computer-Aided Clinical Trial Recruitment Based on Domain-Specific Language Translation: A Case Study of Retinopathy of Prematurity.

PubMed

Zhang, Yinsheng; Zhang, Guoming; Shang, Qian

2017-01-01

Reusing the data from healthcare information systems can effectively facilitate clinical trials (CTs). How to select candidate patients eligible for CT recruitment criteria is a central task. Related work either depends on DBA (database administrator) to convert the recruitment criteria to native SQL queries or involves the data mapping between a standard ontology/information model and individual data source schema. This paper proposes an alternative computer-aided CT recruitment paradigm, based on syntax translation between different DSLs (domain-specific languages). In this paradigm, the CT recruitment criteria are first formally represented as production rules. The referenced rule variables are all from the underlying database schema. Then the production rule is translated to an intermediate query-oriented DSL (e.g., LINQ). Finally, the intermediate DSL is directly mapped to native database queries (e.g., SQL) automated by ORM (object-relational mapping).

Evaluating a NoSQL Alternative for Chilean Virtual Observatory Services

NASA Astrophysics Data System (ADS)

Antognini, J.; Araya, M.; Solar, M.; Valenzuela, C.; Lira, F.

2015-09-01

Currently, the standards and protocols for data access in the Virtual Observatory architecture (DAL) are generally implemented with relational databases based on SQL. In particular, the Astronomical Data Query Language (ADQL), language used by IVOA to represent queries to VO services, was created to satisfy the different data access protocols, such as Simple Cone Search. ADQL is based in SQL92, and has extra functionality implemented using PgSphere. An emergent alternative to SQL are the so called NoSQL databases, which can be classified in several categories such as Column, Document, Key-Value, Graph, Object, etc.; each one recommended for different scenarios. Within their notable characteristics we can find: schema-free, easy replication support, simple API, Big Data, etc. The Chilean Virtual Observatory (ChiVO) is developing a functional prototype based on the IVOA architecture, with the following relevant factors: Performance, Scalability, Flexibility, Complexity, and Functionality. Currently, it's very difficult to compare these factors, due to a lack of alternatives. The objective of this paper is to compare NoSQL alternatives with SQL through the implementation of a Web API REST that satisfies ChiVO's needs: a SESAME-style name resolver for the data from ALMA. Therefore, we propose a test scenario by configuring a NoSQL database with data from different sources and evaluating the feasibility of creating a Simple Cone Search service and its performance. This comparison will allow to pave the way for the application of Big Data databases in the Virtual Observatory.

Examining Learning Styles and Perceived Benefits of Analogical Problem Construction on SQL Knowledge Acquisition

ERIC Educational Resources Information Center

Mills, Robert J.; Dupin-Bryant, Pamela A.; Johnson, John D.; Beaulieu, Tanya Y.

2015-01-01

The demand for Information Systems (IS) graduates with expertise in Structured Query Language (SQL) and database management is vast and projected to increase as "big data" becomes ubiquitous. To prepare students to solve complex problems in a data-driven world, educators must explore instructional strategies to help link prior knowledge…

Development and validation of a structured query language implementation of the Elixhauser comorbidity index.

PubMed

Epstein, Richard H; Dexter, Franklin

2017-07-01

Comorbidity adjustment is often performed during outcomes and health care resource utilization research. Our goal was to develop an efficient algorithm in structured query language (SQL) to determine the Elixhauser comorbidity index. We wrote an SQL algorithm to calculate the Elixhauser comorbidities from Diagnosis Related Group and International Classification of Diseases (ICD) codes. Validation was by comparison to expected comorbidities from combinations of these codes and to the 2013 Nationwide Readmissions Database (NRD). The SQL algorithm matched perfectly with expected comorbidities for all combinations of ICD-9 or ICD-10, and Diagnosis Related Groups. Of 13 585 859 evaluable NRD records, the algorithm matched 100% of the listed comorbidities. Processing time was ∼0.05 ms/record. The SQL Elixhauser code was efficient and computationally identical to the SAS algorithm used for the NRD. This algorithm may be useful where preprocessing of large datasets in a relational database environment and comorbidity determination is desired before statistical analysis. A validated SQL procedure to calculate Elixhauser comorbidities and the van Walraven index from ICD-9 or ICD-10 discharge diagnosis codes has been published. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

PubMed Central

2010-01-01

Background Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file formats, or directly from external databases through specialized third party plugins. However, molecular data are often stored in relational databases with their own specific structure, for which dedicated plugins do not exist. Therefore, a more generic solution is presented. Results A new Cytoscape plugin 'CytoSQL' is developed to connect Cytoscape to any relational database. It allows to launch SQL ('Structured Query Language') queries from within Cytoscape, with the option to inject node or edge features of an existing network as SQL arguments, and to convert the retrieved data to Cytoscape network components. Supported by a set of case studies we demonstrate the flexibility and the power of the CytoSQL plugin in converting specific data subsets into meaningful network representations. Conclusions CytoSQL offers a unified approach to let Cytoscape interact with relational databases. Thanks to the power of the SQL syntax, this tool can rapidly generate and enrich networks according to very complex criteria. The plugin is available at http://www.ptools.ua.ac.be/CytoSQL. PMID:20594316

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.

PubMed

Laukens, Kris; Hollunder, Jens; Dang, Thanh Hai; De Jaeger, Geert; Kuiper, Martin; Witters, Erwin; Verschoren, Alain; Van Leemput, Koenraad

2010-07-01

Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file formats, or directly from external databases through specialized third party plugins. However, molecular data are often stored in relational databases with their own specific structure, for which dedicated plugins do not exist. Therefore, a more generic solution is presented. A new Cytoscape plugin 'CytoSQL' is developed to connect Cytoscape to any relational database. It allows to launch SQL ('Structured Query Language') queries from within Cytoscape, with the option to inject node or edge features of an existing network as SQL arguments, and to convert the retrieved data to Cytoscape network components. Supported by a set of case studies we demonstrate the flexibility and the power of the CytoSQL plugin in converting specific data subsets into meaningful network representations. CytoSQL offers a unified approach to let Cytoscape interact with relational databases. Thanks to the power of the SQL syntax, this tool can rapidly generate and enrich networks according to very complex criteria. The plugin is available at http://www.ptools.ua.ac.be/CytoSQL.

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.

An XML-Based Knowledge Management System of Port Information for U.S. Coast Guard Cutters

DTIC Science & Technology

2003-03-01

using DTDs was not chosen. XML Schema performs many of the same functions as SQL type schemas, but differ by the unique structure of XML documents...to access data from content files within the developed system. XPath is not equivalent to SQL . While XPath is very powerful at reaching into an XML...document and finding nodes or node sets, it is not a complete query language. For operations like joins, unions, intersections, etc., SQL is far

Agile Datacube Analytics (not just) for the Earth Sciences

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Merticariu, Vlad; Baumann, Peter

2017-04-01

Metadata are considered small, smart, and queryable; data, on the other hand, are known as big, clumsy, hard to analyze. Consequently, gridded data - such as images, image timeseries, and climate datacubes - are managed separately from the metadata, and with different, restricted retrieval capabilities. One reason for this silo approach is that databases, while good at tables, XML hierarchies, RDF graphs, etc., traditionally do not support multi-dimensional arrays well. This gap is being closed by Array Databases which extend the SQL paradigm of "any query, anytime" to NoSQL arrays. They introduce semantically rich modelling combined with declarative, high-level query languages on n-D arrays. On Server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. This way, they offer new vistas in flexibility, scalability, performance, and data integration. In this respect, the forthcoming ISO SQL extension MDA ("Multi-dimensional Arrays") will be a game changer in Big Data Analytics. We introduce concepts and opportunities through the example of rasdaman ("raster data manager") which in fact has pioneered the field of Array Databases and forms the blueprint for ISO SQL/MDA and further Big Data standards, such as OGC WCPS for querying spatio-temporal Earth datacubes. With operational installations exceeding 140 TB queries have been split across more than one thousand cloud nodes, using CPUs as well as GPUs. Installations can easily be mashed up securely, enabling large-scale location-transparent query processing in federations. Federation queries have been demonstrated live at EGU 2016 spanning Europe and Australia in the context of the intercontinental EarthServer initiative, visualized through NASA WorldWind.

Agile Datacube Analytics (not just) for the Earth Sciences

NASA Astrophysics Data System (ADS)

Baumann, P.

2016-12-01

Metadata are considered small, smart, and queryable; data, on the other hand, are known as big, clumsy, hard to analyze. Consequently, gridded data - such as images, image timeseries, and climate datacubes - are managed separately from the metadata, and with different, restricted retrieval capabilities. One reason for this silo approach is that databases, while good at tables, XML hierarchies, RDF graphs, etc., traditionally do not support multi-dimensional arrays well.This gap is being closed by Array Databases which extend the SQL paradigm of "any query, anytime" to NoSQL arrays. They introduce semantically rich modelling combined with declarative, high-level query languages on n-D arrays. On Server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. This way, they offer new vistas in flexibility, scalability, performance, and data integration. In this respect, the forthcoming ISO SQL extension MDA ("Multi-dimensional Arrays") will be a game changer in Big Data Analytics.We introduce concepts and opportunities through the example of rasdaman ("raster data manager") which in fact has pioneered the field of Array Databases and forms the blueprint for ISO SQL/MDA and further Big Data standards, such as OGC WCPS for querying spatio-temporal Earth datacubes. With operational installations exceeding 140 TB queries have been split across more than one thousand cloud nodes, using CPUs as well as GPUs. Installations can easily be mashed up securely, enabling large-scale location-transparent query processing in federations. Federation queries have been demonstrated live at EGU 2016 spanning Europe and Australia in the context of the intercontinental EarthServer initiative, visualized through NASA WorldWind.

An SQL query generator for CLIPS

NASA Technical Reports Server (NTRS)

Snyder, James; Chirica, Laurian

1990-01-01

As expert systems become more widely used, their access to large amounts of external information becomes increasingly important. This information exists in several forms such as statistical, tabular data, knowledge gained by experts and large databases of information maintained by companies. Because many expert systems, including CLIPS, do not provide access to this external information, much of the usefulness of expert systems is left untapped. The scope of this paper is to describe a database extension for the CLIPS expert system shell. The current industry standard database language is SQL. Due to SQL standardization, large amounts of information stored on various computers, potentially at different locations, will be more easily accessible. Expert systems should be able to directly access these existing databases rather than requiring information to be re-entered into the expert system environment. The ORACLE relational database management system (RDBMS) was used to provide a database connection within the CLIPS environment. To facilitate relational database access a query generation system was developed as a CLIPS user function. The queries are entered in a CLlPS-like syntax and are passed to the query generator, which constructs and submits for execution, an SQL query to the ORACLE RDBMS. The query results are asserted as CLIPS facts. The query generator was developed primarily for use within the ICADS project (Intelligent Computer Aided Design System) currently being developed by the CAD Research Unit in the California Polytechnic State University (Cal Poly). In ICADS, there are several parallel or distributed expert systems accessing a common knowledge base of facts. Expert system has a narrow domain of interest and therefore needs only certain portions of the information. The query generator provides a common method of accessing this information and allows the expert system to specify what data is needed without specifying how to retrieve it.

Datacube Services in Action, Using Open Source and Open Standards

NASA Astrophysics Data System (ADS)

Baumann, P.; Misev, D.

2016-12-01

Array Databases comprise novel, promising technology for massive spatio-temporal datacubes, extending the SQL paradigm of "any query, anytime" to n-D arrays. On server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. The rasdaman ("raster data manager") system, which has pioneered Array Databases, is available in open source on www.rasdaman.org. Its declarative query language extends SQL with array operators which are optimized and parallelized on server side. The rasdaman engine, which is part of OSGeo Live, is mature and in operational use databases individually holding dozens of Terabytes. Further, the rasdaman concepts have strongly impacted international Big Data standards in the field, including the forthcoming MDA ("Multi-Dimensional Array") extension to ISO SQL, the OGC Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS) standards, and the forthcoming INSPIRE WCS/WCPS; in both OGC and INSPIRE, OGC is WCS Core Reference Implementation. In our talk we present concepts, architecture, operational services, and standardization impact of open-source rasdaman, as well as experiences made.

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.

The Comparison of SQL, QBE, and DFQL as Query Languages for Relational Databases

DTIC Science & Technology

1994-03-01

is: Dname F-mune Laame Headquarter James Borg b. Query 7: RetieMl involving explicit sets Retrieve the Social Security Numbers of employees who worked...i •••,• I• i , i I I • I 10. Ka Dispullahta MABES TNI-AL Cilangkap-Jakarta Timur Indonesia 11. Parunmungan Girsang 3 Jl. Cawang Baru 34-36 Jakarta

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

ERIC Educational Resources Information Center

Breeding, Marshall

2000-01-01

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

Improved Information Retrieval Performance on SQL Database Using Data Adapter

NASA Astrophysics Data System (ADS)

Husni, M.; Djanali, S.; Ciptaningtyas, H. T.; Wicaksana, I. G. N. A.

2018-02-01

The NoSQL databases, short for Not Only SQL, are increasingly being used as the number of big data applications increases. Most systems still use relational databases (RDBs), but as the number of data increases each year, the system handles big data with NoSQL databases to analyze and access data more quickly. NoSQL emerged as a result of the exponential growth of the internet and the development of web applications. The query syntax in the NoSQL database differs from the SQL database, therefore requiring code changes in the application. Data adapter allow applications to not change their SQL query syntax. Data adapters provide methods that can synchronize SQL databases with NotSQL databases. In addition, the data adapter provides an interface which is application can access to run SQL queries. Hence, this research applied data adapter system to synchronize data between MySQL database and Apache HBase using direct access query approach, where system allows application to accept query while synchronization process in progress. From the test performed using data adapter, the results obtained that the data adapter can synchronize between SQL databases, MySQL, and NoSQL database, Apache HBase. This system spends the percentage of memory resources in the range of 40% to 60%, and the percentage of processor moving from 10% to 90%. In addition, from this system also obtained the performance of database NoSQL better than SQL database.

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

START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries.

PubMed

Zhu, Xinjie; Zhang, Qiang; Ho, Eric Dun; Yu, Ken Hung-On; Liu, Chris; Huang, Tim H; Cheng, Alfred Sze-Lok; Kao, Ben; Lo, Eric; Yip, Kevin Y

2017-09-22

A genomic signal track is a set of genomic intervals associated with values of various types, such as measurements from high-throughput experiments. Analysis of signal tracks requires complex computational methods, which often make the analysts focus too much on the detailed computational steps rather than on their biological questions. Here we propose Signal Track Query Language (STQL) for simple analysis of signal tracks. It is a Structured Query Language (SQL)-like declarative language, which means one only specifies what computations need to be done but not how these computations are to be carried out. STQL provides a rich set of constructs for manipulating genomic intervals and their values. To run STQL queries, we have developed the Signal Track Analytical Research Tool (START, http://yiplab.cse.cuhk.edu.hk/start/ ), a system that includes a Web-based user interface and a back-end execution system. The user interface helps users select data from our database of around 10,000 commonly-used public signal tracks, manage their own tracks, and construct, store and share STQL queries. The back-end system automatically translates STQL queries into optimized low-level programs and runs them on a computer cluster in parallel. We use STQL to perform 14 representative analytical tasks. By repeating these analyses using bedtools, Galaxy and custom Python scripts, we show that the STQL solution is usually the simplest, and the parallel execution achieves significant speed-up with large data files. Finally, we describe how a biologist with minimal formal training in computer programming self-learned STQL to analyze DNA methylation data we produced from 60 pairs of hepatocellular carcinoma (HCC) samples. Overall, STQL and START provide a generic way for analyzing a large number of genomic signal tracks in parallel easily.

Blind Seer: A Scalable Private DBMS

DTIC Science & Technology

2014-05-01

searchable index terms per DB row, in time comparable to (insecure) MySQL (many practical queries can be privately executed with work 1.2-3 times slower...than MySQL , although some queries are costlier). We support a rich query set, including searching on arbitrary boolean formulas on keywords and ranges...index terms per DB row, in time comparable to (insecure) MySQL (many practical queries can be privately executed with work 1.2-3 times slower than MySQL

Flexible Decision Support in Device-Saturated Environments

DTIC Science & Technology

2003-10-01

also output tuples to a remote MySQL or Postgres database. 3.3 GUI The GUI allows the user to pose queries using SQL and to display query...DatabaseConnection.java – handles connections to an external database (such as MySQL or Postgres ). • Debug.java – contains the code for printing out Debug messages...also provided. It is possible to output the results of queries to a MySQL or Postgres database for archival and the GUI can query those results

Constructing a Graph Database for Semantic Literature-Based Discovery.

PubMed

Hristovski, Dimitar; Kastrin, Andrej; Dinevski, Dejan; Rindflesch, Thomas C

2015-01-01

Literature-based discovery (LBD) generates discoveries, or hypotheses, by combining what is already known in the literature. Potential discoveries have the form of relations between biomedical concepts; for example, a drug may be determined to treat a disease other than the one for which it was intended. LBD views the knowledge in a domain as a network; a set of concepts along with the relations between them. As a starting point, we used SemMedDB, a database of semantic relations between biomedical concepts extracted with SemRep from Medline. SemMedDB is distributed as a MySQL relational database, which has some problems when dealing with network data. We transformed and uploaded SemMedDB into the Neo4j graph database, and implemented the basic LBD discovery algorithms with the Cypher query language. We conclude that storing the data needed for semantic LBD is more natural in a graph database. Also, implementing LBD discovery algorithms is conceptually simpler with a graph query language when compared with standard SQL.

Python Winding Itself Around Datacubes: How to Access Massive Multi-Dimensional Arrays in a Pythonic Way

NASA Astrophysics Data System (ADS)

Merticariu, Vlad; Misev, Dimitar; Baumann, Peter

2017-04-01

While python has developed into the lingua franca in Data Science there is often a paradigm break when accessing specialized tools. In particular for one of the core data categories in science and engineering, massive multi-dimensional arrays, out-of-memory solutions typically employ their own, different models. We discuss this situation on the example of the scalable open-source array engine, rasdaman ("raster data manager") which offers access to and processing of Petascale multi-dimensional arrays through an SQL-style array query language, rasql. Such queries are executed in the server on a storage engine utilizing adaptive array partitioning and based on a processing engine implementing a "tile streaming" paradigm to allow processing of arrays massively larger than server RAM. The rasdaman QL has acted as blueprint for forthcoming ISO Array SQL and the Open Geospatial Consortium (OGC) geo analytics language, Web Coverage Processing Service, adopted in 2008. Not surprisingly, rasdaman is OGC and INSPIRE Reference Implementation for their "Big Earth Data" standards suite. Recently, rasdaman has been augmented with a python interface which allows to transparently interact with the database (credits go to Siddharth Shukla's Master Thesis at Jacobs University). Programmers do not need to know the rasdaman query language, as the operators are silently transformed, through lazy evaluation, into queries. Arrays delivered are likewise automatically transformed into their python representation. In the talk, the rasdaman concept will be illustrated with the help of large-scale real-life examples of operational satellite image and weather data services, and sample python code.

ADVICE--Educational System for Teaching Database Courses

ERIC Educational Resources Information Center

Cvetanovic, M.; Radivojevic, Z.; Blagojevic, V.; Bojovic, M.

2011-01-01

This paper presents a Web-based educational system, ADVICE, that helps students to bridge the gap between database management system (DBMS) theory and practice. The usage of ADVICE is presented through a set of laboratory exercises developed to teach students conceptual and logical modeling, SQL, formal query languages, and normalization. While…

Network Configuration of Oracle and Database Programming Using SQL

NASA Technical Reports Server (NTRS)

Davis, Melton; Abdurrashid, Jibril; Diaz, Philip; Harris, W. C.

2000-01-01

A database can be defined as a collection of information organized in such a way that it can be retrieved and used. A database management system (DBMS) can further be defined as the tool that enables us to manage and interact with the database. The Oracle 8 Server is a state-of-the-art information management environment. It is a repository for very large amounts of data, and gives users rapid access to that data. The Oracle 8 Server allows for sharing of data between applications; the information is stored in one place and used by many systems. My research will focus primarily on SQL (Structured Query Language) programming. SQL is the way you define and manipulate data in Oracle's relational database. SQL is the industry standard adopted by all database vendors. When programming with SQL, you work on sets of data (i.e., information is not processed one record at a time).

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.

Automatically Preparing Safe SQL Queries

NASA Astrophysics Data System (ADS)

Bisht, Prithvi; Sistla, A. Prasad; Venkatakrishnan, V. N.

We present the first sound program source transformation approach for automatically transforming the code of a legacy web application to employ PREPARE statements in place of unsafe SQL queries. Our approach therefore opens the way for eradicating the SQL injection threat vector from legacy web applications.

Using PHP/MySQL to Manage Potential Mass Impacts

NASA Technical Reports Server (NTRS)

Hager, Benjamin I.

2010-01-01

This paper presents a new application using commercially available software to manage mass properties for spaceflight vehicles. PHP/MySQL(PHP: Hypertext Preprocessor and My Structured Query Language) are a web scripting language and a database language commonly used in concert with each other. They open up new opportunities to develop cutting edge mass properties tools, and in particular, tools for the management of potential mass impacts (threats and opportunities). The paper begins by providing an overview of the functions and capabilities of PHP/MySQL. The focus of this paper is on how PHP/MySQL are being used to develop an advanced "web accessible" database system for identifying and managing mass impacts on NASA's Ares I Upper Stage program, managed by the Marshall Space Flight Center. To fully describe this application, examples of the data, search functions, and views are provided to promote, not only the function, but the security, ease of use, simplicity, and eye-appeal of this new application. This paper concludes with an overview of the other potential mass properties applications and tools that could be developed using PHP/MySQL. The premise behind this paper is that PHP/MySQL are software tools that are easy to use and readily available for the development of cutting edge mass properties applications. These tools are capable of providing "real-time" searching and status of an active database, automated report generation, and other capabilities to streamline and enhance mass properties management application. By using PHP/MySQL, proven existing methods for managing mass properties can be adapted to present-day information technology to accelerate mass properties data gathering, analysis, and reporting, allowing mass property management to keep pace with today's fast-pace design and development processes.

TabSQL: a MySQL tool to facilitate mapping user data to public databases.

PubMed

Xia, Xiao-Qin; McClelland, Michael; Wang, Yipeng

2010-06-23

With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data.

TabSQL: a MySQL tool to facilitate mapping user data to public databases

PubMed Central

2010-01-01

Background With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. Results We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. Conclusions TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data. PMID:20573251

Integrated Array/Metadata Analytics

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Baumann, Peter

2015-04-01

Data comes in various forms and types, and integration usually presents a problem that is often simply ignored and solved with ad-hoc solutions. Multidimensional arrays are an ubiquitous data type, that we find at the core of virtually all science and engineering domains, as sensor, model, image, statistics data. Naturally, arrays are richly described by and intertwined with additional metadata (alphanumeric relational data, XML, JSON, etc). Database systems, however, a fundamental building block of what we call "Big Data", lack adequate support for modelling and expressing these array data/metadata relationships. Array analytics is hence quite primitive or non-existent at all in modern relational DBMS. Recognizing this, we extended SQL with a new SQL/MDA part seamlessly integrating multidimensional array analytics into the standard database query language. We demonstrate the benefits of SQL/MDA with real-world examples executed in ASQLDB, an open-source mediator system based on HSQLDB and rasdaman, that already implements SQL/MDA.

Framework for Evaluating Loop Invariant Detection Games in Relation to Automated Dynamic Invariant Detectors

DTIC Science & Technology

2015-09-01

Detectability ...............................................................................................37 Figure 20. Excel VBA Codes for Checker...National Vulnerability Database OS Operating System SQL Structured Query Language VC Verification Condition VBA Visual Basic for Applications...checks each of these assertions for detectability by Daikon. The checker is an Excel Visual Basic for Applications ( VBA ) script that checks the

An integrated information retrieval and document management system

NASA Technical Reports Server (NTRS)

Coles, L. Stephen; Alvarez, J. Fernando; Chen, James; Chen, William; Cheung, Lai-Mei; Clancy, Susan; Wong, Alexis

1993-01-01

This paper describes the requirements and prototype development for an intelligent document management and information retrieval system that will be capable of handling millions of pages of text or other data. Technologies for scanning, Optical Character Recognition (OCR), magneto-optical storage, and multiplatform retrieval using a Standard Query Language (SQL) will be discussed. The semantic ambiguity inherent in the English language is somewhat compensated-for through the use of coefficients or weighting factors for partial synonyms. Such coefficients are used both for defining structured query trees for routine queries and for establishing long-term interest profiles that can be used on a regular basis to alert individual users to the presence of relevant documents that may have just arrived from an external source, such as a news wire service. Although this attempt at evidential reasoning is limited in comparison with the latest developments in AI Expert Systems technology, it has the advantage of being commercially available.

MRML: an extensible communication protocol for interoperability and benchmarking of multimedia information retrieval systems

NASA Astrophysics Data System (ADS)

Mueller, Wolfgang; Mueller, Henning; Marchand-Maillet, Stephane; Pun, Thierry; Squire, David M.; Pecenovic, Zoran; Giess, Christoph; de Vries, Arjen P.

2000-10-01

While in the area of relational databases interoperability is ensured by common communication protocols (e.g. ODBC/JDBC using SQL), Content Based Image Retrieval Systems (CBIRS) and other multimedia retrieval systems are lacking both a common query language and a common communication protocol. Besides its obvious short term convenience, interoperability of systems is crucial for the exchange and analysis of user data. In this paper, we present and describe an extensible XML-based query markup language, called MRML (Multimedia Retrieval markup Language). MRML is primarily designed so as to ensure interoperability between different content-based multimedia retrieval systems. Further, MRML allows researchers to preserve their freedom in extending their system as needed. MRML encapsulates multimedia queries in a way that enable multimedia (MM) query languages, MM content descriptions, MM query engines, and MM user interfaces to grow independently from each other, reaching a maximum of interoperability while ensuring a maximum of freedom for the developer. For benefitting from this, only a few simple design principles have to be respected when extending MRML for one's fprivate needs. The design of extensions withing the MRML framework will be described in detail in the paper. MRML has been implemented and tested for the CBIRS Viper, using the user interface Snake Charmer. Both are part of the GNU project and can be downloaded at our site.

The Armed Forces Casualty Assistance Readiness Enhancement System (CARES): Design for Flexibility

DTIC Science & Technology

2006-06-01

Special Form SQL Structured Query Language SSA Social Security Administration U USMA United States Military Academy V VB Visual Basic VBA Visual Basic for...of Abbreviations ................................................................... 26 Appendix B: Key VBA Macros and MS Excel Coding...internet portal, CARES Version 1.0 is a MS Excel spreadsheet application that contains a considerable number of Visual Basic for Applications ( VBA

Geographic Video 3d Data Model And Retrieval

NASA Astrophysics Data System (ADS)

Han, Z.; Cui, C.; Kong, Y.; Wu, H.

2014-04-01

Geographic video includes both spatial and temporal geographic features acquired through ground-based or non-ground-based cameras. With the popularity of video capture devices such as smartphones, the volume of user-generated geographic video clips has grown significantly and the trend of this growth is quickly accelerating. Such a massive and increasing volume poses a major challenge to efficient video management and query. Most of the today's video management and query techniques are based on signal level content extraction. They are not able to fully utilize the geographic information of the videos. This paper aimed to introduce a geographic video 3D data model based on spatial information. The main idea of the model is to utilize the location, trajectory and azimuth information acquired by sensors such as GPS receivers and 3D electronic compasses in conjunction with video contents. The raw spatial information is synthesized to point, line, polygon and solid according to the camcorder parameters such as focal length and angle of view. With the video segment and video frame, we defined the three categories geometry object using the geometry model of OGC Simple Features Specification for SQL. We can query video through computing the spatial relation between query objects and three categories geometry object such as VFLocation, VSTrajectory, VSFOView and VFFovCone etc. We designed the query methods using the structured query language (SQL) in detail. The experiment indicate that the model is a multiple objective, integration, loosely coupled, flexible and extensible data model for the management of geographic stereo video.

Evaluation of relational and NoSQL database architectures to manage genomic annotations.

PubMed

Schulz, Wade L; Nelson, Brent G; Felker, Donn K; Durant, Thomas J S; Torres, Richard

2016-12-01

While the adoption of next generation sequencing has rapidly expanded, the informatics infrastructure used to manage the data generated by this technology has not kept pace. Historically, relational databases have provided much of the framework for data storage and retrieval. Newer technologies based on NoSQL architectures may provide significant advantages in storage and query efficiency, thereby reducing the cost of data management. But their relative advantage when applied to biomedical data sets, such as genetic data, has not been characterized. To this end, we compared the storage, indexing, and query efficiency of a common relational database (MySQL), a document-oriented NoSQL database (MongoDB), and a relational database with NoSQL support (PostgreSQL). When used to store genomic annotations from the dbSNP database, we found the NoSQL architectures to outperform traditional, relational models for speed of data storage, indexing, and query retrieval in nearly every operation. These findings strongly support the use of novel database technologies to improve the efficiency of data management within the biological sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

An Ada/SQL (Structured Query Language) Application Scanner.

DTIC Science & Technology

1988-03-01

Digital ...8217 (" DIGITS "), 46 new STRING’ ("DO"), new STRING’ ("ELSE"), new STRING’ ("ELSIF"), new STRING’ ("END"), new STRING’ ("ENTRY"), new STRING’ ("EXCEPTION...INTEGERPRINT; generic type NUM is digits <>; package FLOATPRINT is package txtprts.ada 18 prcdr PR (FL inFL %YE LINE n LINTYPE UNCLASSIFIED procedure

Are Models Easier to Understand than Code? An Empirical Study on Comprehension of Entity-Relationship (ER) Models vs. Structured Query Language (SQL) Code

ERIC Educational Resources Information Center

Sanchez, Pablo; Zorrilla, Marta; Duque, Rafael; Nieto-Reyes, Alicia

2011-01-01

Models in Software Engineering are considered as abstract representations of software systems. Models highlight relevant details for a certain purpose, whereas irrelevant ones are hidden. Models are supposed to make system comprehension easier by reducing complexity. Therefore, models should play a key role in education, since they would ease the…

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.

A method to implement fine-grained access control for personal health records through standard relational database queries.

PubMed

Sujansky, Walter V; Faus, Sam A; Stone, Ethan; Brennan, Patricia Flatley

2010-10-01

Online personal health records (PHRs) enable patients to access, manage, and share certain of their own health information electronically. This capability creates the need for precise access-controls mechanisms that restrict the sharing of data to that intended by the patient. The authors describe the design and implementation of an access-control mechanism for PHR repositories that is modeled on the eXtensible Access Control Markup Language (XACML) standard, but intended to reduce the cognitive and computational complexity of XACML. The authors implemented the mechanism entirely in a relational database system using ANSI-standard SQL statements. Based on a set of access-control rules encoded as relational table rows, the mechanism determines via a single SQL query whether a user who accesses patient data from a specific application is authorized to perform a requested operation on a specified data object. Testing of this query on a moderately large database has demonstrated execution times consistently below 100ms. The authors include the details of the implementation, including algorithms, examples, and a test database as Supplementary materials. Copyright © 2010 Elsevier Inc. All rights reserved.

HBVPathDB: a database of HBV infection-related molecular interaction network.

PubMed

Zhang, Yi; Bo, Xiao-Chen; Yang, Jing; Wang, Sheng-Qi

2005-03-21

To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

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.

Systematic Assessment of the Impact of User Roles on Network Flow Patterns

DTIC Science & Technology

2017-09-01

Protocol SNMP Simple Network Management Protocol SQL Structured Query Language SSH Secure Shell SYN TCP Sync Flag SVDD Support Vector Data Description SVM...and evaluating users based on roles provide the best approach for defining normal digital behaviors? People are individuals, with different interests...activities on the network. We evaluate the assumption that users sharing similar roles exhibit similar network behaviors, and contrast the level of similarity

Analyzing Enron Data: Bitmap Indexing Outperforms MySQL Queries bySeveral Orders of Magnitude

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

Stockinger, Kurt; Rotem, Doron; Shoshani, Arie

2006-01-28

FastBit is an efficient, compressed bitmap indexing technology that was developed in our group. In this report we evaluate the performance of MySQL and FastBit for analyzing the email traffic of the Enron dataset. The first finding shows that materializing the join results of several tables significantly improves the query performance. The second finding shows that FastBit outperforms MySQL by several orders of magnitude.

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.

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.

SQL-RAMS

NASA Technical Reports Server (NTRS)

Alfaro, Victor O.; Casey, Nancy J.

2005-01-01

SQL-RAMS (where "SQL" signifies Structured Query Language and "RAMS" signifies Rocketdyne Automated Management System) is a successor to the legacy version of RAMS -- a computer program used to manage all work, nonconformance, corrective action, and configuration management on rocket engines and ground support equipment at Stennis Space Center. The legacy version resided in the File-Maker Pro software system and was constructed in modules that could act as standalone programs. There was little or no integration among modules. Because of limitations on file-management capabilities in FileMaker Pro, and because of difficulty of integration of FileMaker Pro with other software systems for exchange of data using such industry standards as SQL, the legacy version of RAMS proved to be limited, and working to circumvent its limitations too time-consuming. In contrast, SQL-RAMS is an integrated SQL-server-based program that supports all data-exchange software industry standards. Whereas in the legacy version, it was necessary to access individual modules to gain insight into a particular workstatus document, SQL-RAMS provides access through a single-screen presentation of core modules. In addition, SQL-RAMS enables rapid and efficient filtering of displayed statuses by predefined categories and test numbers. SQL-RAMS is rich in functionality and encompasses significant improvements over the legacy system. It provides users the ability to perform many tasks, which in the past required administrator intervention. Additionally, many of the design limitations have been corrected, allowing for a robust application that is user centric.

SQL-RAMS

NASA Technical Reports Server (NTRS)

Alfaro, Victor O.; Casey, Nancy J.

2005-01-01

SQL-RAMS (where "SQL" signifies Structured Query Language and "RAMS" signifies Rocketdyne Automated Management System) is a successor to the legacy version of RAMS a computer program used to manage all work, nonconformance, corrective action, and configuration management on rocket engines and ground support equipment at Stennis Space Center. The legacy version resided in the FileMaker Pro software system and was constructed in modules that could act as stand-alone programs. There was little or no integration among modules. Because of limitations on file-management capabilities in FileMaker Pro, and because of difficulty of integration of FileMaker Pro with other software systems for exchange of data using such industry standards as SQL, the legacy version of RAMS proved to be limited, and working to circumvent its limitations too time-consuming. In contrast, SQL-RAMS is an integrated SQL-server-based program that supports all data-exchange software industry standards. Whereas in the legacy version, it was necessary to access individual modules to gain insight to a particular work-status documents, SQL-RAMS provides access through a single-screen presentation of core modules. In addition, SQL-RAMS enable rapid and efficient filtering of displayed statuses by predefined categories and test numbers. SQL-RAMS is rich in functionality and encompasses significant improvements over the legacy system. It provides users the ability to perform many tasks which in the past required administrator intervention. Additionally many of the design limitations have been corrected allowing for a robust application that is user centric.

Examining database persistence of ISO/EN 13606 standardized electronic health record extracts: relational vs. NoSQL approaches.

PubMed

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Lozano-Rubí, Raimundo; Serrano-Balazote, Pablo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

2017-08-18

The objective of this research is to compare the relational and non-relational (NoSQL) database systems approaches in order to store, recover, query and persist standardized medical information in the form of ISO/EN 13606 normalized Electronic Health Record XML extracts, both in isolation and concurrently. NoSQL database systems have recently attracted much attention, but few studies in the literature address their direct comparison with relational databases when applied to build the persistence layer of a standardized medical information system. One relational and two NoSQL databases (one document-based and one native XML database) of three different sizes have been created in order to evaluate and compare the response times (algorithmic complexity) of six different complexity growing queries, which have been performed on them. Similar appropriate results available in the literature have also been considered. Relational and non-relational NoSQL database systems show almost linear algorithmic complexity query execution. However, they show very different linear slopes, the former being much steeper than the two latter. Document-based NoSQL databases perform better in concurrency than in isolation, and also better than relational databases in concurrency. Non-relational NoSQL databases seem to be more appropriate than standard relational SQL databases when database size is extremely high (secondary use, research applications). Document-based NoSQL databases perform in general better than native XML NoSQL databases. EHR extracts visualization and edition are also document-based tasks more appropriate to NoSQL database systems. However, the appropriate database solution much depends on each particular situation and specific problem.

Software Engineering Laboratory (SEL) database organization and user's guide, revision 2

NASA Technical Reports Server (NTRS)

Morusiewicz, Linda; Bristow, John

1992-01-01

The organization of the Software Engineering Laboratory (SEL) database is presented. Included are definitions and detailed descriptions of the database tables and views, the SEL data, and system support data. The mapping from the SEL and system support data to the base table is described. In addition, techniques for accessing the database through the Database Access Manager for the SEL (DAMSEL) system and via the ORACLE structured query language (SQL) are discussed.

Software Engineering Laboratory (SEL) database organization and user's guide

NASA Technical Reports Server (NTRS)

So, Maria; Heller, Gerard; Steinberg, Sandra; Spiegel, Douglas

1989-01-01

The organization of the Software Engineering Laboratory (SEL) database is presented. Included are definitions and detailed descriptions of the database tables and views, the SEL data, and system support data. The mapping from the SEL and system support data to the base tables is described. In addition, techniques for accessing the database, through the Database Access Manager for the SEL (DAMSEL) system and via the ORACLE structured query language (SQL), are discussed.

A Customizable Dashboarding System for Watershed Model Interpretation

NASA Astrophysics Data System (ADS)

Easton, Z. M.; Collick, A.; Wagena, M. B.; Sommerlot, A.; Fuka, D.

2017-12-01

Stakeholders, including policymakers, agricultural water managers, and small farm managers, can benefit from the outputs of commonly run watershed models. However, the information that each stakeholder needs is be different. While policy makers are often interested in the broader effects that small farm management may have on a watershed during extreme events or over long periods, farmers are often interested in field specific effects at daily or seasonal period. To provide stakeholders with the ability to analyze and interpret data from large scale watershed models, we have developed a framework that can support custom exploration of the large datasets produced. For the volume of data produced by these models, SQL-based data queries are not efficient; thus, we employ a "Not Only SQL" (NO-SQL) query language, which allows data to scale in both quantity and query volumes. We demonstrate a stakeholder customizable Dashboarding system that allows stakeholders to create custom `dashboards' to summarize model output specific to their needs. Dashboarding is a dynamic and purpose-based visual interface needed to display one-to-many database linkages so that the information can be presented for a single time period or dynamically monitored over time and allows a user to quickly define focus areas of interest for their analysis. We utilize a single watershed model that is run four times daily with a combined set of climate projections, which are then indexed, and added to an ElasticSearch datastore. ElasticSearch is a NO-SQL search engine built on top of Apache Lucene, a free and open-source information retrieval software library. Aligned with the ElasticSearch project is the open source visualization and analysis system, Kibana, which we utilize for custom stakeholder dashboarding. The dashboards create a visualization of the stakeholder selected analysis and can be extended to recommend robust strategies to support decision-making.

Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data

PubMed Central

Freire, Sergio Miranda; Teodoro, Douglas; Wei-Kleiner, Fang; Sundvall, Erik; Karlsson, Daniel; Lambrix, Patrick

2016-01-01

This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest. PMID:26958859

Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data.

PubMed

Freire, Sergio Miranda; Teodoro, Douglas; Wei-Kleiner, Fang; Sundvall, Erik; Karlsson, Daniel; Lambrix, Patrick

2016-01-01

This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest.

Concept locator: a client-server application for retrieval of UMLS metathesaurus concepts through complex boolean query.

PubMed

Nadkarni, P M

1997-08-01

Concept Locator (CL) is a client-server application that accesses a Sybase relational database server containing a subset of the UMLS Metathesaurus for the purpose of retrieval of concepts corresponding to one or more query expressions supplied to it. CL's query grammar permits complex Boolean expressions, wildcard patterns, and parenthesized (nested) subexpressions. CL translates the query expressions supplied to it into one or more SQL statements that actually perform the retrieval. The generated SQL is optimized by the client to take advantage of the strengths of the server's query optimizer, and sidesteps its weaknesses, so that execution is reasonably efficient.

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)''.

Intelligent search in Big Data

NASA Astrophysics Data System (ADS)

Birialtsev, E.; Bukharaev, N.; Gusenkov, A.

2017-10-01

An approach to data integration, aimed on the ontology-based intelligent search in Big Data, is considered in the case when information objects are represented in the form of relational databases (RDB), structurally marked by their schemes. The source of information for constructing an ontology and, later on, the organization of the search are texts in natural language, treated as semi-structured data. For the RDBs, these are comments on the names of tables and their attributes. Formal definition of RDBs integration model in terms of ontologies is given. Within framework of the model universal RDB representation ontology, oil production subject domain ontology and linguistic thesaurus of subject domain language are built. Technique of automatic SQL queries generation for subject domain specialists is proposed. On the base of it, information system for TATNEFT oil-producing company RDBs was implemented. Exploitation of the system showed good relevance with majority of queries.

Developing an Excel Decision Support System Using In-Transit Visibility to Decrease DoD Transportation Delays

DTIC Science & Technology

2008-03-01

Fortunately, built into Excel is the capability to use ActiveX Data Objects (ADO), a software feature which uses VBA to interface with external...part of Excel’s ActiveX Direct Objects (ADO) functionality, Excel can execute SQL queries in Access with VBA. An SQL query statement can be written

An Implementation Methodology and Software Tool for an Entropy Based Engineering Model for Evolving Systems

DTIC Science & Technology

2003-06-01

delivery Data Access (1980s) "What were unit sales in New England last March?" Relational databases (RDBMS), Structured Query Language ( SQL ...macros written in Visual Basic for Applications ( VBA ). 32 Iteration Two: Class Diagram Tech OASIS Export ScriptImport Filter Data ProcessingMethod 1...MS Excel * 1 VBA Macro*1 contains sends data to co nt ai ns executes * * 1 1 contains contains Figure 20. Iteration two class diagram The

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

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.

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

NASA Technical Reports Server (NTRS)

Steeman, Gerald; Connell, Christopher

2000-01-01

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

Brave New World: Data Intensive Science with SDSS and the VO

NASA Astrophysics Data System (ADS)

Thakar, A. R.; Szalay, A. S.; O'Mullane, W.; Nieto-Santisteban, M.; Budavari, T.; Li, N.; Carliles, S.; Haridas, V.; Malik, T.; Gray, J.

2004-12-01

With the advent of digital archives and the VO, astronomy is quickly changing from a data-hungry to a data-intensive science. Local and specialized access to data will remain the most direct and efficient way to get data out of individual archives, especially if you know what you are looking for. However, the enormous sizes of the upcoming archives will preclude this type of access for most institutions, and will not allow researchers to tap the vast potential for discovery in cross-matching and comparing data between different archives. The VO makes this type of interoperability and distributed data access possible by adopting industry standards for data access (SQL) and data interchange (SOAP/XML) with platform independence (Web services). As a sneak preview of this brave new world where astronomers may need to become SQL warriors, we present a look at VO-enabled access to catalog data in the SDSS Catalog Archive Server (CAS): CasJobs - a workbench environment that allows arbitrarily complex SQL queries and your own personal database (MyDB) that you can share with collaborators; OpenSkyQuery - an IVOA (International Virtual Observatory Alliance) compliant federation of multiple archives (OpenSkyNodes) that currently links nearly 20 catalogs and allows cross-match queries (in ADQL - Astronomical Data Query Language) between them; Spectrum and Filter Profile Web services that provide access to an open database of spectra (registered users may add their own spectra); and VO-enabled Mirage - a Java visualizatiion tool developed at Bell Labs and enhanced at JHU that allows side-by-side comparison of SDSS catalog and FITS image data. Anticipating the next generation of Petabyte archives like LSST by the end of the decade, we are developing a parallel cross-match engine for all-sky cross-matches between large surveys, along with a 100-Terabyte data intensive science laboratory with high-speed parallel data access.

SiC: An Agent Based Architecture for Preventing and Detecting Attacks to Ubiquitous Databases

NASA Astrophysics Data System (ADS)

Pinzón, Cristian; de Paz, Yanira; Bajo, Javier; Abraham, Ajith; Corchado, Juan M.

One of the main attacks to ubiquitous databases is the structure query language (SQL) injection attack, which causes severe damages both in the commercial aspect and in the user’s confidence. This chapter proposes the SiC architecture as a solution to the SQL injection attack problem. This is a hierarchical distributed multiagent architecture, which involves an entirely new approach with respect to existing architectures for the prevention and detection of SQL injections. SiC incorporates a kind of intelligent agent, which integrates a case-based reasoning system. This agent, which is the core of the architecture, allows the application of detection techniques based on anomalies as well as those based on patterns, providing a great degree of autonomy, flexibility, robustness and dynamic scalability. The characteristics of the multiagent system allow an architecture to detect attacks from different types of devices, regardless of the physical location. The architecture has been tested on a medical database, guaranteeing safe access from various devices such as PDAs and notebook computers.

BioWarehouse: a bioinformatics database warehouse toolkit

PubMed Central

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

2006-01-01

Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the database integration problem for bioinformatics. PMID:16556315

BioWarehouse: a bioinformatics database warehouse toolkit.

PubMed

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

2006-03-23

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

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

Madduri, Kamesh; Wu, Kesheng

The Resource Description Framework (RDF) is a popular data model for representing linked data sets arising from the web, as well as large scienti c data repositories such as UniProt. RDF data intrinsically represents a labeled and directed multi-graph. SPARQL is a query language for RDF that expresses subgraph pattern- nding queries on this implicit multigraph in a SQL- like syntax. SPARQL queries generate complex intermediate join queries; to compute these joins e ciently, we propose a new strategy based on bitmap indexes. We store the RDF data in column-oriented structures as compressed bitmaps along with two dictionaries. This papermore » makes three new contributions. (i) We present an e cient parallel strategy for parsing the raw RDF data, building dictionaries of unique entities, and creating compressed bitmap indexes of the data. (ii) We utilize the constructed bitmap indexes to e ciently answer SPARQL queries, simplifying the join evaluations. (iii) To quantify the performance impact of using bitmap indexes, we compare our approach to the state-of-the-art triple-store RDF-3X. We nd that our bitmap index-based approach to answering queries is up to an order of magnitude faster for a variety of SPARQL queries, on gigascale RDF data sets.« less

Example Level 1 Ada/SQL (Structured Query Language) System Software

DTIC Science & Technology

1987-09-01

PUTLINE ("EMPNAME JOB SALARY COMMISSION"); loop FETCH ( CURSOR ); INTO ( VEMP NAME , STR LAST ); T LEN INTEGER (STR LAST - V EMP NAME’FIRST + 1); for I in 1...begin PUT_LINE ("EMPNAME JOB SALARY DEPT"); loop FETCH (CURSOR); INTO ( VEMP NAME , STRLAST ); T_LEN := INTEGER (STRLAST - V_EMPNAME’FIRST + 1); for I in...NUMBERS OPEN ( CURSOR ); begin PUT_LINE ("EMP_NAME SALARY JOB"); loop FETCH ( CURSOR ); INTO ( VEMP NAME , STRLAST ); T_LEN := INTEGER (STR_LAST

Abstracting data warehousing issues in scientific research.

PubMed

Tews, Cody; Bracio, Boris R

2002-01-01

This paper presents the design and implementation of the Idaho Biomedical Data Management System (IBDMS). This system preprocesses biomedical data from the IMPROVE (Improving Control of Patient Status in Critical Care) library via an Open Database Connectivity (ODBC) connection. The ODBC connection allows for local and remote simulations to access filtered, joined, and sorted data using the Structured Query Language (SQL). The tool is capable of providing an overview of available data in addition to user defined data subset for verification of models of the human respiratory system.

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.

Development of a replicated database of DHCP data for evaluation of drug use.

PubMed Central

Graber, S E; Seneker, J A; Stahl, A A; Franklin, K O; Neel, T E; Miller, R A

1996-01-01

This case report describes development and testing of a method to extract clinical information stored in the Veterans Affairs (VA) Decentralized Hospital Computer System (DHCP) for the purpose of analyzing data about groups of patients. The authors used a microcomputer-based, structured query language (SQL)-compatible, relational database system to replicate a subset of the Nashville VA Hospital's DHCP patient database. This replicated database contained the complete current Nashville DHCP prescription, provider, patient, and drug data sets, and a subset of the laboratory data. A pilot project employed this replicated database to answer questions that might arise in drug-use evaluation, such as identification of cases of polypharmacy, suboptimal drug regimens, and inadequate laboratory monitoring of drug therapy. These database queries included as candidates for review all prescriptions for all outpatients. The queries demonstrated that specific drug-use events could be identified for any time interval represented in the replicated database. PMID:8653451

Development of a replicated database of DHCP data for evaluation of drug use.

PubMed

Graber, S E; Seneker, J A; Stahl, A A; Franklin, K O; Neel, T E; Miller, R A

1996-01-01

This case report describes development and testing of a method to extract clinical information stored in the Veterans Affairs (VA) Decentralized Hospital Computer System (DHCP) for the purpose of analyzing data about groups of patients. The authors used a microcomputer-based, structured query language (SQL)-compatible, relational database system to replicate a subset of the Nashville VA Hospital's DHCP patient database. This replicated database contained the complete current Nashville DHCP prescription, provider, patient, and drug data sets, and a subset of the laboratory data. A pilot project employed this replicated database to answer questions that might arise in drug-use evaluation, such as identification of cases of polypharmacy, suboptimal drug regimens, and inadequate laboratory monitoring of drug therapy. These database queries included as candidates for review all prescriptions for all outpatients. The queries demonstrated that specific drug-use events could be identified for any time interval represented in the replicated database.

Engineering the ATLAS TAG Browser

NASA Astrophysics Data System (ADS)

Zhang, Qizhi; ATLAS Collaboration

2011-12-01

ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services are discussed. We also describe strategies for dealing with data that may vary over time, such as run-dependent trigger decision decoding. Along with examples, we illustrate how programming techniques in multiple languages (PHP, JAVASCRIPT, XML, AJAX, and PL/SQL) have been blended to achieve the required results. Finally, we evaluate features of the ELSSI service in terms of functionality, scalability, and performance.

Improved oilfield GHG accounting using a global oilfield database

NASA Astrophysics Data System (ADS)

Roberts, S.; Brandt, A. R.; Masnadi, M.

2016-12-01

The definition of oil is shifting in considerable ways. Conventional oil resources are declining as oil sands, heavy oils, and others emerge. Technological advances mean that these unconventional hydrocarbons are now viable resources. Meanwhile, scientific evidence is mounting that climate change is occurring. The oil sector is responsible for 35% of global greenhouse gas (GHG) emissions, but the climate impacts of these new unconventional oils are not well understood. As such, the Oil Climate Index (OCI) project has been an international effort to evaluate the total life-cycle environmental GHG emissions of different oil fields globally. Over the course of the first and second phases of the project, 30 and 75 global oil fields have been investigated, respectively. The 75 fields account for about 25% of global oil production. For the third phase of the project, it is aimed to expand the OCI to contain closing to 100% of global oil production; leading to the analysis of 8000 fields. To accomplish this, a robust database system is required to handle and manipulate the data. Therefore, the integration of the data into the computer science language SQL (Structured Query Language) was performed. The implementation of SQL allows users to process the data more efficiently than would be possible by using the previously established program (Microsoft Excel). Next, a graphic user interface (gui) was implemented, in the computer science language of C#, in order to make the data interactive; enabling people to update the database without prior knowledge of SQL being necessary.

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

PubMed

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

2017-03-01

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

Use of Graph Database for the Integration of Heterogeneous Biological Data

PubMed Central

Yoon, Byoung-Ha; Kim, Seon-Kyu

2017-01-01

Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data. PMID:28416946

High dimensional biological data retrieval optimization with NoSQL technology.

PubMed

Wang, Shicai; Pandis, Ioannis; Wu, Chao; He, Sijin; Johnson, David; Emam, Ibrahim; Guitton, Florian; Guo, Yike

2014-01-01

High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies. Although microarray data is supported in data warehouses such as tranSMART, when querying relational databases for hundreds of different patient gene expression records queries are slow due to poor performance. Non-relational data models, such as the key-value model implemented in NoSQL databases, hold promise to be more performant solutions. Our motivation is to improve the performance of the tranSMART data warehouse with a view to supporting Next Generation Sequencing data. In this paper we introduce a new data model better suited for high-dimensional data storage and querying, optimized for database scalability and performance. We have designed a key-value pair data model to support faster queries over large-scale microarray data and implemented the model using HBase, an implementation of Google's BigTable storage system. An experimental performance comparison was carried out against the traditional relational data model implemented in both MySQL Cluster and MongoDB, using a large publicly available transcriptomic data set taken from NCBI GEO concerning Multiple Myeloma. Our new key-value data model implemented on HBase exhibits an average 5.24-fold increase in high-dimensional biological data query performance compared to the relational model implemented on MySQL Cluster, and an average 6.47-fold increase on query performance on MongoDB. The performance evaluation found that the new key-value data model, in particular its implementation in HBase, outperforms the relational model currently implemented in tranSMART. We propose that NoSQL technology holds great promise for large-scale data management, in particular for high-dimensional biological data such as that demonstrated in the performance evaluation described in this paper. We aim to use this new data model as a basis for migrating tranSMART's implementation to a more scalable solution for Big Data.

High dimensional biological data retrieval optimization with NoSQL technology

PubMed Central

2014-01-01

Background High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies. Although microarray data is supported in data warehouses such as tranSMART, when querying relational databases for hundreds of different patient gene expression records queries are slow due to poor performance. Non-relational data models, such as the key-value model implemented in NoSQL databases, hold promise to be more performant solutions. Our motivation is to improve the performance of the tranSMART data warehouse with a view to supporting Next Generation Sequencing data. Results In this paper we introduce a new data model better suited for high-dimensional data storage and querying, optimized for database scalability and performance. We have designed a key-value pair data model to support faster queries over large-scale microarray data and implemented the model using HBase, an implementation of Google's BigTable storage system. An experimental performance comparison was carried out against the traditional relational data model implemented in both MySQL Cluster and MongoDB, using a large publicly available transcriptomic data set taken from NCBI GEO concerning Multiple Myeloma. Our new key-value data model implemented on HBase exhibits an average 5.24-fold increase in high-dimensional biological data query performance compared to the relational model implemented on MySQL Cluster, and an average 6.47-fold increase on query performance on MongoDB. Conclusions The performance evaluation found that the new key-value data model, in particular its implementation in HBase, outperforms the relational model currently implemented in tranSMART. We propose that NoSQL technology holds great promise for large-scale data management, in particular for high-dimensional biological data such as that demonstrated in the performance evaluation described in this paper. We aim to use this new data model as a basis for migrating tranSMART's implementation to a more scalable solution for Big Data. PMID:25435347

The Ruby UCSC API: accessing the UCSC genome database using Ruby.

PubMed

Mishima, Hiroyuki; Aerts, Jan; Katayama, Toshiaki; Bonnal, Raoul J P; Yoshiura, Koh-ichiro

2012-09-21

The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast.The API uses the bin index-if available-when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/.

The Ruby UCSC API: accessing the UCSC genome database using Ruby

PubMed Central

2012-01-01

Background The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. Results The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast. The API uses the bin index—if available—when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Conclusions Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/. PMID:22994508

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

PubMed

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

2005-12-01

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

Reactome graph database: Efficient access to complex pathway data

PubMed Central

Korninger, Florian; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D’Eustachio, Peter

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types. PMID:29377902

An approach for heterogeneous and loosely coupled geospatial data distributed computing

NASA Astrophysics Data System (ADS)

Chen, Bin; Huang, Fengru; Fang, Yu; Huang, Zhou; Lin, Hui

2010-07-01

Most GIS (Geographic Information System) applications tend to have heterogeneous and autonomous geospatial information resources, and the availability of these local resources is unpredictable and dynamic under a distributed computing environment. In order to make use of these local resources together to solve larger geospatial information processing problems that are related to an overall situation, in this paper, with the support of peer-to-peer computing technologies, we propose a geospatial data distributed computing mechanism that involves loosely coupled geospatial resource directories and a term named as Equivalent Distributed Program of global geospatial queries to solve geospatial distributed computing problems under heterogeneous GIS environments. First, a geospatial query process schema for distributed computing as well as a method for equivalent transformation from a global geospatial query to distributed local queries at SQL (Structured Query Language) level to solve the coordinating problem among heterogeneous resources are presented. Second, peer-to-peer technologies are used to maintain a loosely coupled network environment that consists of autonomous geospatial information resources, thus to achieve decentralized and consistent synchronization among global geospatial resource directories, and to carry out distributed transaction management of local queries. Finally, based on the developed prototype system, example applications of simple and complex geospatial data distributed queries are presented to illustrate the procedure of global geospatial information processing.

Reactome graph database: Efficient access to complex pathway data.

PubMed

Fabregat, Antonio; Korninger, Florian; Viteri, Guilherme; Sidiropoulos, Konstantinos; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types.

Incremental Query Rewriting with Resolution

NASA Astrophysics Data System (ADS)

Riazanov, Alexandre; Aragão, Marcelo A. T.

We address the problem of semantic querying of relational databases (RDB) modulo knowledge bases using very expressive knowledge representation formalisms, such as full first-order logic or its various fragments. We propose to use a resolution-based first-order logic (FOL) reasoner for computing schematic answers to deductive queries, with the subsequent translation of these schematic answers to SQL queries which are evaluated using a conventional relational DBMS. We call our method incremental query rewriting, because an original semantic query is rewritten into a (potentially infinite) series of SQL queries. In this chapter, we outline the main idea of our technique - using abstractions of databases and constrained clauses for deriving schematic answers, and provide completeness and soundness proofs to justify the applicability of this technique to the case of resolution for FOL without equality. The proposed method can be directly used with regular RDBs, including legacy databases. Moreover, we propose it as a potential basis for an efficient Web-scale semantic search technology.

Named Entity Recognition in a Hungarian NL Based QA System

NASA Astrophysics Data System (ADS)

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

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

Shark: SQL and Analytics with Cost-Based Query Optimization on Coarse-Grained Distributed Memory

DTIC Science & Technology

2014-01-13

RDBMS and contains a database (often MySQL or Derby) with a namespace for tables, table metadata and partition information. Table data is stored in an...serialization/deserialization) Java interface implementations with corresponding object inspectors. The Hive driver controls the processing of queries, coordinat...native API, RDD operations are invoked through a functional interface similar to DryadLINQ [32] in Scala, Java or Python. For example, the Scala code for

Array Databases: Agile Analytics (not just) for the Earth Sciences

NASA Astrophysics Data System (ADS)

Baumann, P.; Misev, D.

2015-12-01

Gridded data, such as images, image timeseries, and climate datacubes, today are managed separately from the metadata, and with different, restricted retrieval capabilities. While databases are good at metadata modelled in tables, XML hierarchies, or RDF graphs, they traditionally do not support multi-dimensional arrays.This gap is being closed by Array Databases, pioneered by the scalable rasdaman ("raster data manager") array engine. Its declarative query language, rasql, extends SQL with array operators which are optimized and parallelized on server side. Installations can easily be mashed up securely, thereby enabling large-scale location-transparent query processing in federations. Domain experts value the integration with their commonly used tools leading to a quick learning curve.Earth, Space, and Life sciences, but also Social sciences as well as business have massive amounts of data and complex analysis challenges that are answered by rasdaman. As of today, rasdaman is mature and in operational use on hundreds of Terabytes of timeseries datacubes, with transparent query distribution across more than 1,000 nodes. Additionally, its concepts have shaped international Big Data standards in the field, including the forthcoming array extension to ISO SQL, many of which are supported by both open-source and commercial systems meantime. In the geo field, rasdaman is reference implementation for the Open Geospatial Consortium (OGC) Big Data standard, WCS, now also under adoption by ISO. Further, rasdaman is in the final stage of OSGeo incubation.In this contribution we present array queries a la rasdaman, describe the architecture and novel optimization and parallelization techniques introduced in 2015, and put this in context of the intercontinental EarthServer initiative which utilizes rasdaman for enabling agile analytics on Petascale datacubes.

An effective model for store and retrieve big health data in cloud computing.

PubMed

Goli-Malekabadi, Zohreh; Sargolzaei-Javan, Morteza; Akbari, Mohammad Kazem

2016-08-01

The volume of healthcare data including different and variable text types, sounds, and images is increasing day to day. Therefore, the storage and processing of these data is a necessary and challenging issue. Generally, relational databases are used for storing health data which are not able to handle the massive and diverse nature of them. This study aimed at presenting the model based on NoSQL databases for the storage of healthcare data. Despite different types of NoSQL databases, document-based DBs were selected by a survey on the nature of health data. The presented model was implemented in the Cloud environment for accessing to the distribution properties. Then, the data were distributed on the database by applying the Shard property. The efficiency of the model was evaluated in comparison with the previous data model, Relational Database, considering query time, data preparation, flexibility, and extensibility parameters. The results showed that the presented model approximately performed the same as SQL Server for "read" query while it acted more efficiently than SQL Server for "write" query. Also, the performance of the presented model was better than SQL Server in the case of flexibility, data preparation and extensibility. Based on these observations, the proposed model was more effective than Relational Databases for handling health data. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Data Processing on Database Management Systems with Fuzzy Query

NASA Astrophysics Data System (ADS)

Şimşek, Irfan; Topuz, Vedat

In this study, a fuzzy query tool (SQLf) for non-fuzzy database management systems was developed. In addition, samples of fuzzy queries were made by using real data with the tool developed in this study. Performance of SQLf was tested with the data about the Marmara University students' food grant. The food grant data were collected in MySQL database by using a form which had been filled on the web. The students filled a form on the web to describe their social and economical conditions for the food grant request. This form consists of questions which have fuzzy and crisp answers. The main purpose of this fuzzy query is to determine the students who deserve the grant. The SQLf easily found the eligible students for the grant through predefined fuzzy values. The fuzzy query tool (SQLf) could be used easily with other database system like ORACLE and SQL server.

PiCO QL: A software library for runtime interactive queries on program data

NASA Astrophysics Data System (ADS)

Fragkoulis, Marios; Spinellis, Diomidis; Louridas, Panos

PiCO QL is an open source C/C++ software whose scientific scope is real-time interactive analysis of in-memory data through SQL queries. It exposes a relational view of a system's or application's data structures, which is queryable through SQL. While the application or system is executing, users can input queries through a web-based interface or issue web service requests. Queries execute on the live data structures through the respective relational views. PiCO QL makes a good candidate for ad-hoc data analysis in applications and for diagnostics in systems settings. Applications of PiCO QL include the Linux kernel, the Valgrind instrumentation framework, a GIS application, a virtual real-time observatory of stellar objects, and a source code analyser.

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

PubMed

Huan, Tianxiao; Sivachenko, Andrey Y; Harrison, Scott H; Chen, Jake Y

2008-08-12

New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed. We developed ProteoLens as a JAVA-based visual analytic software tool for creating, annotating and exploring multi-scale biological networks. It supports direct database connectivity to either Oracle or PostgreSQL database tables/views, on which SQL statements using both Data Definition Languages (DDL) and Data Manipulation languages (DML) may be specified. The robust query languages embedded directly within the visualization software help users to bring their network data into a visualization context for annotation and exploration. ProteoLens supports graph/network represented data in standard Graph Modeling Language (GML) formats, and this enables interoperation with a wide range of other visual layout tools. The architectural design of ProteoLens enables the de-coupling of complex network data visualization tasks into two distinct phases: 1) creating network data association rules, which are mapping rules between network node IDs or edge IDs and data attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation of graph nodes and edges according to associated data values. We demonstrated the advantages of these new capabilities through three biological network visualization case studies: human disease association network, drug-target interaction network and protein-peptide mapping network. The architectural design of ProteoLens makes it suitable for bioinformatics expert data analysts who are experienced with relational database management to perform large-scale integrated network visual explorations. ProteoLens is a promising visual analytic platform that will facilitate knowledge discoveries in future network and systems biology studies.

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.

An academic radiology information system (RIS): a review of the commercial RIS systems, and how an individualized academic RIS can be created and utilized.

PubMed

Tamm, E P; Kawashima, A; Silverman, P

2001-06-01

Current commercial radiology information systems (RIS) are designed for scheduling, billing, charge collection, and report dissemination. Academic institutions have additional requirements for their missions for teaching, research and clinical care. The newest versions of commercial RIS offer greater flexibility than prior systems. We sent questionnaires to Cerner Corporation, ADAC Health Care Information Systems, IDX Systems, Per-Se' Technologies, and Siemens Health Services regarding features of their products. All of the products we surveyed offer user customizable fields. However, most products did not allow the user to expand their product's data table. The search capabilities of the products varied. All of the products supported the Health Level 7 (HL-7) interface and the use of structured query language (SQL). All of the products were offered with an SQL editor for creating customized queries and custom reports. All products included capabilities for collecting data for quality assurance and included capabilities for tracking "interesting cases," though they varied in the functionality offered. No product offered dedicated functions for research. Alternatively, radiology departments can create their own client-server Windows-based database systems to supplement the capabilities of commercial systems. Such systems can be developed with "web-enabled" database products like Microsoft Access or Apple Filemaker Pro.

Comparative study on the customization of natural language interfaces to databases.

PubMed

Pazos R, Rodolfo A; Aguirre L, Marco A; González B, Juan J; Martínez F, José A; Pérez O, Joaquín; Verástegui O, Andrés A

2016-01-01

In the last decades the popularity of natural language interfaces to databases (NLIDBs) has increased, because in many cases information obtained from them is used for making important business decisions. Unfortunately, the complexity of their customization by database administrators make them difficult to use. In order for a NLIDB to obtain a high percentage of correctly translated queries, it is necessary that it is correctly customized for the database to be queried. In most cases the performance reported in NLIDB literature is the highest possible; i.e., the performance obtained when the interfaces were customized by the implementers. However, for end users it is more important the performance that the interface can yield when the NLIDB is customized by someone different from the implementers. Unfortunately, there exist very few articles that report NLIDB performance when the NLIDBs are not customized by the implementers. This article presents a semantically-enriched data dictionary (which permits solving many of the problems that occur when translating from natural language to SQL) and an experiment in which two groups of undergraduate students customized our NLIDB and English language frontend (ELF), considered one of the best available commercial NLIDBs. The experimental results show that, when customized by the first group, our NLIDB obtained a 44.69 % of correctly answered queries and ELF 11.83 % for the ATIS database, and when customized by the second group, our NLIDB attained 77.05 % and ELF 13.48 %. The performance attained by our NLIDB, when customized by ourselves was 90 %.

Data-driven decision support for radiologists: re-using the National Lung Screening Trial dataset for pulmonary nodule management.

PubMed

Morrison, James J; Hostetter, Jason; Wang, Kenneth; Siegel, Eliot L

2015-02-01

Real-time mining of large research trial datasets enables development of case-based clinical decision support tools. Several applicable research datasets exist including the National Lung Screening Trial (NLST), a dataset unparalleled in size and scope for studying population-based lung cancer screening. Using these data, a clinical decision support tool was developed which matches patient demographics and lung nodule characteristics to a cohort of similar patients. The NLST dataset was converted into Structured Query Language (SQL) tables hosted on a web server, and a web-based JavaScript application was developed which performs real-time queries. JavaScript is used for both the server-side and client-side language, allowing for rapid development of a robust client interface and server-side data layer. Real-time data mining of user-specified patient cohorts achieved a rapid return of cohort cancer statistics and lung nodule distribution information. This system demonstrates the potential of individualized real-time data mining using large high-quality clinical trial datasets to drive evidence-based clinical decision-making.

EmptyHeaded: A Relational Engine for Graph Processing

PubMed Central

Aberger, Christopher R.; Tu, Susan; Olukotun, Kunle; Ré, Christopher

2016-01-01

There are two types of high-performance graph processing engines: low- and high-level engines. Low-level engines (Galois, PowerGraph, Snap) provide optimized data structures and computation models but require users to write low-level imperative code, hence ensuring that efficiency is the burden of the user. In high-level engines, users write in query languages like datalog (SociaLite) or SQL (Grail). High-level engines are easier to use but are orders of magnitude slower than the low-level graph engines. We present EmptyHeaded, a high-level engine that supports a rich datalog-like query language and achieves performance comparable to that of low-level engines. At the core of EmptyHeaded’s design is a new class of join algorithms that satisfy strong theoretical guarantees but have thus far not achieved performance comparable to that of specialized graph processing engines. To achieve high performance, EmptyHeaded introduces a new join engine architecture, including a novel query optimizer and data layouts that leverage single-instruction multiple data (SIMD) parallelism. With this architecture, EmptyHeaded outperforms high-level approaches by up to three orders of magnitude on graph pattern queries, PageRank, and Single-Source Shortest Paths (SSSP) and is an order of magnitude faster than many low-level baselines. We validate that EmptyHeaded competes with the best-of-breed low-level engine (Galois), achieving comparable performance on PageRank and at most 3× worse performance on SSSP. PMID:28077912

DAS: A Data Management System for Instrument Tests and Operations

NASA Astrophysics Data System (ADS)

Frailis, M.; Sartor, S.; Zacchei, A.; Lodi, M.; Cirami, R.; Pasian, F.; Trifoglio, M.; Bulgarelli, A.; Gianotti, F.; Franceschi, E.; Nicastro, L.; Conforti, V.; Zoli, A.; Smart, R.; Morbidelli, R.; Dadina, M.

2014-05-01

The Data Access System (DAS) is a and data management software system, providing a reusable solution for the storage of data acquired both from telescopes and auxiliary data sources during the instrument development phases and operations. It is part of the Customizable Instrument WorkStation system (CIWS-FW), a framework for the storage, processing and quick-look at the data acquired from scientific instruments. The DAS provides a data access layer mainly targeted to software applications: quick-look displays, pre-processing pipelines and scientific workflows. It is logically organized in three main components: an intuitive and compact Data Definition Language (DAS DDL) in XML format, aimed for user-defined data types; an Application Programming Interface (DAS API), automatically adding classes and methods supporting the DDL data types, and providing an object-oriented query language; a data management component, which maps the metadata of the DDL data types in a relational Data Base Management System (DBMS), and stores the data in a shared (network) file system. With the DAS DDL, developers define the data model for a particular project, specifying for each data type the metadata attributes, the data format and layout (if applicable), and named references to related or aggregated data types. Together with the DDL user-defined data types, the DAS API acts as the only interface to store, query and retrieve the metadata and data in the DAS system, providing both an abstract interface and a data model specific one in C, C++ and Python. The mapping of metadata in the back-end database is automatic and supports several relational DBMSs, including MySQL, Oracle and PostgreSQL.

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

PubMed

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

2013-04-01

Clinical data are dynamic in nature, often arranged hierarchically and stored as free text and numbers. Effective management of clinical data and the transformation of the data into structured format for data analysis are therefore challenging issues in electronic health records development. Despite the popularity of relational databases, the scalability of the NoSQL database model and the document-centric data structure of XML databases appear to be promising features for effective clinical data management. In this paper, three database approaches--NoSQL, XML-enabled and native XML--are investigated to evaluate their suitability for structured clinical data. The database query performance is reported, together with our experience in the databases development. The results show that NoSQL database is the best choice for query speed, whereas XML databases are advantageous in terms of scalability, flexibility and extensibility, which are essential to cope with the characteristics of clinical data. While NoSQL and XML technologies are relatively new compared to the conventional relational database, both of them demonstrate potential to become a key database technology for clinical data management as the technology further advances. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

CGDM: collaborative genomic data model for molecular profiling data using NoSQL.

PubMed

Wang, Shicai; Mares, Mihaela A; Guo, Yi-Ke

2016-12-01

High-throughput molecular profiling has greatly improved patient stratification and mechanistic understanding of diseases. With the increasing amount of data used in translational medicine studies in recent years, there is a need to improve the performance of data warehouses in terms of data retrieval and statistical processing. Both relational and Key Value models have been used for managing molecular profiling data. Key Value models such as SeqWare have been shown to be particularly advantageous in terms of query processing speed for large datasets. However, more improvement can be achieved, particularly through better indexing techniques of the Key Value models, taking advantage of the types of queries which are specific for the high-throughput molecular profiling data. In this article, we introduce a Collaborative Genomic Data Model (CGDM), aimed at significantly increasing the query processing speed for the main classes of queries on genomic databases. CGDM creates three Collaborative Global Clustering Index Tables (CGCITs) to solve the velocity and variety issues at the cost of limited extra volume. Several benchmarking experiments were carried out, comparing CGDM implemented on HBase to the traditional SQL data model (TDM) implemented on both HBase and MySQL Cluster, using large publicly available molecular profiling datasets taken from NCBI and HapMap. In the microarray case, CGDM on HBase performed up to 246 times faster than TDM on HBase and 7 times faster than TDM on MySQL Cluster. In single nucleotide polymorphism case, CGDM on HBase outperformed TDM on HBase by up to 351 times and TDM on MySQL Cluster by up to 9 times. The CGDM source code is available at https://github.com/evanswang/CGDM. y.guo@imperial.ac.uk. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

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.

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

Computerized database management system for breast cancer patients.

PubMed

Sim, Kok Swee; Chong, Sze Siang; Tso, Chih Ping; Nia, Mohsen Esmaeili; Chong, Aun Kee; Abbas, Siti Fathimah

2014-01-01

Data analysis based on breast cancer risk factors such as age, race, breastfeeding, hormone replacement therapy, family history, and obesity was conducted on breast cancer patients using a new enhanced computerized database management system. My Structural Query Language (MySQL) is selected as the application for database management system to store the patient data collected from hospitals in Malaysia. An automatic calculation tool is embedded in this system to assist the data analysis. The results are plotted automatically and a user-friendly graphical user interface is developed that can control the MySQL database. Case studies show breast cancer incidence rate is highest among Malay women, followed by Chinese and Indian. The peak age for breast cancer incidence is from 50 to 59 years old. Results suggest that the chance of developing breast cancer is increased in older women, and reduced with breastfeeding practice. The weight status might affect the breast cancer risk differently. Additional studies are needed to confirm these findings.

StreptomycesInforSys: A web-enabled information repository

PubMed Central

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. Availability www.sis.biowaves.org PMID:23275736

StreptomycesInforSys: A web-enabled information repository.

PubMed

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. www.sis.biowaves.org.

Design of Instant Messaging System of Multi-language E-commerce Platform

NASA Astrophysics Data System (ADS)

Yang, Heng; Chen, Xinyi; Li, Jiajia; Cao, Yaru

2017-09-01

This paper aims at researching the message system in the instant messaging system based on the multi-language e-commerce platform in order to design the instant messaging system in multi-language environment and exhibit the national characteristics based information as well as applying national languages to e-commerce. In order to develop beautiful and friendly system interface for the front end of the message system and reduce the development cost, the mature jQuery framework is adopted in this paper. The high-performance server Tomcat is adopted at the back end to process user requests, and MySQL database is adopted for data storage to persistently store user data, and meanwhile Oracle database is adopted as the message buffer for system optimization. Moreover, AJAX technology is adopted for the client to actively pull the newest data from the server at the specified time. In practical application, the system has strong reliability, good expansibility, short response time, high system throughput capacity and high user concurrency.

Nosql for Storage and Retrieval of Large LIDAR Data Collections

NASA Astrophysics Data System (ADS)

Boehm, J.; Liu, K.

2015-08-01

Developments in LiDAR technology over the past decades have made LiDAR to become a mature and widely accepted source of geospatial information. This in turn has led to an enormous growth in data volume. The central idea for a file-centric storage of LiDAR point clouds is the observation that large collections of LiDAR data are typically delivered as large collections of files, rather than single files of terabyte size. This split of the dataset, commonly referred to as tiling, was usually done to accommodate a specific processing pipeline. It makes therefore sense to preserve this split. A document oriented NoSQL database can easily emulate this data partitioning, by representing each tile (file) in a separate document. The document stores the metadata of the tile. The actual files are stored in a distributed file system emulated by the NoSQL database. We demonstrate the use of MongoDB a highly scalable document oriented NoSQL database for storing large LiDAR files. MongoDB like any NoSQL database allows for queries on the attributes of the document. As a specialty MongoDB also allows spatial queries. Hence we can perform spatial queries on the bounding boxes of the LiDAR tiles. Inserting and retrieving files on a cloud-based database is compared to native file system and cloud storage transfer speed.

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.

TOBA

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

Bauer, Travis

2007-01-26

Toba is an extensible personal information retrieval system. It supports various plugins which the user uses to create and store bits of information. It comes configured to store meeting notes, task items, issue, and business development opportunities. Plugins could be written to support almost any kind of digital information. So with the right plugins, Toba could become a full fledged contact manager, project management application, programmer's toolkit, or almost any other type of data storage/search/retrieval application imaginable. Toba comes with a built in command line interface and via a plugin it has a fully scripting language (jython). The information storedmore » can be searched by keyword or through SQL queries.« less

Large Survey Database: A Distributed Framework for Storage and Analysis of Large Datasets

NASA Astrophysics Data System (ADS)

Juric, Mario

2011-01-01

The Large Survey Database (LSD) is a Python framework and DBMS for distributed storage, cross-matching and querying of large survey catalogs (>10^9 rows, >1 TB). The primary driver behind its development is the analysis of Pan-STARRS PS1 data. It is specifically optimized for fast queries and parallel sweeps of positionally and temporally indexed datasets. It transparently scales to more than >10^2 nodes, and can be made to function in "shared nothing" architectures. An LSD database consists of a set of vertically and horizontally partitioned tables, physically stored as compressed HDF5 files. Vertically, we partition the tables into groups of related columns ('column groups'), storing together logically related data (e.g., astrometry, photometry). Horizontally, the tables are partitioned into partially overlapping ``cells'' by position in space (lon, lat) and time (t). This organization allows for fast lookups based on spatial and temporal coordinates, as well as data and task distribution. The design was inspired by the success of Google BigTable (Chang et al., 2006). Our programming model is a pipelined extension of MapReduce (Dean and Ghemawat, 2004). An SQL-like query language is used to access data. For complex tasks, map-reduce ``kernels'' that operate on query results on a per-cell basis can be written, with the framework taking care of scheduling and execution. The combination leverages users' familiarity with SQL, while offering a fully distributed computing environment. LSD adds little overhead compared to direct Python file I/O. In tests, we sweeped through 1.1 Grows of PanSTARRS+SDSS data (220GB) less than 15 minutes on a dual CPU machine. In a cluster environment, we achieved bandwidths of 17Gbits/sec (I/O limited). Based on current experience, we believe LSD should scale to be useful for analysis and storage of LSST-scale datasets. It can be downloaded from http://mwscience.net/lsd.

Comparing IndexedHBase and Riak for Serving Truthy: Performance of Data Loading and Query Evaluation

DTIC Science & Technology

2013-08-01

Research Triangle Park, NC 27709-2211 15. SUBJECT TERMS performance evaluation, distributed database, noSQL , HBase, indexing Xiaoming Gao, Judy Qiu...common hashtags created during a given time window. With the purpose of finding a solution for these challenges, we evaluate NoSQL databases such as

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

Extending SQL to Support Privacy Policies

NASA Astrophysics Data System (ADS)

Ghazinour, Kambiz; Pun, Sampson; Majedi, Maryam; Chinaci, Amir H.; Barker, Ken

Increasing concerns over Internet applications that violate user privacy by exploiting (back-end) database vulnerabilities must be addressed to protect both customer privacy and to ensure corporate strategic assets remain trustworthy. This chapter describes an extension onto database catalogues and Structured Query Language (SQL) for supporting privacy in Internet applications, such as in social networks, e-health, e-governmcnt, etc. The idea is to introduce new predicates to SQL commands to capture common privacy requirements, such as purpose, visibility, generalization, and retention for both mandatory and discretionary access control policies. The contribution is that corporations, when creating the underlying databases, will be able to define what their mandatory privacy policies arc with which all application users have to comply. Furthermore, each application user, when providing their own data, will be able to define their own privacy policies with which other users have to comply. The extension is supported with underlying catalogues and algorithms. The experiments demonstrate a very reasonable overhead for the extension. The result is a low-cost mechanism to create new systems that arc privacy aware and also to transform legacy databases to their privacy-preserving equivalents. Although the examples arc from social networks, one can apply the results to data security and user privacy of other enterprises as well.

Development of a Web-based Glaucoma Registry at King Khaled Eye Specialist Hospital, Saudi Arabia: A Cost-Effective Methodology

PubMed Central

Zaman, Babar; Khandekar, Rajiv; Al Shahwan, Sami; Song, Jonathan; Al Jadaan, Ibrahim; Al Jiasim, Leyla; Owaydha, Ohood; Asghar, Nasira; Hijazi, Amar; Edward, Deepak P.

2014-01-01

In this brief communication, we present the steps used to establish a web-based congenital glaucoma registry at our institution. The contents of a case report form (CRF) were developed by a group of glaucoma subspecialists. Information Technology (IT) specialists used Lime Survey softwareTM to create an electronic CRF. A MY Structured Query Language (MySQL) server was used as a database with a virtual machine operating system. Two ophthalmologists and 2 IT specialists worked for 7 hours, and a biostatistician and a data registrar worked for 24 hours each to establish the electronic CRF. Using the CRF which was transferred to the Lime survey tool, and the MYSQL server application, data could be directly stored in spreadsheet programs that included Microsoft Excel, SPSS, and R-Language and queried in real-time. In a pilot test, clinical data from 80 patients with congenital glaucoma were entered into the registry and successful descriptive analysis and data entry validation was performed. A web-based disease registry was established in a short period of time in a cost-efficient manner using available resources and a team-based approach. PMID:24791112

Development of a web-based glaucoma registry at King Khaled Eye Specialist Hospital, Saudi Arabia: a cost-effective methodology.

PubMed

Zaman, Babar; Khandekar, Rajiv; Al Shahwan, Sami; Song, Jonathan; Al Jadaan, Ibrahim; Al Jiasim, Leyla; Owaydha, Ohood; Asghar, Nasira; Hijazi, Amar; Edward, Deepak P

2014-01-01

In this brief communication, we present the steps used to establish a web-based congenital glaucoma registry at our institution. The contents of a case report form (CRF) were developed by a group of glaucoma subspecialists. Information Technology (IT) specialists used Lime Survey softwareTM to create an electronic CRF. A MY Structured Query Language (MySQL) server was used as a database with a virtual machine operating system. Two ophthalmologists and 2 IT specialists worked for 7 hours, and a biostatistician and a data registrar worked for 24 hours each to establish the electronic CRF. Using the CRF which was transferred to the Lime survey tool, and the MYSQL server application, data could be directly stored in spreadsheet programs that included Microsoft Excel, SPSS, and R-Language and queried in real-time. In a pilot test, clinical data from 80 patients with congenital glaucoma were entered into the registry and successful descriptive analysis and data entry validation was performed. A web-based disease registry was established in a short period of time in a cost-efficient manner using available resources and a team-based approach.

Enhancing SAMOS Data Access in DOMS via a Neo4j Property Graph Database.

NASA Astrophysics Data System (ADS)

Stallard, A. P.; Smith, S. R.; Elya, J. L.

2016-12-01

The Shipboard Automated Meteorological and Oceanographic System (SAMOS) initiative provides routine access to high-quality marine meteorological and near-surface oceanographic observations from research vessels. The Distributed Oceanographic Match-Up Service (DOMS) under development is a centralized service that allows researchers to easily match in situ and satellite oceanographic data from distributed sources to facilitate satellite calibration, validation, and retrieval algorithm development. The service currently uses Apache Solr as a backend search engine on each node in the distributed network. While Solr is a high-performance solution that facilitates creation and maintenance of indexed data, it is limited in the sense that its schema is fixed. The property graph model escapes this limitation by creating relationships between data objects. The authors will present the development of the SAMOS Neo4j property graph database including new search possibilities that take advantage of the property graph model, performance comparisons with Apache Solr, and a vision for graph databases as a storage tool for oceanographic data. The integration of the SAMOS Neo4j graph into DOMS will also be described. Currently, Neo4j contains spatial and temporal records from SAMOS which are modeled into a time tree and r-tree using Graph Aware and Spatial plugin tools for Neo4j. These extensions provide callable Java procedures within CYPHER (Neo4j's query language) that generate in-graph structures. Once generated, these structures can be queried using procedures from these libraries, or directly via CYPHER statements. Neo4j excels at performing relationship and path-based queries, which challenge relational-SQL databases because they require memory intensive joins due to the limitation of their design. Consider a user who wants to find records over several years, but only for specific months. If a traditional database only stores timestamps, this type of query would be complex and likely prohibitively slow. Using the time tree model, one can specify a path from the root to the data which restricts resolutions to certain timeframes (e.g., months). This query can be executed without joins, unions, or other compute-intensive operations, putting Neo4j at a computational advantage to the SQL database alternative.

A distributed query execution engine of big attributed graphs.

PubMed

Batarfi, Omar; Elshawi, Radwa; Fayoumi, Ayman; Barnawi, Ahmed; Sakr, Sherif

2016-01-01

A graph is a popular data model that has become pervasively used for modeling structural relationships between objects. In practice, in many real-world graphs, the graph vertices and edges need to be associated with descriptive attributes. Such type of graphs are referred to as attributed graphs. G-SPARQL has been proposed as an expressive language, with a centralized execution engine, for querying attributed graphs. G-SPARQL supports various types of graph querying operations including reachability, pattern matching and shortest path where any G-SPARQL query may include value-based predicates on the descriptive information (attributes) of the graph edges/vertices in addition to the structural predicates. In general, a main limitation of centralized systems is that their vertical scalability is always restricted by the physical limits of computer systems. This article describes the design, implementation in addition to the performance evaluation of DG-SPARQL, a distributed, hybrid and adaptive parallel execution engine of G-SPARQL queries. In this engine, the topology of the graph is distributed over the main memory of the underlying nodes while the graph data are maintained in a relational store which is replicated on the disk of each of the underlying nodes. DG-SPARQL evaluates parts of the query plan via SQL queries which are pushed to the underlying relational stores while other parts of the query plan, as necessary, are evaluated via indexless memory-based graph traversal algorithms. Our experimental evaluation shows the efficiency and the scalability of DG-SPARQL on querying massive attributed graph datasets in addition to its ability to outperform the performance of Apache Giraph, a popular distributed graph processing system, by orders of magnitudes.

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

PubMed Central

Zhu, Yuelin; Davis, Sean; Stephens, Robert; Meltzer, Paul S.; Chen, Yidong

2008-01-01

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R. Availability: The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website. Contact: yidong@mail.nih.gov PMID:18842599

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

Big Geo Data Services: From More Bytes to More Barrels

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Baumann, Peter

2016-04-01

The data deluge is affecting the oil and gas industry just as much as many other industries. However, aside from the sheer volume there is the challenge of data variety, such as regular and irregular grids, multi-dimensional space/time grids, point clouds, and TINs and other meshes. A uniform conceptualization for modelling and serving them could save substantial effort, such as the proverbial "department of reformatting". The notion of a coverage actually can accomplish this. Its abstract model in ISO 19123 together with the concrete, interoperable OGC Coverage Implementation Schema (CIS), which is currently under adoption as ISO 19123-2, provieds a common platform for representing any n-D grid type, point clouds, and general meshes. This is paired by the OGC Web Coverage Service (WCS) together with its datacube analytics language, the OGC Web Coverage Processing Service (WCPS). The OGC WCS Core Reference Implementation, rasdaman, relies on Array Database technology, i.e. a NewSQL/NoSQL approach. It supports the grid part of coverages, with installations of 100+ TB known and single queries parallelized across 1,000+ cloud nodes. Recent research attempts to address the point cloud and mesh part through a unified query model. The Holy Grail envisioned is that these approaches can be merged into a single service interface at some time. We present both grid amd point cloud / mesh approaches and discuss status, implementation, standardization, and research perspectives, including a live demo.

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.

PhyloExplorer: a web server to validate, explore and query phylogenetic trees

PubMed Central

Ranwez, Vincent; Clairon, Nicolas; Delsuc, Frédéric; Pourali, Saeed; Auberval, Nicolas; Diser, Sorel; Berry, Vincent

2009-01-01

Background Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees. Results We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database. Conclusion PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: and the source code can be downloaded from: . PMID:19450253

Thriving on Chaos: The Development of a Surgical Information System

PubMed Central

Olund, Steven R.

1988-01-01

Hospitals present unique challenges to the computer industry, generating a greater quantity and variety of data than nearly any other enterprise. This is complicated by the fact that a hospital is not one homogenous organization, but a bundle of semi-independent groups with unique data requirements. Therefore hospital information systems must be fast, flexible, reliable, easy to use and maintain, and cost-effective. The Surgical Information System at Rush Presbyterian-St. Luke's Medical Center, Chicago is such system. It uses a Sequent Balance 21000 multi-processor superminicomputer, running industry standard tools such as the Unix operating system, a 4th generation programming language (4GL), and Structured Query Language (SQL) relational database management software. This treatise illustrates a comprehensive yet generic approach which can be applied to almost any clinical situation where access to patient data is required by a variety of medical professionals.

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)

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

Enders, Alexander L.; Lousteau, Angela L.

The Desktop Analysis Reporting Tool (DART) is a software package that allows users to easily view and analyze daily files that span long periods. DART gives users the capability to quickly determine the state of health of a radiation portal monitor (RPM), troubleshoot and diagnose problems, and view data in various time frames to perform trend analysis. In short, it converts the data strings written in the daily files into meaningful tables and plots. The standalone version of DART (“soloDART”) utilizes a database engine that is included with the application; no additional installations are necessary. There is also a networkedmore » version of DART (“polyDART”) that is designed to maximize the benefit of a centralized data repository while distributing the workload to individual desktop machines. This networked approach requires a more complex database manager Structured Query Language (SQL) Server; however, SQL Server is not currently provided with DART. Regardless of which version is used, DART will import daily files from RPMs, store the relevant data in its database, and it can produce reports for status, trend analysis, and reporting purposes.« less

Providing R-Tree Support for Mongodb

NASA Astrophysics Data System (ADS)

Xiang, Longgang; Shao, Xiaotian; Wang, Dehao

2016-06-01

Supporting large amounts of spatial data is a significant characteristic of modern databases. However, unlike some mature relational databases, such as Oracle and PostgreSQL, most of current burgeoning NoSQL databases are not well designed for storing geospatial data, which is becoming increasingly important in various fields. In this paper, we propose a novel method to provide R-tree index, as well as corresponding spatial range query and nearest neighbour query functions, for MongoDB, one of the most prevalent NoSQL databases. First, after in-depth analysis of MongoDB's features, we devise an efficient tabular document structure which flattens R-tree index into MongoDB collections. Further, relevant mechanisms of R-tree operations are issued, and then we discuss in detail how to integrate R-tree into MongoDB. Finally, we present the experimental results which show that our proposed method out-performs the built-in spatial index of MongoDB. Our research will greatly facilitate big data management issues with MongoDB in a variety of geospatial information applications.

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.

Mynodbcsv: lightweight zero-config database solution for handling very large CSV files.

PubMed

Adaszewski, Stanisław

2014-01-01

Volumes of data used in science and industry are growing rapidly. When researchers face the challenge of analyzing them, their format is often the first obstacle. Lack of standardized ways of exploring different data layouts requires an effort each time to solve the problem from scratch. Possibility to access data in a rich, uniform manner, e.g. using Structured Query Language (SQL) would offer expressiveness and user-friendliness. Comma-separated values (CSV) are one of the most common data storage formats. Despite its simplicity, with growing file size handling it becomes non-trivial. Importing CSVs into existing databases is time-consuming and troublesome, or even impossible if its horizontal dimension reaches thousands of columns. Most databases are optimized for handling large number of rows rather than columns, therefore, performance for datasets with non-typical layouts is often unacceptable. Other challenges include schema creation, updates and repeated data imports. To address the above-mentioned problems, I present a system for accessing very large CSV-based datasets by means of SQL. It's characterized by: "no copy" approach--data stay mostly in the CSV files; "zero configuration"--no need to specify database schema; written in C++, with boost [1], SQLite [2] and Qt [3], doesn't require installation and has very small size; query rewriting, dynamic creation of indices for appropriate columns and static data retrieval directly from CSV files ensure efficient plan execution; effortless support for millions of columns; due to per-value typing, using mixed text/numbers data is easy; very simple network protocol provides efficient interface for MATLAB and reduces implementation time for other languages. The software is available as freeware along with educational videos on its website [4]. It doesn't need any prerequisites to run, as all of the libraries are included in the distribution package. I test it against existing database solutions using a battery of benchmarks and discuss the results.

Mynodbcsv: Lightweight Zero-Config Database Solution for Handling Very Large CSV Files

PubMed Central

Adaszewski, Stanisław

2014-01-01

Volumes of data used in science and industry are growing rapidly. When researchers face the challenge of analyzing them, their format is often the first obstacle. Lack of standardized ways of exploring different data layouts requires an effort each time to solve the problem from scratch. Possibility to access data in a rich, uniform manner, e.g. using Structured Query Language (SQL) would offer expressiveness and user-friendliness. Comma-separated values (CSV) are one of the most common data storage formats. Despite its simplicity, with growing file size handling it becomes non-trivial. Importing CSVs into existing databases is time-consuming and troublesome, or even impossible if its horizontal dimension reaches thousands of columns. Most databases are optimized for handling large number of rows rather than columns, therefore, performance for datasets with non-typical layouts is often unacceptable. Other challenges include schema creation, updates and repeated data imports. To address the above-mentioned problems, I present a system for accessing very large CSV-based datasets by means of SQL. It's characterized by: “no copy” approach – data stay mostly in the CSV files; “zero configuration” – no need to specify database schema; written in C++, with boost [1], SQLite [2] and Qt [3], doesn't require installation and has very small size; query rewriting, dynamic creation of indices for appropriate columns and static data retrieval directly from CSV files ensure efficient plan execution; effortless support for millions of columns; due to per-value typing, using mixed text/numbers data is easy; very simple network protocol provides efficient interface for MATLAB and reduces implementation time for other languages. The software is available as freeware along with educational videos on its website [4]. It doesn't need any prerequisites to run, as all of the libraries are included in the distribution package. I test it against existing database solutions using a battery of benchmarks and discuss the results. PMID:25068261

Footprint Representation of Planetary Remote Sensing Data

NASA Astrophysics Data System (ADS)

Walter, S. H. G.; Gasselt, S. V.; Michael, G.; Neukum, G.

The geometric outline of remote sensing image data, the so called footprint, can be represented as a number of coordinate tuples. These polygons are associated with according attribute information such as orbit name, ground- and image resolution, solar longitude and illumination conditions to generate a powerful base for classification of planetary experiment data. Speed, handling and extended capabilites are the reasons for using geodatabases to store and access these data types. Techniques for such a spatial database of footprint data are demonstrated using the Relational Database Management System (RDBMS) PostgreSQL, spatially enabled by the PostGIS extension. Exemplary, footprints of the HRSC and OMEGA instruments, both onboard ESA's Mars Express Orbiter, are generated and connected to attribute information. The aim is to provide high-resolution footprints of the OMEGA instrument to the science community for the first time and make them available for web-based mapping applications like the "Planetary Interactive GIS-on-the-Web Analyzable Database" (PIG- WAD), produced by the USGS. Map overlays with HRSC or other instruments like MOC and THEMIS (footprint maps are already available for these instruments and can be integrated into the database) allow on-the-fly intersection and comparison as well as extended statistics of the data. Footprint polygons are generated one by one using standard software provided by the instrument teams. Attribute data is calculated and stored together with the geometric information. In the case of HRSC, the coordinates of the footprints are already available in the VICAR label of each image file. Using the VICAR RTL and PostgreSQL's libpq C library they are loaded into the database using the Well-Known Text (WKT) notation by the Open Geospatial Consortium, Inc. (OGC). For the OMEGA instrument, image data is read using IDL routines developed and distributed by the OMEGA team. Image outlines are exported together with relevant attribute data to the industry standard Shapefile format. These files are translated to a Structured Query Language (SQL) command sequence suitable for insertion into the PostGIS/PostgrSQL database using the shp2pgsql data loader provided by the PostGIS software. PostgreSQL's advanced features such as geometry types, rules, operators and functions allow complex spatial queries and on-the-fly processing of data on DBMS level e.g. generalisation of the outlines. Processing done by the DBMS, visualisation via GIS systems and utilisation for web-based applications like mapservers will be demonstrated.

Informatics in radiology: use of CouchDB for document-based storage of DICOM objects.

PubMed

Rascovsky, Simón J; Delgado, Jorge A; Sanz, Alexander; Calvo, Víctor D; Castrillón, Gabriel

2012-01-01

Picture archiving and communication systems traditionally have depended on schema-based Structured Query Language (SQL) databases for imaging data management. To optimize database size and performance, many such systems store a reduced set of Digital Imaging and Communications in Medicine (DICOM) metadata, discarding informational content that might be needed in the future. As an alternative to traditional database systems, document-based key-value stores recently have gained popularity. These systems store documents containing key-value pairs that facilitate data searches without predefined schemas. Document-based key-value stores are especially suited to archive DICOM objects because DICOM metadata are highly heterogeneous collections of tag-value pairs conveying specific information about imaging modalities, acquisition protocols, and vendor-supported postprocessing options. The authors used an open-source document-based database management system (Apache CouchDB) to create and test two such databases; CouchDB was selected for its overall ease of use, capability for managing attachments, and reliance on HTTP and Representational State Transfer standards for accessing and retrieving data. A large database was created first in which the DICOM metadata from 5880 anonymized magnetic resonance imaging studies (1,949,753 images) were loaded by using a Ruby script. To provide the usual DICOM query functionality, several predefined "views" (standard queries) were created by using JavaScript. For performance comparison, the same queries were executed in both the CouchDB database and a SQL-based DICOM archive. The capabilities of CouchDB for attachment management and database replication were separately assessed in tests of a similar, smaller database. Results showed that CouchDB allowed efficient storage and interrogation of all DICOM objects; with the use of information retrieval algorithms such as map-reduce, all the DICOM metadata stored in the large database were searchable with only a minimal increase in retrieval time over that with the traditional database management system. Results also indicated possible uses for document-based databases in data mining applications such as dose monitoring, quality assurance, and protocol optimization. RSNA, 2012

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

Image query and indexing for digital x rays

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Thoma, George R.

1998-12-01

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

SU-E-T-255: Development of a Michigan Quality Assurance (MQA) Database for Clinical Machine Operations

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

Roberts, D

Purpose: A unified database system was developed to allow accumulation, review and analysis of quality assurance (QA) data for measurement, treatment, imaging and simulation equipment in our department. Recording these data in a database allows a unified and structured approach to review and analysis of data gathered using commercial database tools. Methods: A clinical database was developed to track records of quality assurance operations on linear accelerators, a computed tomography (CT) scanner, high dose rate (HDR) afterloader and imaging systems such as on-board imaging (OBI) and Calypso in our department. The database was developed using Microsoft Access database and visualmore » basic for applications (VBA) programming interface. Separate modules were written for accumulation, review and analysis of daily, monthly and annual QA data. All modules were designed to use structured query language (SQL) as the basis of data accumulation and review. The SQL strings are dynamically re-written at run time. The database also features embedded documentation, storage of documents produced during QA activities and the ability to annotate all data within the database. Tests are defined in a set of tables that define test type, specific value, and schedule. Results: Daily, Monthly and Annual QA data has been taken in parallel with established procedures to test MQA. The database has been used to aggregate data across machines to examine the consistency of machine parameters and operations within the clinic for several months. Conclusion: The MQA application has been developed as an interface to a commercially available SQL engine (JET 5.0) and a standard database back-end. The MQA system has been used for several months for routine data collection.. The system is robust, relatively simple to extend and can be migrated to a commercial SQL server.« less

TreeQ-VISTA: An Interactive Tree Visualization Tool withFunctional Annotation Query Capabilities

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

Gu, Shengyin; Anderson, Iain; Kunin, Victor

2007-05-07

Summary: We describe a general multiplatform exploratorytool called TreeQ-Vista, designed for presenting functional annotationsin a phylogenetic context. Traits, such as phenotypic and genomicproperties, are interactively queried from a relational database with auser-friendly interface which provides a set of tools for users with orwithout SQL knowledge. The query results are projected onto aphylogenetic tree and can be displayed in multiple color groups. A richset of browsing, grouping and query tools are provided to facilitatetrait exploration, comparison and analysis.Availability: The program,detailed tutorial and examples are available online athttp://genome-test.lbl.gov/vista/TreeQVista.

Ultrabroadband photonic internet: safety aspects

NASA Astrophysics Data System (ADS)

Kalicki, Arkadiusz; Romaniuk, Ryszard

2008-11-01

Web applications became most popular medium in the Internet. Popularity, easiness of web application frameworks together with careless development results in high number of vulnerabilities and attacks. There are several types of attacks possible because of improper input validation. SQL injection is ability to execute arbitrary SQL queries in a database through an existing application. Cross-site scripting is the vulnerability which allows malicious web users to inject code into the web pages viewed by other users. Cross-Site Request Forgery (CSRF) is an attack that tricks the victim into loading a page that contains malicious request. Web spam in blogs. There are several techniques to mitigate attacks. Most important are web application strong design, correct input validation, defined data types for each field and parameterized statements in SQL queries. Server hardening with firewall, modern security policies systems and safe web framework interpreter configuration are essential. It is advised to keep proper security level on client side, keep updated software and install personal web firewalls or IDS/IPS systems. Good habits are logging out from services just after finishing work and using even separate web browser for most important sites, like e-banking.

ExplorEnz: the primary source of the IUBMB enzyme list

PubMed Central

McDonald, Andrew G.; Boyce, Sinéad; Tipton, Keith F.

2009-01-01

ExplorEnz is the MySQL database that is used for the curation and dissemination of the International Union of Biochemistry and Molecular Biology (IUBMB) Enzyme Nomenclature. A simple web-based query interface is provided, along with an advanced search engine for more complex Boolean queries. The WWW front-end is accessible at http://www.enzyme-database.org, from where downloads of the database as SQL and XML are also available. An associated form-based curatorial application has been developed to facilitate the curation of enzyme data as well as the internal and public review processes that occur before an enzyme entry is made official. Suggestions for new enzyme entries, or modifications to existing ones, can be made using the forms provided at http://www.enzyme-database.org/forms.php. PMID:18776214

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

Development of a platform-independent receiver control system for SISIFOS

NASA Astrophysics Data System (ADS)

Lemke, Roland; Olberg, Michael

1998-05-01

Up to now receiver control software was a time consuming development usually written by receiver engineers who had mainly the hardware in mind. We are presenting a low-cost and very flexible system which uses a minimal interface to the real hardware, and which makes it easy to adapt to new receivers. Our system uses Tcl/Tk as a graphical user interface (GUI), SpecTcl as a GUI builder, Pgplot as plotting software, a simple query language (SQL) database for information storage and retrieval, Ethernet socket to socket communication and SCPI as a command control language. The complete system is in principal platform independent but for cost saving reasons we are using it actually on a PC486 running Linux 2.0.30, which is a copylefted Unix. The only hardware dependent part are the digital input/output boards, analog to digital and digital to analog convertors. In the case of the Linux PC we are using a device driver development kit to integrate the boards fully into the kernel of the operating system, which indeed makes them look like an ordinary device. The advantage of this system is firstly the low price and secondly the clear separation between the different software components which are available for many operating systems. If it is not possible, due to CPU performance limitations, to run all the software in a single machine,the SQL-database or the graphical user interface could be installed on separate computers.

Shark: SQL and Rich Analytics at Scale

DTIC Science & Technology

2012-11-26

learning programs up to 100 faster than Hadoop. Unlike previous systems, Shark shows that it is possible to achieve these speedups while retaining a...Shark to run SQL queries up to 100× faster than Apache Hive, and machine learning programs up to 100× faster than Hadoop. Unlike previous systems, Shark...so using a runtime that is optimized for such workloads and a programming model that is designed to express machine learn - ing algorithms. 4.1

Advances in Data Management in Remote Sensing and Climate Modeling

NASA Astrophysics Data System (ADS)

Brown, P. G.

2014-12-01

Recent commercial interest in "Big Data" information systems has yielded little more than a sense of deja vu among scientists whose work has always required getting their arms around extremely large databases, and writing programs to explore and analyze it. On the flip side, there are some commercial DBMS startups building "Big Data" platform using techniques taken from earth science, astronomy, high energy physics and high performance computing. In this talk, we will introduce one such platform; Paradigm4's SciDB, the first DBMS designed from the ground up to combine the kinds of quality-of-service guarantees made by SQL DBMS platforms—high level data model, query languages, extensibility, transactions—with the kinds of functionality familiar to scientific users—arrays as structural building blocks, integrated linear algebra, and client language interfaces that minimize the learning curve. We will review how SciDB is used to manage and analyze earth science data by several teams of scientific users.

"Science SQL" as a Building Block for Flexible, Standards-based Data Infrastructures

NASA Astrophysics Data System (ADS)

Baumann, Peter

2016-04-01

We have learnt to live with the pain of separating data and metadata into non-interoperable silos. For metadata, we enjoy the flexibility of databases, be they relational, graph, or some other NoSQL. Contrasting this, users still "drown in files" as an unstructured, low-level archiving paradigm. It is time to bridge this chasm which once was technologically induced, but today can be overcome. One building block towards a common re-integrated information space is to support massive multi-dimensional spatio-temporal arrays. These "datacubes" appear as sensor, image, simulation, and statistics data in all science and engineering domains, and beyond. For example, 2-D satellilte imagery, 2-D x/y/t image timeseries and x/y/z geophysical voxel data, and 4-D x/y/z/t climate data contribute to today's data deluge in the Earth sciences. Virtual observatories in the Space sciences routinely generate Petabytes of such data. Life sciences deal with microarray data, confocal microscopy, human brain data, which all fall into the same category. The ISO SQL/MDA (Multi-Dimensional Arrays) candidate standard is extending SQL with modelling and query support for n-D arrays ("datacubes") in a flexible, domain-neutral way. This heralds a new generation of services with new quality parameters, such as flexibility, ease of access, embedding into well-known user tools, and scalability mechanisms that remain completely transparent to users. Technology like the EU rasdaman ("raster data manager") Array Database system can support all of the above examples simultaneously, with one technology. This is practically proven: As of today, rasdaman is in operational use on hundreds of Terabytes of satellite image timeseries datacubes, with transparent query distribution across more than 1,000 nodes. Therefore, Array Databases offering SQL/MDA constitute a natural common building block for next-generation data infrastructures. Being initiator and editor of the standard we present principles, implementation facets, and application examples as a basis for further discussion. Further, we highlight recent implementation progress in parallelization, data distribution, and query optimization showing their effects on real-life use cases.

Toward An Unstructured Mesh Database

NASA Astrophysics Data System (ADS)

Rezaei Mahdiraji, Alireza; Baumann, Peter Peter

2014-05-01

Unstructured meshes are used in several application domains such as earth sciences (e.g., seismology), medicine, oceanography, cli- mate modeling, GIS as approximate representations of physical objects. Meshes subdivide a domain into smaller geometric elements (called cells) which are glued together by incidence relationships. The subdivision of a domain allows computational manipulation of complicated physical structures. For instance, seismologists model earthquakes using elastic wave propagation solvers on hexahedral meshes. The hexahedral con- tains several hundred millions of grid points and millions of hexahedral cells. Each vertex node in the hexahedrals stores a multitude of data fields. To run simulation on such meshes, one needs to iterate over all the cells, iterate over incident cells to a given cell, retrieve coordinates of cells, assign data values to cells, etc. Although meshes are used in many application domains, to the best of our knowledge there is no database vendor that support unstructured mesh features. Currently, the main tool for querying and manipulating unstructured meshes are mesh libraries, e.g., CGAL and GRAL. Mesh li- braries are dedicated libraries which includes mesh algorithms and can be run on mesh representations. The libraries do not scale with dataset size, do not have declarative query language, and need deep C++ knowledge for query implementations. Furthermore, due to high coupling between the implementations and input file structure, the implementations are less reusable and costly to maintain. A dedicated mesh database offers the following advantages: 1) declarative querying, 2) ease of maintenance, 3) hiding mesh storage structure from applications, and 4) transparent query optimization. To design a mesh database, the first challenge is to define a suitable generic data model for unstructured meshes. We proposed ImG-Complexes data model as a generic topological mesh data model which extends incidence graph model to multi-incidence relationships. We instrument ImG model with sets of optional and application-specific constraints which can be used to check validity of meshes for a specific class of object such as manifold, pseudo-manifold, and simplicial manifold. We conducted experiments to measure the performance of the graph database solution in processing mesh queries and compare it with GrAL mesh library and PostgreSQL database on synthetic and real mesh datasets. The experiments show that each system perform well on specific types of mesh queries, e.g., graph databases perform well on global path-intensive queries. In the future, we investigate database operations for the ImG model and design a mesh query language.

SQLGEN: a framework for rapid client-server database application development.

PubMed

Nadkarni, P M; Cheung, K H

1995-12-01

SQLGEN is a framework for rapid client-server relational database application development. It relies on an active data dictionary on the client machine that stores metadata on one or more database servers to which the client may be connected. The dictionary generates dynamic Structured Query Language (SQL) to perform common database operations; it also stores information about the access rights of the user at log-in time, which is used to partially self-configure the behavior of the client to disable inappropriate user actions. SQLGEN uses a microcomputer database as the client to store metadata in relational form, to transiently capture server data in tables, and to allow rapid application prototyping followed by porting to client-server mode with modest effort. SQLGEN is currently used in several production biomedical databases.

Chapter 51: How to Build a Simple Cone Search Service Using a Local Database

NASA Astrophysics Data System (ADS)

Kent, B. R.; Greene, G. R.

The cone search service protocol will be examined from the server side in this chapter. A simple cone search service will be setup and configured locally using MySQL. Data will be read into a table, and the Java JDBC will be used to connect to the database. Readers will understand the VO cone search specification and how to use it to query a database on their local systems and return an XML/VOTable file based on an input of RA/DEC coordinates and a search radius. The cone search in this example will be deployed as a Java servlet. The resulting cone search can be tested with a verification service. This basic setup can be used with other languages and relational databases.

An approach in building a chemical compound search engine in oracle database.

PubMed

Wang, H; Volarath, P; Harrison, R

2005-01-01

A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework.

JBioWH: an open-source Java framework for bioinformatics data integration

PubMed Central

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh PMID:23846595

JBioWH: an open-source Java framework for bioinformatics data integration.

PubMed

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh.

Kinota: An Open-Source NoSQL implementation of OGC SensorThings for large-scale high-resolution real-time environmental monitoring

NASA Astrophysics Data System (ADS)

Miles, B.; Chepudira, K.; LaBar, W.

2017-12-01

The Open Geospatial Consortium (OGC) SensorThings API (STA) specification, ratified in 2016, is a next-generation open standard for enabling real-time communication of sensor data. Building on over a decade of OGC Sensor Web Enablement (SWE) Standards, STA offers a rich data model that can represent a range of sensor and phenomena types (e.g. fixed sensors sensing fixed phenomena, fixed sensors sensing moving phenomena, mobile sensors sensing fixed phenomena, and mobile sensors sensing moving phenomena) and is data agnostic. Additionally, and in contrast to previous SWE standards, STA is developer-friendly, as is evident from its convenient JSON serialization, and expressive OData-based query language (with support for geospatial queries); with its Message Queue Telemetry Transport (MQTT), STA is also well-suited to efficient real-time data publishing and discovery. All these attributes make STA potentially useful for use in environmental monitoring sensor networks. Here we present Kinota(TM), an Open-Source NoSQL implementation of OGC SensorThings for large-scale high-resolution real-time environmental monitoring. Kinota, which roughly stands for Knowledge from Internet of Things Analyses, relies on Cassandra its underlying data store, which is a horizontally scalable, fault-tolerant open-source database that is often used to store time-series data for Big Data applications (though integration with other NoSQL or rational databases is possible). With this foundation, Kinota can scale to store data from an arbitrary number of sensors collecting data every 500 milliseconds. Additionally, Kinota architecture is very modular allowing for customization by adopters who can choose to replace parts of the existing implementation when desirable. The architecture is also highly portable providing the flexibility to choose between cloud providers like azure, amazon, google etc. The scalable, flexible and cloud friendly architecture of Kinota makes it ideal for use in next-generation large-scale and high-resolution real-time environmental monitoring networks used in domains such as hydrology, geomorphology, and geophysics, as well as management applications such as flood early warning, and regulatory enforcement.

Web-based Hyper Suprime-Cam Data Providing System

NASA Astrophysics Data System (ADS)

Koike, M.; Furusawa, H.; Takata, T.; Price, P.; Okura, Y.; Yamada, Y.; Yamanoi, H.; Yasuda, N.; Bickerton, S.; Katayama, N.; Mineo, S.; Lupton, R.; Bosch, J.; Loomis, C.

2014-05-01

We describe a web-based user interface to retrieve Hyper Suprime-Cam data products, including images and. Users can access data directly from a graphical user interface or by writing a database SQL query. The system provides raw images, reduced images and stacked images (from multiple individual exposures), with previews available. Catalog queries can be executed in preview or queue mode, allowing for both exploratory and comprehensive investigations.

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.

Integrating Scientific Array Processing into Standard SQL

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Bachhuber, Johannes; Baumann, Peter

2014-05-01

We live in a time that is dominated by data. Data storage is cheap and more applications than ever accrue vast amounts of data. Storing the emerging multidimensional data sets efficiently, however, and allowing them to be queried by their inherent structure, is a challenge many databases have to face today. Despite the fact that multidimensional array data is almost always linked to additional, non-array information, array databases have mostly developed separately from relational systems, resulting in a disparity between the two database categories. The current SQL standard and SQL DBMS supports arrays - and in an extension also multidimensional arrays - but does so in a very rudimentary and inefficient way. This poster demonstrates the practicality of an SQL extension for array processing, implemented in a proof-of-concept multi-faceted system that manages a federation of array and relational database systems, providing transparent, efficient and scalable access to the heterogeneous data in them.

Similarity extraction mechanism concerning historical personalities based on SQL queries in an RDBMS environment

NASA Astrophysics Data System (ADS)

Barouchou, Alexandra; Dendrinos, Markos

2015-02-01

An interesting issue in the domain of history of science and ideas is the concept of similarity of historical personalities. Similar objects of research of philosophers and scientists indicate prospective influences, caused either from one another's reading or meetings, communication or even cooperation. Key methodological role in the surfacing of the sought similarities play the keywords extracted from their works as well as their placement in a philosophical and scientific term taxonomy. The case study examined in the framework of this paper concerns scientists and philosophers, who lived in ancient Greece or Renaissance periods and dealt, in at least one work, with the subject God. All the available data (scientists, studies, recorded relations between scientists, keywords, and thematic hierarchy) have been organized in an RDBMS environment, aiming at the emergence of similarities and influences between scientists through properly created SQL queries based on date and thematic hierarchy criteria.

EarthServer: Use of Rasdaman as a data store for use in visualisation of complex EO data

NASA Astrophysics Data System (ADS)

Clements, Oliver; Walker, Peter; Grant, Mike

2013-04-01

The European Commission FP7 project EarthServer is establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending cutting-edge Array Database technology. EarthServer is built around the Rasdaman Raster Data Manager which extends standard relational database systems with the ability to store and retrieve multi-dimensional raster data of unlimited size through an SQL style query language. Rasdaman facilitates visualisation of data by providing several Open Geospatial Consortium (OGC) standard interfaces through its web services wrapper, Petascope. These include the well established standards, Web Coverage Service (WCS) and Web Map Service (WMS) as well as the emerging standard, Web Coverage Processing Service (WCPS). The WCPS standard allows the running of ad-hoc queries on the data stored within Rasdaman, creating an infrastructure where users are not restricted by bandwidth when manipulating or querying huge datasets. Here we will show that the use of EarthServer technologies and infrastructure allows access and visualisation of massive scale data through a web client with only marginal bandwidth use as opposed to the current mechanism of copying huge amounts of data to create visualisations locally. For example if a user wanted to generate a plot of global average chlorophyll for a complete decade time series they would only have to download the result instead of Terabytes of data. Firstly we will present a brief overview of the capabilities of Rasdaman and the WCPS query language to introduce the ways in which it is used in a visualisation tool chain. We will show that there are several ways in which WCPS can be utilised to create both standard and novel web based visualisations. An example of a standard visualisation is the production of traditional 2d plots, allowing users the ability to plot data products easily. However, the query language allows the creation of novel/custom products, which can then immediately be plotted with the same system. For more complex multi-spectral data, WCPS allows the user to explore novel combinations of bands in standard band-ratio algorithms through a web browser with dynamic updating of the resultant image. To visualise very large datasets Rasdaman has the capability to dynamically scale a dataset or query result so that it can be appraised quickly for use in later unscaled queries. All of these techniques are accessible through a web based GIS interface increasing the number of potential users of the system. Lastly we will show the advances in dynamic web based 3D visualisations being explored within the EarthServer project. By utilising the emerging declarative 3D web standard X3DOM as a tool to visualise the results of WCPS queries we introduce several possible benefits, including quick appraisal of data for outliers or anomalous data points and visualisation of the uncertainty of data alongside the actual data values.

Meta sequence analysis of human blood peptides and their parent proteins.

PubMed

Bowden, Peter; Pendrak, Voitek; Zhu, Peihong; Marshall, John G

2010-04-18

Sequence analysis of the blood peptides and their qualities will be key to understanding the mechanisms that contribute to error in LC-ESI-MS/MS. Analysis of peptides and their proteins at the level of sequences is much more direct and informative than the comparison of disparate accession numbers. A portable database of all blood peptide and protein sequences with descriptor fields and gene ontology terms might be useful for designing immunological or MRM assays from human blood. The results of twelve studies of human blood peptides and/or proteins identified by LC-MS/MS and correlated against a disparate array of genetic libraries were parsed and matched to proteins from the human ENSEMBL, SwissProt and RefSeq databases by SQL. The reported peptide and protein sequences were organized into an SQL database with full protein sequences and up to five unique peptides in order of prevalence along with the peptide count for each protein. Structured query language or BLAST was used to acquire descriptive information in current databases. Sampling error at the level of peptides is the largest source of disparity between groups. Chi Square analysis of peptide to protein distributions confirmed the significant agreement between groups on identified proteins. Copyright 2010. Published by Elsevier B.V.

SORTEZ: a relational translator for NCBI's ASN.1 database.

PubMed

Hart, K W; Searls, D B; Overton, G C

1994-07-01

The National Center for Biotechnology Information (NCBI) has created a database collection that includes several protein and nucleic acid sequence databases, a biosequence-specific subset of MEDLINE, as well as value-added information such as links between similar sequences. Information in the NCBI database is modeled in Abstract Syntax Notation 1 (ASN.1) an Open Systems Interconnection protocol designed for the purpose of exchanging structured data between software applications rather than as a data model for database systems. While the NCBI database is distributed with an easy-to-use information retrieval system, ENTREZ, the ASN.1 data model currently lacks an ad hoc query language for general-purpose data access. For that reason, we have developed a software package, SORTEZ, that transforms the ASN.1 database (or other databases with nested data structures) to a relational data model and subsequently to a relational database management system (Sybase) where information can be accessed through the relational query language, SQL. Because the need to transform data from one data model and schema to another arises naturally in several important contexts, including efficient execution of specific applications, access to multiple databases and adaptation to database evolution this work also serves as a practical study of the issues involved in the various stages of database transformation. We show that transformation from the ASN.1 data model to a relational data model can be largely automated, but that schema transformation and data conversion require considerable domain expertise and would greatly benefit from additional support tools.

Efficient hemodynamic event detection utilizing relational databases and wavelet analysis

NASA Technical Reports Server (NTRS)

Saeed, M.; Mark, R. G.

2001-01-01

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

Integrating Radar Image Data with Google Maps

NASA Technical Reports Server (NTRS)

Chapman, Bruce D.; Gibas, Sarah

2010-01-01

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

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.

A distributed computing environment with support for constraint-based task scheduling and scientific experimentation

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

Ahrens, J.P.; Shapiro, L.G.; Tanimoto, S.L.

1997-04-01

This paper describes a computing environment which supports computer-based scientific research work. Key features include support for automatic distributed scheduling and execution and computer-based scientific experimentation. A new flexible and extensible scheduling technique that is responsive to a user`s scheduling constraints, such as the ordering of program results and the specification of task assignments and processor utilization levels, is presented. An easy-to-use constraint language for specifying scheduling constraints, based on the relational database query language SQL, is described along with a search-based algorithm for fulfilling these constraints. A set of performance studies show that the environment can schedule and executemore » program graphs on a network of workstations as the user requests. A method for automatically generating computer-based scientific experiments is described. Experiments provide a concise method of specifying a large collection of parameterized program executions. The environment achieved significant speedups when executing experiments; for a large collection of scientific experiments an average speedup of 3.4 on an average of 5.5 scheduled processors was obtained.« less

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

Scale-Independent Relational Query Processing

DTIC Science & Technology

2013-10-04

source options are also available, including Postgresql, MySQL , and SQLite. These mod- ern relational databases are generally very complex software systems...and Their Application to Data Stream Management. IGI Global, 2010. [68] George Reese. Database Programming with JDBC and Java , Second Edition. Ed. by

NoSQL Based 3D City Model Management System

NASA Astrophysics Data System (ADS)

Mao, B.; Harrie, L.; Cao, J.; Wu, Z.; Shen, J.

2014-04-01

To manage increasingly complicated 3D city models, a framework based on NoSQL database is proposed in this paper. The framework supports import and export of 3D city model according to international standards such as CityGML, KML/COLLADA and X3D. We also suggest and implement 3D model analysis and visualization in the framework. For city model analysis, 3D geometry data and semantic information (such as name, height, area, price and so on) are stored and processed separately. We use a Map-Reduce method to deal with the 3D geometry data since it is more complex, while the semantic analysis is mainly based on database query operation. For visualization, a multiple 3D city representation structure CityTree is implemented within the framework to support dynamic LODs based on user viewpoint. Also, the proposed framework is easily extensible and supports geoindexes to speed up the querying. Our experimental results show that the proposed 3D city management system can efficiently fulfil the analysis and visualization requirements.

An experiment in big data: storage, querying and visualisation of data taken from the Liverpool Telescope's wide field cameras

NASA Astrophysics Data System (ADS)

Barnsley, R. M.; Steele, Iain A.; Smith, R. J.; Mawson, Neil R.

2014-07-01

The Small Telescopes Installed at the Liverpool Telescope (STILT) project has been in operation since March 2009, collecting data with three wide field unfiltered cameras: SkycamA, SkycamT and SkycamZ. To process the data, a pipeline was developed to automate source extraction, catalogue cross-matching, photometric calibration and database storage. In this paper, modifications and further developments to this pipeline will be discussed, including a complete refactor of the pipeline's codebase into Python, migration of the back-end database technology from MySQL to PostgreSQL, and changing the catalogue used for source cross-matching from USNO-B1 to APASS. In addition to this, details will be given relating to the development of a preliminary front-end to the source extracted database which will allow a user to perform common queries such as cone searches and light curve comparisons of catalogue and non-catalogue matched objects. Some next steps and future ideas for the project will also be presented.

An anaesthesia information management system as a tool for a quality assurance program: 10years of experience.

PubMed

Motamed, Cyrus; Bourgain, Jean Louis

2016-06-01

Anaesthesia Information Management Systems (AIMS) generate large amounts of data, which might be useful for quality assurance programs. This study was designed to highlight the multiple contributions of our AIMS system in extracting quality indicators over a period of 10years. The study was conducted from 2002 to 2011. Two methods were used to extract anaesthesia indicators: the manual extraction of individual files for monitoring neuromuscular relaxation and structured query language (SQL) extraction for other indicators which were postoperative nausea and vomiting (PONV), pain, sedation scores, pain-related medications, scores and postoperative hypothermia. For each indicator, a program of information/meetings and adaptation/suggestions for operating room and PACU personnel was initiated to improve quality assurance, while data were extracted each year. The study included 77,573 patients. The mean overall completeness of data for the initial years ranged from 55 to 85% and was indicator-dependent, which then improved to 95% completeness for the last 5years. The incidence of neuromuscular monitoring was initially 67% and then increased to 95% (P<0.05). The rate of pharmacological reversal remained around 53% throughout the study. Regarding SQL data, an improvement of severe postoperative pain and PONV scores was observed throughout the study, while mild postoperative hypothermia remained a challenge, despite efforts for improvement. The AIMS system permitted the follow-up of certain indicators through manual sampling and many more via SQL extraction in a sustained and non-time-consuming way across years. However, it requires competent and especially dedicated resources to handle the database. Copyright © 2016 Société française d'anesthésie et de réanimation (Sfar). Published by Elsevier Masson SAS. All rights reserved.

A Look Under the Hood: How the JPL Tropical Cyclone Information System Uses Database Technologies to Present Big Data to Users

NASA Astrophysics Data System (ADS)

Knosp, B.; Gangl, M.; Hristova-Veleva, S. M.; Kim, R. M.; Li, P.; Turk, J.; Vu, Q. A.

2015-12-01

The JPL Tropical Cyclone Information System (TCIS) brings together satellite, aircraft, and model forecast data from several NASA, NOAA, and other data centers to assist researchers in comparing and analyzing data and model forecast related to tropical cyclones. The TCIS has been running a near-real time (NRT) data portal during North Atlantic hurricane season that typically runs from June through October each year, since 2010. Data collected by the TCIS varies by type, format, contents, and frequency and is served to the user in two ways: (1) as image overlays on a virtual globe and (2) as derived output from a suite of analysis tools. In order to support these two functions, the data must be collected and then made searchable by criteria such as date, mission, product, pressure level, and geospatial region. Creating a database architecture that is flexible enough to manage, intelligently interrogate, and ultimately present this disparate data to the user in a meaningful way has been the primary challenge. The database solution for the TCIS has been to use a hybrid MySQL + Solr implementation. After testing other relational database and NoSQL solutions, such as PostgreSQL and MongoDB respectively, this solution has given the TCIS the best offerings in terms of query speed and result reliability. This database solution also supports the challenging (and memory overwhelming) geospatial queries that are necessary to support analysis tools requested by users. Though hardly new technologies on their own, our implementation of MySQL + Solr had to be customized and tuned to be able to accurately store, index, and search the TCIS data holdings. In this presentation, we will discuss how we arrived on our MySQL + Solr database architecture, why it offers us the most consistent fast and reliable results, and how it supports our front end so that we can offer users a look into our "big data" holdings.

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

NASA Astrophysics Data System (ADS)

Velazquez, Enrique Israel

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

Enhanced DIII-D Data Management Through a Relational Database

NASA Astrophysics Data System (ADS)

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

2000-10-01

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

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.

A veterinary anatomy tutoring system.

PubMed

Theodoropoulos, G; Loumos, V; Antonopoulos, J

1994-02-14

A veterinary anatomy tutoring system was developed by using Knowledge Pro, an object-oriented software development tool with hypermedia capabilities, and MS Access, a relational database. Communication between them is facilitated by using the Structured Query Language (SQL). The architecture of the system is based on knowledge sets, each of which covers four different descriptions of an organ, namely gross anatomy (general description), gross anatomy (comparative features), histology, and embryology, which constitute the knowledge units. These knowledge units are linked with three global variables that define the animals, the topographies, and the system to which this organ belongs, creating three data-bases. These three data-bases are interrelated through the organ field in order to establish a relational model. This system allows versatility in the student's navigation through the information space by offering different modes for information location and presentation. These include course mode, review mode, reference mode, dissection mode, and comparison mode. In addition, the system provides a self-evaluation mode.

Research on sudden environmental pollution public service platform construction based on WebGIS

NASA Astrophysics Data System (ADS)

Bi, T. P.; Gao, D. Y.; Zhong, X. Y.

2016-08-01

In order to actualize the social sharing and service of the emergency-response information for sudden pollution accidents, the public can share the risk source information service, dangerous goods control technology service and so on, The SQL Server and ArcSDE software are used to establish a spatial database to restore all kinds of information including risk sources, hazardous chemicals and handling methods in case of accidents. Combined with Chinese atmospheric environmental assessment standards, the SCREEN3 atmospheric dispersion model and one-dimensional liquid diffusion model are established to realize the query of related information and the display of the diffusion effect under B/S structure. Based on the WebGIS technology, C#.Net language is used to develop the sudden environmental pollution public service platform. As a result, the public service platform can make risk assessments and provide the best emergency processing services.

LSST communications middleware implementation

NASA Astrophysics Data System (ADS)

Mills, Dave; Schumacher, German; Lotz, Paul

2016-07-01

The LSST communications middleware is based on a set of software abstractions; which provide standard interfaces for common communications services. The observatory requires communication between diverse subsystems, implemented by different contractors, and comprehensive archiving of subsystem status data. The Service Abstraction Layer (SAL) is implemented using open source packages that implement open standards of DDS (Data Distribution Service1) for data communication, and SQL (Standard Query Language) for database access. For every subsystem, abstractions for each of the Telemetry datastreams, along with Command/Response and Events, have been agreed with the appropriate component vendor (such as Dome, TMA, Hexapod), and captured in ICD's (Interface Control Documents).The OpenSplice (Prismtech) Community Edition of DDS provides an LGPL licensed distribution which may be freely redistributed. The availability of the full source code provides assurances that the project will be able to maintain it over the full 10 year survey, independent of the fortunes of the original providers.

Development of Human Face Literature Database Using Text Mining Approach: Phase I.

PubMed

Kaur, Paramjit; Krishan, Kewal; Sharma, Suresh K

2018-06-01

The face is an important part of the human body by which an individual communicates in the society. Its importance can be highlighted by the fact that a person deprived of face cannot sustain in the living world. The amount of experiments being performed and the number of research papers being published under the domain of human face have surged in the past few decades. Several scientific disciplines, which are conducting research on human face include: Medical Science, Anthropology, Information Technology (Biometrics, Robotics, and Artificial Intelligence, etc.), Psychology, Forensic Science, Neuroscience, etc. This alarms the need of collecting and managing the data concerning human face so that the public and free access of it can be provided to the scientific community. This can be attained by developing databases and tools on human face using bioinformatics approach. The current research emphasizes on creating a database concerning literature data of human face. The database can be accessed on the basis of specific keywords, journal name, date of publication, author's name, etc. The collected research papers will be stored in the form of a database. Hence, the database will be beneficial to the research community as the comprehensive information dedicated to the human face could be found at one place. The information related to facial morphologic features, facial disorders, facial asymmetry, facial abnormalities, and many other parameters can be extracted from this database. The front end has been developed using Hyper Text Mark-up Language and Cascading Style Sheets. The back end has been developed using hypertext preprocessor (PHP). The JAVA Script has used as scripting language. MySQL (Structured Query Language) is used for database development as it is most widely used Relational Database Management System. XAMPP (X (cross platform), Apache, MySQL, PHP, Perl) open source web application software has been used as the server.The database is still under the developmental phase and discusses the initial steps of its creation. The current paper throws light on the work done till date.

Visual query tool for finding patient cohorts from a clinical data warehouse of the partners HealthCare system

PubMed Central

Murphy, SN; Barnett, GO; Chueh, HC

2000-01-01

The patient base of the Partners HealthCare System in Boston exceeds 1.8 million. Many of these patients are desirable for participation in research studies. To facilitate their discovery, we developed a data warehouse to contain clinical characteristics of these patients. The data warehouse contains diagnosis and procedures from administrative databases. The patients are indexed across institutions and their demographics provided by an Enterprise Master Patient Indexing service. Characteristics of the diagnoses and procedures such as associated providers, dates of service, inpatient/outpatient status, and other visit-related characteristics are also fed from the administrative systems. The targeted users of this system are research clinician s interested in finding patient cohorts for research studies. Their data requirements were analyzed and have been reported elsewhere. We did not expect the clinicians to become expert users of the system. Tools for querying healthcare data have traditionally been text based, although graphical interfaces have been pursued. In order to support the simple drag and drop visual model, as well as the identification and distribution of the patient data, a three-tier software architecture was developed. The user interface was developed in Visual Basic and distributed as an ActiveX object embedded in an HTML page. The middle layer was developed in Java and Microsoft COM. The queries are represented throughout their lifetime as XML objects, and the Microsoft SQL7 database is queried and managed in standard SQL. PMID:11080028

Visual query tool for finding patient cohorts from a clinical data warehouse of the partners HealthCare system

PubMed

Murphy; Barnett; Chueh

2000-01-01

The patient base of the Partners HealthCare System in Boston exceeds 1.8 million. Many of these patients are desirable for participation in research studies. To facilitate their discovery, we developed a data warehouse to contain clinical characteristics of these patients. The data warehouse contains diagnosis and procedures from administrative databases. The patients are indexed across institutions and their demographics provided by an Enterprise Master Patient Indexing service. Characteristics of the diagnoses and procedures such as associated providers, dates of service, inpatient/outpatient status, and other visit-related characteristics are also fed from the administrative systems. The targeted users of this system are research clinician s interested in finding patient cohorts for research studies. Their data requirements were analyzed and have been reported elsewhere. We did not expect the clinicians to become expert users of the system. Tools for querying healthcare data have traditionally been text based, although graphical interfaces have been pursued. In order to support the simple drag and drop visual model, as well as the identification and distribution of the patient data, a three-tier software architecture was developed. The user interface was developed in Visual Basic and distributed as an ActiveX object embedded in an HTML page. The middle layer was developed in Java and Microsoft COM. The queries are represented throughout their lifetime as XML objects, and the Microsoft SQL7 database is queried and managed in standard SQL.

ESTminer: a Web interface for mining EST contig and cluster databases.

PubMed

Huang, Yecheng; Pumphrey, Janie; Gingle, Alan R

2005-03-01

ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster datasets. The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or a threshold number of members. The results are displayed as color-coded tree nodes, where the color indicates the fractional size of each cDNA library component. The nodes are expandable, revealing library statistics as well as EST or contig members, with links to sequence data, GenBank records or user configurable links. Also, the interface allows 'queries within queries' where the result set of a query is further filtered by the subsequent query. ESTminer is implemented in Java/JSP and the package, including MySQL and Oracle schema creation scripts, is available from http://cggc.agtec.uga.edu/Data/download.asp agingle@uga.edu.

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…

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.

Model-based query language for analyzing clinical processes.

PubMed

Barzdins, Janis; Barzdins, Juris; Rencis, Edgars; Sostaks, Agris

2013-01-01

Nowadays large databases of clinical process data exist in hospitals. However, these data are rarely used in full scope. In order to perform queries on hospital processes, one must either choose from the predefined queries or develop queries using MS Excel-type software system, which is not always a trivial task. In this paper we propose a new query language for analyzing clinical processes that is easily perceptible also by non-IT professionals. We develop this language based on a process modeling language which is also described in this paper. Prototypes of both languages have already been verified using real examples from hospitals.

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

PubMed

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

1995-01-01

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

Microsoft Repository Version 2 and the Open Information Model.

ERIC Educational Resources Information Center

Bernstein, Philip A.; Bergstraesser, Thomas; Carlson, Jason; Pal, Shankar; Sanders, Paul; Shutt, David

1999-01-01

Describes the programming interface and implementation of the repository engine and the Open Information Model for Microsoft Repository, an object-oriented meta-data management facility that ships in Microsoft Visual Studio and Microsoft SQL Server. Discusses Microsoft's component object model, object manipulation, queries, and information…

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)

Ingredients for an Integrated Dinner: Parsley, Sage, Rosemary and Thyme

NASA Astrophysics Data System (ADS)

Baumann, Peter

2013-04-01

In 1966, Simon and Garfunkel combined the English traditional "Scarborough Fair" with a counter melody. This is one of the manifold techniques of the Kontrapunktik described by Bach around 1745 in "The Art of the Fugue": combining completely different and seemingly independent melodies (or motifs) into a coherent piece of music, pleasant for the audience. This achievement, transposed into Computer Science, could be of great benefit for geo services as we look at the currently disparate situation: On the one hand, we have metadata - traditionally, they are understood as being small in volume, but rich in content and semantics, and flexibly queryable through the rich body of technologies established over several decades of database research, centering around query languages like SQL. On the other hand, we have data themselves, such as remote sensing and other measured and observed data sets - they are considered difficult to interpret, semantic-poor, and only for clumsy download, as they are the main constituent of what we today call Big Data. The traditional advantages of databases, such as information integration, query flexibility, and scalability seem to be unavailable. These are the melodies that require a kontrapunctic harmonization, leading to a Holy Grail where different information categories enjoy individually tailored support, while an overall integrating framework allows seamless and convenient access and processing by the user. Most of the data categories to be integrated are well known in fact: ontologies, geospatial meshes, spatiotemporal arrays, and free text constitute major ingredients in this orchestration. For many of them, isolated solutions have been presented, and for some of them (like ontologies and text) integration has been achieved already; a complete harmonic integration, though, is still lacking as of today. In our talk, we detail our vision on such integration through query models and languages which merge established concepts and novel paradigms in a harmonic way. We present the EarthServer initiative which has set out to demonstrate flexible ad-hoc processing and filtering on massive Earth data sets.

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)

A Natural Language Interface Concordant with a Knowledge Base.

PubMed

Han, Yong-Jin; Park, Seong-Bae; Park, Se-Young

2016-01-01

The discordance between expressions interpretable by a natural language interface (NLI) system and those answerable by a knowledge base is a critical problem in the field of NLIs. In order to solve this discordance problem, this paper proposes a method to translate natural language questions into formal queries that can be generated from a graph-based knowledge base. The proposed method considers a subgraph of a knowledge base as a formal query. Thus, all formal queries corresponding to a concept or a predicate in the knowledge base can be generated prior to query time and all possible natural language expressions corresponding to each formal query can also be collected in advance. A natural language expression has a one-to-one mapping with a formal query. Hence, a natural language question is translated into a formal query by matching the question with the most appropriate natural language expression. If the confidence of this matching is not sufficiently high the proposed method rejects the question and does not answer it. Multipredicate queries are processed by regarding them as a set of collected expressions. The experimental results show that the proposed method thoroughly handles answerable questions from the knowledge base and rejects unanswerable ones effectively.

Design Recommendations for Query Languages

DTIC Science & Technology

1980-09-01

DESIGN RECOMMENDATIONS FOR QUERY LANGUAGES S.L. Ehrenreich Submitted by: Stanley M. Halpin, Acting Chief HUMAN FACTORS TECHNICAL AREA Approved by: Edgar ...respond to que- ries that it recognizes as faulty. Codd (1974) states that in designing a nat- ural query language, attention must be given to dealing...impaired. Codd (1974) also regarded the user’s perception of the data base to be of critical importance in properly designing a query language system

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.

NoSQL data model for semi-automatic integration of ethnomedicinal plant data from multiple sources.

PubMed

Ningthoujam, Sanjoy Singh; Choudhury, Manabendra Dutta; Potsangbam, Kumar Singh; Chetia, Pankaj; Nahar, Lutfun; Sarker, Satyajit D; Basar, Norazah; Das Talukdar, Anupam

2014-01-01

Sharing traditional knowledge with the scientific community could refine scientific approaches to phytochemical investigation and conservation of ethnomedicinal plants. As such, integration of traditional knowledge with scientific data using a single platform for sharing is greatly needed. However, ethnomedicinal data are available in heterogeneous formats, which depend on cultural aspects, survey methodology and focus of the study. Phytochemical and bioassay data are also available from many open sources in various standards and customised formats. To design a flexible data model that could integrate both primary and curated ethnomedicinal plant data from multiple sources. The current model is based on MongoDB, one of the Not only Structured Query Language (NoSQL) databases. Although it does not contain schema, modifications were made so that the model could incorporate both standard and customised ethnomedicinal plant data format from different sources. The model presented can integrate both primary and secondary data related to ethnomedicinal plants. Accommodation of disparate data was accomplished by a feature of this database that supported a different set of fields for each document. It also allowed storage of similar data having different properties. The model presented is scalable to a highly complex level with continuing maturation of the database, and is applicable for storing, retrieving and sharing ethnomedicinal plant data. It can also serve as a flexible alternative to a relational and normalised database. Copyright © 2014 John Wiley & Sons, Ltd.

The establishment and use of the point source catalog database of the 2MASS near infrared survey

NASA Astrophysics Data System (ADS)

Gao, Y. F.; Shan, H. G.; Cheng, D.

2003-02-01

The 2MASS near infrared survey project is introduced briefly. The 2MASS point sources catalog (2MASS PSC) database and the network query system are established by using the PHP Hypertext Preprocessor and MySQL database server. By using the system, one can not only query information of sources listed in the catalog, but also draw the plots related. Moreover, after the 2MASS data are diagnosed , some research fields which can be benefited from this database are suggested.

The MAO NASU Plate Archive Database. Current Status and Perspectives

NASA Astrophysics Data System (ADS)

Pakuliak, L. K.; Sergeeva, T. P.

2006-04-01

The preliminary online version of the database of the MAO NASU plate archive is constructed on the basis of the relational database management system MySQL and permits an easy supplement of database with new collections of astronegatives, provides a high flexibility in constructing SQL-queries for data search optimization, PHP Basic Authorization protected access to administrative interface and wide range of search parameters. The current status of the database will be reported and the brief description of the search engine and means of the database integrity support will be given. Methods and means of the data verification and tasks for the further development will be discussed.

2MASS Catalog Server Kit Version 2.1

NASA Astrophysics Data System (ADS)

Yamauchi, C.

2013-10-01

The 2MASS Catalog Server Kit is open source software for use in easily constructing a high performance search server for important astronomical catalogs. This software utilizes the open source RDBMS PostgreSQL, therefore, any users can setup the database on their local computers by following step-by-step installation guide. The kit provides highly optimized stored functions for positional searchs similar to SDSS SkyServer. Together with these, the powerful SQL environment of PostgreSQL will meet various user's demands. We released 2MASS Catalog Server Kit version 2.1 in 2012 May, which supports the latest WISE All-Sky catalog (563,921,584 rows) and 9 major all-sky catalogs. Local databases are often indispensable for observatories with unstable or narrow-band networks or severe use, such as retrieving large numbers of records within a small period of time. This software is the best for such purposes, and increasing supported catalogs and improvements of version 2.1 can cover a wider range of applications including advanced calibration system, scientific studies using complicated SQL queries, etc. Official page: http://www.ir.isas.jaxa.jp/~cyamauch/2masskit/

Information Security Considerations for Applications Using Apache Accumulo

DTIC Science & Technology

2014-09-01

Distributed File System INSCOM United States Army Intelligence and Security Command JPA Java Persistence API JSON JavaScript Object Notation MAC Mandatory... MySQL [13]. BigTable can process 20 petabytes per day [14]. High degree of scalability on commodity hardware. NoSQL databases do not rely on highly...manipulation in relational databases. NoSQL databases each have a unique programming interface that uses a lower level procedural language (e.g., Java

Learning Asset Technology Integration Support Tool Design Document

DTIC Science & Technology

2010-05-11

language known as Hypertext Preprocessor ( PHP ) and by MySQL – a relational database management system that can also be used for content management. It...Requirements The LATIST tool will be implemented utilizing a WordPress platform with MySQL as the database. Also the LATIST system must effectively work... MySQL . When designing the LATIST system there are several considerations which must be accounted for in the working prototype. These include: • DAU

EasyKSORD: A Platform of Keyword Search Over Relational Databases

NASA Astrophysics Data System (ADS)

Peng, Zhaohui; Li, Jing; Wang, Shan

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

In-database processing of a large collection of remote sensing data: applications and implementation

NASA Astrophysics Data System (ADS)

Kikhtenko, Vladimir; Mamash, Elena; Chubarov, Dmitri; Voronina, Polina

2016-04-01

Large archives of remote sensing data are now available to scientists, yet the need to work with individual satellite scenes or product files constrains studies that span a wide temporal range or spatial extent. The resources (storage capacity, computing power and network bandwidth) required for such studies are often beyond the capabilities of individual geoscientists. This problem has been tackled before in remote sensing research and inspired several information systems. Some of them such as NASA Giovanni [1] and Google Earth Engine have already proved their utility for science. Analysis tasks involving large volumes of numerical data are not unique to Earth Sciences. Recent advances in data science are enabled by the development of in-database processing engines that bring processing closer to storage, use declarative query languages to facilitate parallel scalability and provide high-level abstraction of the whole dataset. We build on the idea of bridging the gap between file archives containing remote sensing data and databases by integrating files into relational database as foreign data sources and performing analytical processing inside the database engine. Thereby higher level query language can efficiently address problems of arbitrary size: from accessing the data associated with a specific pixel or a grid cell to complex aggregation over spatial or temporal extents over a large number of individual data files. This approach was implemented using PostgreSQL for a Siberian regional archive of satellite data products holding hundreds of terabytes of measurements from multiple sensors and missions taken over a decade-long span. While preserving the original storage layout and therefore compatibility with existing applications the in-database processing engine provides a toolkit for provisioning remote sensing data in scientific workflows and applications. The use of SQL - a widely used higher level declarative query language - simplifies interoperability between desktop GIS, web applications and geographic web services and interactive scientific applications (MATLAB, IPython). The system is also automatically ingesting direct readout data from meteorological and research satellites in near-real time with distributed acquisition workflows managed by Taverna workflow engine [2]. The system has demonstrated its utility in performing non-trivial analytic processing such as the computation of the Robust Satellite Technique (RST) indices [3]. It had been useful in different tasks such as studying urban heat islands, analyzing patterns in the distribution of wildfire occurrences, detecting phenomena related to seismic and earthquake activity. Initial experience has highlighted several limitations of the proposed approach yet it has demonstrated ability to facilitate the use of large archives of remote sensing data by geoscientists. 1. J.G. Acker, G. Leptoukh, Online analysis enhances use of NASA Earth science data. EOS Trans. AGU, 2007, 88(2), P. 14-17. 2. D. Hull, K. Wolsfencroft, R. Stevens, C. Goble, M.R. Pocock, P. Li and T. Oinn, Taverna: a tool for building and running workflows of services. Nucleic Acids Research. 2006. V. 34. P. W729-W732. 3. V. Tramutoli, G. Di Bello, N. Pergola, S. Piscitelli, Robust satellite techniques for remote sensing of seismically active areas // Annals of Geophysics. 2001. no. 44(2). P. 295-312.

[Establishment of a comprehensive database for laryngeal cancer related genes and the miRNAs].

PubMed

Li, Mengjiao; E, Qimin; Liu, Jialin; Huang, Tingting; Liang, Chuanyu

2015-09-01

By collecting and analyzing the laryngeal cancer related genes and the miRNAs, to build a comprehensive laryngeal cancer-related gene database, which differs from the current biological information database with complex and clumsy structure and focuses on the theme of gene and miRNA, and it could make the research and teaching more convenient and efficient. Based on the B/S architecture, using Apache as a Web server, MySQL as coding language of database design and PHP as coding language of web design, a comprehensive database for laryngeal cancer-related genes was established, providing with the gene tables, protein tables, miRNA tables and clinical information tables of the patients with laryngeal cancer. The established database containsed 207 laryngeal cancer related genes, 243 proteins, 26 miRNAs, and their particular information such as mutations, methylations, diversified expressions, and the empirical references of laryngeal cancer relevant molecules. The database could be accessed and operated via the Internet, by which browsing and retrieval of the information were performed. The database were maintained and updated regularly. The database for laryngeal cancer related genes is resource-integrated and user-friendly, providing a genetic information query tool for the study of laryngeal cancer.

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.

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.

Performance Prediction of a MongoDB-Based Traceability System in Smart Factory Supply Chains

PubMed Central

Kang, Yong-Shin; Park, Il-Ha; Youm, Sekyoung

2016-01-01

In the future, with the advent of the smart factory era, manufacturing and logistics processes will become more complex, and the complexity and criticality of traceability will further increase. This research aims at developing a performance assessment method to verify scalability when implementing traceability systems based on key technologies for smart factories, such as Internet of Things (IoT) and BigData. To this end, based on existing research, we analyzed traceability requirements and an event schema for storing traceability data in MongoDB, a document-based Not Only SQL (NoSQL) database. Next, we analyzed the algorithm of the most representative traceability query and defined a query-level performance model, which is composed of response times for the components of the traceability query algorithm. Next, this performance model was solidified as a linear regression model because the response times increase linearly by a benchmark test. Finally, for a case analysis, we applied the performance model to a virtual automobile parts logistics. As a result of the case study, we verified the scalability of a MongoDB-based traceability system and predicted the point when data node servers should be expanded in this case. The traceability system performance assessment method proposed in this research can be used as a decision-making tool for hardware capacity planning during the initial stage of construction of traceability systems and during their operational phase. PMID:27983654

Rasdaman for Big Spatial Raster Data

NASA Astrophysics Data System (ADS)

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

2015-12-01

Spatial raster data have grown exponentially over the past decade. Recent advancements on data acquisition technology, such as remote sensing, have allowed us to collect massive observation data of various spatial resolution and domain coverage. The volume, velocity, and variety of such spatial data, along with the computational intensive nature of spatial queries, pose grand challenge to the storage technologies for effective big data management. While high performance computing platforms (e.g., cloud computing) can be used to solve the computing-intensive issues in big data analysis, data has to be managed in a way that is suitable for distributed parallel processing. Recently, rasdaman (raster data manager) has emerged as a scalable and cost-effective database solution to store and retrieve massive multi-dimensional arrays, such as sensor, image, and statistics data. Within this paper, the pros and cons of using rasdaman to manage and query spatial raster data will be examined and compared with other common approaches, including file-based systems, relational databases (e.g., PostgreSQL/PostGIS), and NoSQL databases (e.g., MongoDB and Hive). Earth Observing System (EOS) data collected from NASA's Atmospheric Scientific Data Center (ASDC) will be used and stored in these selected database systems, and a set of spatial and non-spatial queries will be designed to benchmark their performance on retrieving large-scale, multi-dimensional arrays of EOS data. Lessons learnt from using rasdaman will be discussed as well.

Performance Prediction of a MongoDB-Based Traceability System in Smart Factory Supply Chains.

PubMed

Kang, Yong-Shin; Park, Il-Ha; Youm, Sekyoung

2016-12-14

In the future, with the advent of the smart factory era, manufacturing and logistics processes will become more complex, and the complexity and criticality of traceability will further increase. This research aims at developing a performance assessment method to verify scalability when implementing traceability systems based on key technologies for smart factories, such as Internet of Things (IoT) and BigData. To this end, based on existing research, we analyzed traceability requirements and an event schema for storing traceability data in MongoDB, a document-based Not Only SQL (NoSQL) database. Next, we analyzed the algorithm of the most representative traceability query and defined a query-level performance model, which is composed of response times for the components of the traceability query algorithm. Next, this performance model was solidified as a linear regression model because the response times increase linearly by a benchmark test. Finally, for a case analysis, we applied the performance model to a virtual automobile parts logistics. As a result of the case study, we verified the scalability of a MongoDB-based traceability system and predicted the point when data node servers should be expanded in this case. The traceability system performance assessment method proposed in this research can be used as a decision-making tool for hardware capacity planning during the initial stage of construction of traceability systems and during their operational phase.

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.

A Priority Fuzzy Logic Extension of the XQuery Language

NASA Astrophysics Data System (ADS)

Škrbić, Srdjan; Wettayaprasit, Wiphada; Saeueng, Pannipa

2011-09-01

In recent years there have been significant research findings in flexible XML querying techniques using fuzzy set theory. Many types of fuzzy extensions to XML data model and XML query languages have been proposed. In this paper, we introduce priority fuzzy logic extensions to XQuery language. Describing these extensions we introduce a new query language. Moreover, we describe a way to implement an interpreter for this language using an existing XML native database.

Natural Language Query System Design for Interactive Information Storage and Retrieval Systems. M.S. Thesis

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Liu, I-Hsiung

1985-01-01

The currently developed multi-level language interfaces of information systems are generally designed for experienced users. These interfaces commonly ignore the nature and needs of the largest user group, i.e., casual users. This research identifies the importance of natural language query system research within information storage and retrieval system development; addresses the topics of developing such a query system; and finally, proposes a framework for the development of natural language query systems in order to facilitate the communication between casual users and information storage and retrieval systems.

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

PubMed

Jamil, Hasan M

2012-06-11

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

A Visual Interface for Querying Heterogeneous Phylogenetic Databases.

PubMed

Jamil, Hasan M

2017-01-01

Despite the recent growth in the number of phylogenetic databases, access to these wealth of resources remain largely tool or form-based interface driven. It is our thesis that the flexibility afforded by declarative query languages may offer the opportunity to access these repositories in a better way, and to use such a language to pose truly powerful queries in unprecedented ways. In this paper, we propose a substantially enhanced closed visual query language, called PhyQL, that can be used to query phylogenetic databases represented in a canonical form. The canonical representation presented helps capture most phylogenetic tree formats in a convenient way, and is used as the storage model for our PhyloBase database for which PhyQL serves as the query language. We have implemented a visual interface for the end users to pose PhyQL queries using visual icons, and drag and drop operations defined over them. Once a query is posed, the interface translates the visual query into a Datalog query for execution over the canonical database. Responses are returned as hyperlinks to phylogenies that can be viewed in several formats using the tree viewers supported by PhyloBase. Results cached in PhyQL buffer allows secondary querying on the computed results making it a truly powerful querying architecture.

Defense Information Systems Agency Technical Integration Support (DISA- TIS). MUMPS Study.

DTIC Science & Technology

1993-01-01

usable in DoD, MUMPS must continue to improve in its support of DoD and OSE standards such as SQL , X-Windows, POSIX, PHIGS, etc. MUMPS and large AlSs...Language ( SQL ), X-Windows, and Graphical Kernel Services (GKS)) 2.2.2.3 FIPS Adoption by NIST The National Institute of Standards and Technology (NIST...many of the performance tuning mechanisms that must be performed explicitly with other systems. The VA looks forward to the SQL binding (1993 ANS) that

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…

Object-Oriented Query Language For Events Detection From Images Sequences

NASA Astrophysics Data System (ADS)

Ganea, Ion Eugen

2015-09-01

In this paper is presented a method to represent the events extracted from images sequences and the query language used for events detection. Using an object oriented model the spatial and temporal relationships between salient objects and also between events are stored and queried. This works aims to unify the storing and querying phases for video events processing. The object oriented language syntax used for events processing allow the instantiation of the indexes classes in order to improve the accuracy of the query results. The experiments were performed on images sequences provided from sport domain and it shows the reliability and the robustness of the proposed language. To extend the language will be added a specific syntax for constructing the templates for abnormal events and for detection of the incidents as the final goal of the research.

National Irrigation Water Quality Program data-synthesis data base

USGS Publications Warehouse

Seiler, Ralph L.; Skorupa, Joseph P.

2001-01-01

Under the National Irrigation Water Quality Program (NIWQP) of the U.S. Department of the Interior, researchers investigated contamination caused by irrigation drainage in 26 areas in the Western United States from 1986 to 1993. From 1992 to 1995, a comprehensive relational data base was built to organize data collected during the 26-area investigations. The data base provided the basis for analysis and synthesis of these data to identify common features of contaminated areas and hence dominant biologic, geologic, climatic, chemical, and physiographic factors that have resulted in contamination of water and biota in irrigated areas in the Western United States. Included in the data base are geologic, hydrologic, climatological, chemical, and cultural data that describe the 26 study areas in 14 Western States. The data base contains information on 1,264 sites from which water and bottom sediment were collected. It also contains chemical data from 6,903 analyses of surface water, 914 analyses of ground water, 707 analyses of inorganic constituents in bottom sediments, 223 analyses of organochlorine pesticides in bottom sediments, 8,217 analyses of inorganic constituents in biota, and 1,088 analyses for organic constituents in biota. The data base is available to the public and can be obtained at the NIWQP homepage http://www.usbr.gov/niwqp as dBase III tables for personal-computer systems or as American Standard Code for Information Exchange structured query language (SQL) command and data files for SQL data bases.

DCMS: A data analytics and management system for molecular simulation.

PubMed

Kumar, Anand; Grupcev, Vladimir; Berrada, Meryem; Fogarty, Joseph C; Tu, Yi-Cheng; Zhu, Xingquan; Pandit, Sagar A; Xia, Yuni

Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface ( i.e. , SQL), data access methods, query processing, and optimization mechanisms of modern DBMSs. A unique challenge is to handle the analytical queries that are often compute-intensive. For that, we developed novel indexing and query processing strategies (including algorithms running on modern co-processors) as integrated components of the DBMS. As a result, researchers can upload and analyze their data using efficient functions implemented inside the DBMS. Index structures are generated to store analysis results that may be interesting to other users, so that the results are readily available without duplicating the analysis. We have developed a prototype of DCMS based on the PostgreSQL system and experiments using real MS data and workload show that DCMS significantly outperforms existing MS software systems. We also used it as a platform to test other data management issues such as security and compression.

A Flexible Monitoring Infrastructure for the Simulation Requests

NASA Astrophysics Data System (ADS)

Spinoso, V.; Missiato, M.

2014-06-01

Running and monitoring simulations usually involves several different aspects of the entire workflow: the configuration of the job, the site issues, the software deployment at the site, the file catalogue, the transfers of the simulated data. In addition, the final product of the simulation is often the result of several sequential steps. This project tries a different approach to monitoring the simulation requests. All the necessary data are collected from the central services which lead the submission of the requests and the data management, and stored by a backend into a NoSQL-based data cache; those data can be queried through a Web Service interface, which returns JSON responses, and allows users, sites, physics groups to easily create their own web frontend, aggregating only the needed information. As an example, it will be shown how it is possible to monitor the CMS services (ReqMgr, DAS/DBS, PhEDEx) using a central backend and multiple customized cross-language frontends.

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.

Generating and Executing Complex Natural Language Queries across Linked Data.

PubMed

Hamon, Thierry; Mougin, Fleur; Grabar, Natalia

2015-01-01

With the recent and intensive research in the biomedical area, the knowledge accumulated is disseminated through various knowledge bases. Links between these knowledge bases are needed in order to use them jointly. Linked Data, SPARQL language, and interfaces in Natural Language question-answering provide interesting solutions for querying such knowledge bases. We propose a method for translating natural language questions in SPARQL queries. We use Natural Language Processing tools, semantic resources, and the RDF triples description. The method is designed on 50 questions over 3 biomedical knowledge bases, and evaluated on 27 questions. It achieves 0.78 F-measure on the test set. The method for translating natural language questions into SPARQL queries is implemented as Perl module available at http://search.cpan.org/ thhamon/RDF-NLP-SPARQLQuery.

Concept-based query language approach to enterprise information systems

NASA Astrophysics Data System (ADS)

Niemi, Timo; Junkkari, Marko; Järvelin, Kalervo

2014-01-01

In enterprise information systems (EISs) it is necessary to model, integrate and compute very diverse data. In advanced EISs the stored data often are based both on structured (e.g. relational) and semi-structured (e.g. XML) data models. In addition, the ad hoc information needs of end-users may require the manipulation of data-oriented (structural), behavioural and deductive aspects of data. Contemporary languages capable of treating this kind of diversity suit only persons with good programming skills. In this paper we present a concept-oriented query language approach to manipulate this diversity so that the programming skill requirements are considerably reduced. In our query language, the features which need technical knowledge are hidden in application-specific concepts and structures. Therefore, users need not be aware of the underlying technology. Application-specific concepts and structures are represented by the modelling primitives of the extended RDOOM (relational deductive object-oriented modelling) which contains primitives for all crucial real world relationships (is-a relationship, part-of relationship, association), XML documents and views. Our query language also supports intensional and extensional-intensional queries, in addition to conventional extensional queries. In its query formulation, the end-user combines available application-specific concepts and structures through shared variables.

Mining Student Data Captured from a Web-Based Tutoring Tool: Initial Exploration and Results

ERIC Educational Resources Information Center

Merceron, Agathe; Yacef, Kalina

2004-01-01

In this article we describe the initial investigations that we have conducted on student data collected from a web-based tutoring tool. We have used some data mining techniques such as association rule and symbolic data analysis, as well as traditional SQL queries to gain further insight on the students' learning and deduce information to improve…

ClimateSpark: An in-memory distributed computing framework for big climate data analytics

NASA Astrophysics Data System (ADS)

Hu, Fei; Yang, Chaowei; Schnase, John L.; Duffy, Daniel Q.; Xu, Mengchao; Bowen, Michael K.; Lee, Tsengdar; Song, Weiwei

2018-06-01

The unprecedented growth of climate data creates new opportunities for climate studies, and yet big climate data pose a grand challenge to climatologists to efficiently manage and analyze big data. The complexity of climate data content and analytical algorithms increases the difficulty of implementing algorithms on high performance computing systems. This paper proposes an in-memory, distributed computing framework, ClimateSpark, to facilitate complex big data analytics and time-consuming computational tasks. Chunking data structure improves parallel I/O efficiency, while a spatiotemporal index is built for the chunks to avoid unnecessary data reading and preprocessing. An integrated, multi-dimensional, array-based data model (ClimateRDD) and ETL operations are developed to address big climate data variety by integrating the processing components of the climate data lifecycle. ClimateSpark utilizes Spark SQL and Apache Zeppelin to develop a web portal to facilitate the interaction among climatologists, climate data, analytic operations and computing resources (e.g., using SQL query and Scala/Python notebook). Experimental results show that ClimateSpark conducts different spatiotemporal data queries/analytics with high efficiency and data locality. ClimateSpark is easily adaptable to other big multiple-dimensional, array-based datasets in various geoscience domains.

Accessing the public MIMIC-II intensive care relational database for clinical research.

PubMed

Scott, Daniel J; Lee, Joon; Silva, Ikaro; Park, Shinhyuk; Moody, George B; Celi, Leo A; Mark, Roger G

2013-01-10

The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge "Predicting mortality of ICU Patients". QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database.

TokSearch: A search engine for fusion experimental data

DOE PAGES

Sammuli, Brian S.; Barr, Jayson L.; Eidietis, Nicholas W.; ...

2018-04-01

At a typical fusion research site, experimental data is stored using archive technologies that deal with each discharge as an independent set of data. These technologies (e.g. MDSplus or HDF5) are typically supplemented with a database that aggregates metadata for multiple shots to allow for efficient querying of certain predefined quantities. Often, however, a researcher will need to extract information from the archives, possibly for many shots, that is not available in the metadata store or otherwise indexed for quick retrieval. To address this need, a new search tool called TokSearch has been added to the General Atomics TokSys controlmore » design and analysis suite [1]. This tool provides the ability to rapidly perform arbitrary, parallelized queries of archived tokamak shot data (both raw and analyzed) over large numbers of shots. The TokSearch query API borrows concepts from SQL, and users can choose to implement queries in either MatlabTM or Python.« less

TokSearch: A search engine for fusion experimental data

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

Sammuli, Brian S.; Barr, Jayson L.; Eidietis, Nicholas W.

At a typical fusion research site, experimental data is stored using archive technologies that deal with each discharge as an independent set of data. These technologies (e.g. MDSplus or HDF5) are typically supplemented with a database that aggregates metadata for multiple shots to allow for efficient querying of certain predefined quantities. Often, however, a researcher will need to extract information from the archives, possibly for many shots, that is not available in the metadata store or otherwise indexed for quick retrieval. To address this need, a new search tool called TokSearch has been added to the General Atomics TokSys controlmore » design and analysis suite [1]. This tool provides the ability to rapidly perform arbitrary, parallelized queries of archived tokamak shot data (both raw and analyzed) over large numbers of shots. The TokSearch query API borrows concepts from SQL, and users can choose to implement queries in either MatlabTM or Python.« less

A future Outlook: Web based Simulation of Hydrodynamic models

NASA Astrophysics Data System (ADS)

Islam, A. S.; Piasecki, M.

2003-12-01

Despite recent advances to present simulation results as 3D graphs or animation contours, the modeling user community still faces some shortcomings when trying to move around and analyze data. Typical problems include the lack of common platforms with standard vocabulary to exchange simulation results from different numerical models, insufficient descriptions about data (metadata), lack of robust search and retrieval tools for data, and difficulties to reuse simulation domain knowledge. This research demonstrates how to create a shared simulation domain in the WWW and run a number of models through multi-user interfaces. Firstly, meta-datasets have been developed to describe hydrodynamic model data based on geographic metadata standard (ISO 19115) that has been extended to satisfy the need of the hydrodynamic modeling community. The Extended Markup Language (XML) is used to publish this metadata by the Resource Description Framework (RDF). Specific domain ontology for Web Based Simulation (WBS) has been developed to explicitly define vocabulary for the knowledge based simulation system. Subsequently, this knowledge based system is converted into an object model using Meta Object Family (MOF). The knowledge based system acts as a Meta model for the object oriented system, which aids in reusing the domain knowledge. Specific simulation software has been developed based on the object oriented model. Finally, all model data is stored in an object relational database. Database back-ends help store, retrieve and query information efficiently. This research uses open source software and technology such as Java Servlet and JSP, Apache web server, Tomcat Servlet Engine, PostgresSQL databases, Protégé ontology editor, RDQL and RQL for querying RDF in semantic level, Jena Java API for RDF. Also, we use international standards such as the ISO 19115 metadata standard, and specifications such as XML, RDF, OWL, XMI, and UML. The final web based simulation product is deployed as Web Archive (WAR) files which is platform and OS independent and can be used by Windows, UNIX, or Linux. Keywords: Apache, ISO 19115, Java Servlet, Jena, JSP, Metadata, MOF, Linux, Ontology, OWL, PostgresSQL, Protégé, RDF, RDQL, RQL, Tomcat, UML, UNIX, Windows, WAR, XML

SPARQL Assist language-neutral query composer

PubMed Central

2012-01-01

Background SPARQL query composition is difficult for the lay-person, and even the experienced bioinformatician in cases where the data model is unfamiliar. Moreover, established best-practices and internationalization concerns dictate that the identifiers for ontological terms should be opaque rather than human-readable, which further complicates the task of synthesizing queries manually. Results We present SPARQL Assist: a Web application that addresses these issues by providing context-sensitive type-ahead completion during SPARQL query construction. Ontological terms are suggested using their multi-lingual labels and descriptions, leveraging existing support for internationalization and language-neutrality. Moreover, the system utilizes the semantics embedded in ontologies, and within the query itself, to help prioritize the most likely suggestions. Conclusions To ensure success, the Semantic Web must be easily available to all users, regardless of locale, training, or preferred language. By enhancing support for internationalization, and moreover by simplifying the manual construction of SPARQL queries through the use of controlled-natural-language interfaces, we believe we have made some early steps towards simplifying access to Semantic Web resources. PMID:22373327

SPARQL assist language-neutral query composer.

PubMed

McCarthy, Luke; Vandervalk, Ben; Wilkinson, Mark

2012-01-25

SPARQL query composition is difficult for the lay-person, and even the experienced bioinformatician in cases where the data model is unfamiliar. Moreover, established best-practices and internationalization concerns dictate that the identifiers for ontological terms should be opaque rather than human-readable, which further complicates the task of synthesizing queries manually. We present SPARQL Assist: a Web application that addresses these issues by providing context-sensitive type-ahead completion during SPARQL query construction. Ontological terms are suggested using their multi-lingual labels and descriptions, leveraging existing support for internationalization and language-neutrality. Moreover, the system utilizes the semantics embedded in ontologies, and within the query itself, to help prioritize the most likely suggestions. To ensure success, the Semantic Web must be easily available to all users, regardless of locale, training, or preferred language. By enhancing support for internationalization, and moreover by simplifying the manual construction of SPARQL queries through the use of controlled-natural-language interfaces, we believe we have made some early steps towards simplifying access to Semantic Web resources.

Querying Proofs

NASA Technical Reports Server (NTRS)

Aspinall, David; Denney, Ewen; Lueth, Christoph

2012-01-01

We motivate and introduce a query language PrQL designed for inspecting machine representations of proofs. PrQL natively supports hiproofs which express proof structure using hierarchical nested labelled trees. The core language presented in this paper is locally structured (first-order), with queries built using recursion and patterns over proof structure and rule names. We define the syntax and semantics of locally structured queries, demonstrate their power, and sketch some implementation experiments.

Querying Proofs (Work in Progress)

NASA Technical Reports Server (NTRS)

Aspinall, David; Denney, Ewen; Lueth, Christoph

2011-01-01

We motivate and introduce the basis for a query language designed for inspecting electronic representations of proofs. We argue that there is much to learn from large proofs beyond their validity, and that a dedicated query language can provide a principled way of implementing a family of useful operations.

Access Based Cost Estimation for Beddown Analysis

DTIC Science & Technology

2006-03-23

logic. This research expands upon the existing research by using Visual Basic for Applications ( VBA ) to further customize and streamline the...methods with the use of VBA . Calculations are completed in either underlying Form VBA code or through global modules accessible throughout the...query and SQL referencing. Attempts were made where possible to align data structures with possible external sources to minimize import errors and

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 New Publicly Available Chemical Query Language, CSRML, to support Chemotype Representations for Application to Data-Mining and Modeling

EPA Science Inventory

A new XML-based query language, CSRML, has been developed for representing chemical substructures, molecules, reaction rules, and reactions. CSRML queries are capable of integrating additional forms of information beyond the simple substructure (e.g., SMARTS) or reaction transfor...

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

Cloud-Based NoSQL Open Database of Pulmonary Nodules for Computer-Aided Lung Cancer Diagnosis and Reproducible Research.

PubMed

Ferreira Junior, José Raniery; Oliveira, Marcelo Costa; de Azevedo-Marques, Paulo Mazzoncini

2016-12-01

Lung cancer is the leading cause of cancer-related deaths in the world, and its main manifestation is pulmonary nodules. Detection and classification of pulmonary nodules are challenging tasks that must be done by qualified specialists, but image interpretation errors make those tasks difficult. In order to aid radiologists on those hard tasks, it is important to integrate the computer-based tools with the lesion detection, pathology diagnosis, and image interpretation processes. However, computer-aided diagnosis research faces the problem of not having enough shared medical reference data for the development, testing, and evaluation of computational methods for diagnosis. In order to minimize this problem, this paper presents a public nonrelational document-oriented cloud-based database of pulmonary nodules characterized by 3D texture attributes, identified by experienced radiologists and classified in nine different subjective characteristics by the same specialists. Our goal with the development of this database is to improve computer-aided lung cancer diagnosis and pulmonary nodule detection and classification research through the deployment of this database in a cloud Database as a Service framework. Pulmonary nodule data was provided by the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), image descriptors were acquired by a volumetric texture analysis, and database schema was developed using a document-oriented Not only Structured Query Language (NoSQL) approach. The proposed database is now with 379 exams, 838 nodules, and 8237 images, 4029 of them are CT scans and 4208 manually segmented nodules, and it is allocated in a MongoDB instance on a cloud infrastructure.

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

PubMed Central

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

1988-01-01

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

Specialized microbial databases for inductive exploration of microbial genome sequences

PubMed Central

Fang, Gang; Ho, Christine; Qiu, Yaowu; Cubas, Virginie; Yu, Zhou; Cabau, Cédric; Cheung, Frankie; Moszer, Ivan; Danchin, Antoine

2005-01-01

Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore , a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya) has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis) associated to related organisms for comparison. PMID:15698474

a Webgis for the Knowledge and Conservation of the Historical Wall Structures of the 13TH-18TH Centuries

NASA Astrophysics Data System (ADS)

Vacca, G.; Pili, D.; Fiorino, D. R.; Pintus, V.

2017-05-01

The presented work is part of the research project, titled "Tecniche murarie tradizionali: conoscenza per la conservazione ed il miglioramento prestazionale" (Traditional building techniques: from knowledge to conservation and performance improvement), with the purpose of studying the building techniques of the 13th-18th centuries in the Sardinia Region (Italy) for their knowledge, conservation, and promotion. The end purpose of the entire study is to improve the performance of the examined structures. In particular, the task of the authors within the research project was to build a WebGIS to manage the data collected during the examination and study phases. This infrastructure was entirely built using Open Source software. The work consisted of designing a database built in PostgreSQL and its spatial extension PostGIS, which allows to store and manage feature geometries and spatial data. The data input is performed via a form built in HTML and PHP. The HTML part is based on Bootstrap, an open tools library for websites and web applications. The implementation of this template used both PHP and Javascript code. The PHP code manages the reading and writing of data to the database, using embedded SQL queries. As of today, we surveyed and archived more than 300 buildings, belonging to three main macro categories: fortification architectures, religious architectures, residential architectures. The masonry samples investigated in relation to the construction techniques are more than 150. The database is published on the Internet as a WebGIS built using the Leaflet Javascript open libraries, which allows creating map sites with background maps and navigation, input and query tools. This too uses an interaction of HTML, Javascript, PHP and SQL code.

SIMS: addressing the problem of heterogeneity in databases

NASA Astrophysics Data System (ADS)

Arens, Yigal

1997-02-01

The heterogeneity of remotely accessible databases -- with respect to contents, query language, semantics, organization, etc. -- presents serious obstacles to convenient querying. The SIMS (single interface to multiple sources) system addresses this global integration problem. It does so by defining a single language for describing the domain about which information is stored in the databases and using this language as the query language. Each database to which SIMS is to provide access is modeled using this language. The model describes a database's contents, organization, and other relevant features. SIMS uses these models, together with a planning system drawing on techniques from artificial intelligence, to decompose a given user's high-level query into a series of queries against the databases and other data manipulation steps. The retrieval plan is constructed so as to minimize data movement over the network and maximize parallelism to increase execution speed. SIMS can recover from network failures during plan execution by obtaining data from alternate sources, when possible. SIMS has been demonstrated in the domains of medical informatics and logistics, using real databases.

A Study of the Efficiency of Spatial Indexing Methods Applied to Large Astronomical Databases

NASA Astrophysics Data System (ADS)

Donaldson, Tom; Berriman, G. Bruce; Good, John; Shiao, Bernie

2018-01-01

Spatial indexing of astronomical databases generally uses quadrature methods, which partition the sky into cells used to create an index (usually a B-tree) written as database column. We report the results of a study to compare the performance of two common indexing methods, HTM and HEALPix, on Solaris and Windows database servers installed with a PostgreSQL database, and a Windows Server installed with MS SQL Server. The indexing was applied to the 2MASS All-Sky Catalog and to the Hubble Source catalog. On each server, the study compared indexing performance by submitting 1 million queries at each index level with random sky positions and random cone search radius, which was computed on a logarithmic scale between 1 arcsec and 1 degree, and measuring the time to complete the query and write the output. These simulated queries, intended to model realistic use patterns, were run in a uniform way on many combinations of indexing method and indexing level. The query times in all simulations are strongly I/O-bound and are linear with number of records returned for large numbers of sources. There are, however, considerable differences between simulations, which reveal that hardware I/O throughput is a more important factor in managing the performance of a DBMS than the choice of indexing scheme. The choice of index itself is relatively unimportant: for comparable index levels, the performance is consistent within the scatter of the timings. At small index levels (large cells; e.g. level 4; cell size 3.7 deg), there is large scatter in the timings because of wide variations in the number of sources found in the cells. At larger index levels, performance improves and scatter decreases, but the improvement at level 8 (14 min) and higher is masked to some extent in the timing scatter caused by the range of query sizes. At very high levels (20; 0.0004 arsec), the granularity of the cells becomes so high that a large number of extraneous empty cells begin to degrade performance. Thus, for the use patterns studied here the database performance is not critically dependent on the exact choices of index or level.

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

Angers, Crystal Plume; Bottema, Ryan; Buckley, Les

Purpose: Treatment unit uptime statistics are typically used to monitor radiation equipment performance. The Ottawa Hospital Cancer Centre has introduced the use of Quality Control (QC) test success as a quality indicator for equipment performance and overall health of the equipment QC program. Methods: Implemented in 2012, QATrack+ is used to record and monitor over 1100 routine machine QC tests each month for 20 treatment and imaging units ( http://qatrackplus.com/ ). Using an SQL (structured query language) script, automated queries of the QATrack+ database are used to generate program metrics such as the number of QC tests executed and themore » percentage of tests passing, at tolerance or at action. These metrics are compared against machine uptime statistics already reported within the program. Results: Program metrics for 2015 show good correlation between pass rate of QC tests and uptime for a given machine. For the nine conventional linacs, the QC test success rate was consistently greater than 97%. The corresponding uptimes for these units are better than 98%. Machines that consistently show higher failure or tolerance rates in the QC tests have lower uptimes. This points to either poor machine performance requiring corrective action or to problems with the QC program. Conclusions: QATrack+ significantly improves the organization of QC data but can also aid in overall equipment management. Complimenting machine uptime statistics with QC test metrics provides a more complete picture of overall machine performance and can be used to identify areas of improvement in the machine service and QC programs.« less

Knowledge portal for Six Sigma DMAIC process

NASA Astrophysics Data System (ADS)

ThanhDat, N.; Claudiu, K. V.; Zobia, R.; Lobont, Lucian

2016-08-01

Knowledge plays a crucial role in success of DMAIC (Define, Measure, Analysis, Improve, and Control) execution. It is therefore necessary to share and renew the knowledge. Yet, one problem arising is how to create a place where knowledge are collected and shared effectively. We believe that Knowledge Portal (KP) is an important solution for the problem. In this article, the works concerning with requirements and functionalities for KP are first reviewed. Afterwards, a procedure with necessary tools to develop and implement a KP for DMAIC (KPD) is proposed. Particularly, KPD is built on the basis of free and open-source content and learning management systems, and Ontology Engineering. In order to structure and store knowledge, tools such as Protégé, OWL, as well as OWL-RDF Parsers are used. A Knowledge Reasoner module is developed in PHP language, ARC2, MySQL and SPARQL endpoint for the purpose of querying and inferring knowledge available from Ontologies. In order to validate the availability of the procedure, a KPD is built with the proposed functionalities and tools. The authors find that the KPD benefits an organization in constructing Web sites by itself with simple steps of implementation and low initial costs. It creates a space of knowledge exchange and supports effectively collecting DMAIC reports as well as sharing knowledge created. The authors’ evaluation result shows that DMAIC knowledge is found exactly with a high success rate and a good level of response time of queries.

Extending Climate Analytics-As to the Earth System Grid Federation

NASA Astrophysics Data System (ADS)

Tamkin, G.; Schnase, J. L.; Duffy, D.; McInerney, M.; Nadeau, D.; Li, J.; Strong, S.; Thompson, J. H.

2015-12-01

We are building three extensions to prior-funded work on climate analytics-as-a-service that will benefit the Earth System Grid Federation (ESGF) as it addresses the Big Data challenges of future climate research: (1) We are creating a cloud-based, high-performance Virtual Real-Time Analytics Testbed supporting a select set of climate variables from six major reanalysis data sets. This near real-time capability will enable advanced technologies like the Cloudera Impala-based Structured Query Language (SQL) query capabilities and Hadoop-based MapReduce analytics over native NetCDF files while providing a platform for community experimentation with emerging analytic technologies. (2) We are building a full-featured Reanalysis Ensemble Service comprising monthly means data from six reanalysis data sets. The service will provide a basic set of commonly used operations over the reanalysis collections. The operations will be made accessible through NASA's climate data analytics Web services and our client-side Climate Data Services (CDS) API. (3) We are establishing an Open Geospatial Consortium (OGC) WPS-compliant Web service interface to our climate data analytics service that will enable greater interoperability with next-generation ESGF capabilities. The CDS API will be extended to accommodate the new WPS Web service endpoints as well as ESGF's Web service endpoints. These activities address some of the most important technical challenges for server-side analytics and support the research community's requirements for improved interoperability and improved access to reanalysis data.

Accessing the public MIMIC-II intensive care relational database for clinical research

PubMed Central

2013-01-01

Background The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. Results QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge “Predicting mortality of ICU Patients”. Conclusions QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database. PMID:23302652

Finding Relevant Data in a Sea of Languages

DTIC Science & Technology

2016-04-26

full machine-translated text , unbiased word clouds , query-biased word clouds , and query-biased sentence...and information retrieval to automate language processing tasks so that the limited number of linguists available for analyzing text and spoken...the crime (stock market). The Cross-LAnguage Search Engine (CLASE) has already preprocessed the documents, extracting text to identify the language

An Object-Oriented View of Backend Databases in a Mobile Environment for Navy and Marine Corps Applications

DTIC Science & Technology

2006-09-01

Each of these layers will be described in more detail to include relevant technologies ( Java , PDA, Hibernate , and PostgreSQL) used to implement...Logic Layer -Object-Relational Mapper ( Hibernate ) Data 35 capable in order to interface with Java applications. Based on meeting the selection...further discussed. Query List Application Logic Layer HibernateApache - Java Servlet - Hibernate Interface -OR Mapper -RDBMS Interface

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

TCW: Transcriptome Computational Workbench

PubMed Central

Soderlund, Carol; Nelson, William; Willer, Mark; Gang, David R.

2013-01-01

Background The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. Methodology The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. Conclusion It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw. PMID:23874959

TCW: transcriptome computational workbench.

PubMed

Soderlund, Carol; Nelson, William; Willer, Mark; Gang, David R

2013-01-01

The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw.

An Expressive and Efficient Language for XML Information Retrieval.

ERIC Educational Resources Information Center

Chinenyanga, Taurai Tapiwa; Kushmerick, Nicholas

2002-01-01

Discusses XML and information retrieval and describes a query language, ELIXIR (expressive and efficient language for XML information retrieval), with a textual similarity operator that can be used for similarity joins. Explains the algorithm for answering ELIXIR queries to generate intermediate relational data. (Author/LRW)

DBPQL: A view-oriented query language for the Intel Data Base Processor

NASA Technical Reports Server (NTRS)

Fishwick, P. A.

1983-01-01

An interactive query language (BDPQL) for the Intel Data Base Processor (DBP) is defined. DBPQL includes a parser generator package which permits the analyst to easily create and manipulate the query statement syntax and semantics. The prototype language, DBPQL, includes trace and performance commands to aid the analyst when implementing new commands and analyzing the execution characteristics of the DBP. The DBPQL grammar file and associated key procedures are included as an appendix to this report.

A New Framework for Textual Information Mining over Parse Trees. CRESST Report 805

ERIC Educational Resources Information Center

Mousavi, Hamid; Kerr, Deirdre; Iseli, Markus R.

2011-01-01

Textual information mining is a challenging problem that has resulted in the creation of many different rule-based linguistic query languages. However, these languages generally are not optimized for the purpose of text mining. In other words, they usually consider queries as individuals and only return raw results for each query. Moreover they…

Graphical modeling and query language for hospitals.

PubMed

Barzdins, Janis; Barzdins, Juris; Rencis, Edgars; Sostaks, Agris

2013-01-01

So far there has been little evidence that implementation of the health information technologies (HIT) is leading to health care cost savings. One of the reasons for this lack of impact by the HIT likely lies in the complexity of the business process ownership in the hospitals. The goal of our research is to develop a business model-based method for hospital use which would allow doctors to retrieve directly the ad-hoc information from various hospital databases. We have developed a special domain-specific process modelling language called the MedMod. Formally, we define the MedMod language as a profile on UML Class diagrams, but we also demonstrate it on examples, where we explain the semantics of all its elements informally. Moreover, we have developed the Process Query Language (PQL) that is based on MedMod process definition language. The purpose of PQL is to allow a doctor querying (filtering) runtime data of hospital's processes described using MedMod. The MedMod language tries to overcome deficiencies in existing process modeling languages, allowing to specify the loosely-defined sequence of the steps to be performed in the clinical process. The main advantages of PQL are in two main areas - usability and efficiency. They are: 1) the view on data through "glasses" of familiar process, 2) the simple and easy-to-perceive means of setting filtering conditions require no more expertise than using spreadsheet applications, 3) the dynamic response to each step in construction of the complete query that shortens the learning curve greatly and reduces the error rate, and 4) the selected means of filtering and data retrieving allows to execute queries in O(n) time regarding the size of the dataset. We are about to continue developing this project with three further steps. First, we are planning to develop user-friendly graphical editors for the MedMod process modeling and query languages. The second step is to do evaluation of usability the proposed language and tool involving the physicians from several hospitals in Latvia and working with real data from these hospitals. Our third step is to develop an efficient implementation of the query language.

Foundations of RDF Databases

NASA Astrophysics Data System (ADS)

Arenas, Marcelo; Gutierrez, Claudio; Pérez, Jorge

The goal of this paper is to give an overview of the basics of the theory of RDF databases. We provide a formal definition of RDF that includes the features that distinguish this model from other graph data models. We then move into the fundamental issue of querying RDF data. We start by considering the RDF query language SPARQL, which is a W3C Recommendation since January 2008. We provide an algebraic syntax and a compositional semantics for this language, study the complexity of the evaluation problem for different fragments of SPARQL, and consider the problem of optimizing the evaluation of SPARQL queries, showing that a natural fragment of this language has some good properties in this respect. We furthermore study the expressive power of SPARQL, by comparing it with some well-known query languages such as relational algebra. We conclude by considering the issue of querying RDF data in the presence of RDFS vocabulary. In particular, we present a recently proposed extension of SPARQL with navigational capabilities.

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.

Read Code Quality Assurance

PubMed Central

Schulz, Erich; Barrett, James W.; Price, Colin

1998-01-01

As controlled clinical vocabularies assume an increasing role in modern clinical information systems, so the issue of their quality demands greater attention. In order to meet the resulting stringent criteria for completeness and correctness, a quality assurance system comprising a database of more than 500 rules is being developed and applied to the Read Thesaurus. The authors discuss the requirement to apply quality assurance processes to their dynamic editing database in order to ensure the quality of exported products. Sources of errors include human, hardware, and software factors as well as new rules and transactions. The overall quality strategy includes prevention, detection, and correction of errors. The quality assurance process encompasses simple data specification, internal consistency, inspection procedures and, eventually, field testing. The quality assurance system is driven by a small number of tables and UNIX scripts, with “business rules” declared explicitly as Structured Query Language (SQL) statements. Concurrent authorship, client-server technology, and an initial failure to implement robust transaction control have all provided valuable lessons. The feedback loop for error management needs to be short. PMID:9670131

[Establishement for regional pelvic trauma database in Hunan Province].

PubMed

Cheng, Liang; Zhu, Yong; Long, Haitao; Yang, Junxiao; Sun, Buhua; Li, Kanghua

2017-04-28

To establish a database for pelvic trauma in Hunan Province, and to start the work of multicenter pelvic trauma registry.
 Methods: To establish the database, literatures relevant to pelvic trauma were screened, the experiences from the established trauma database in China and abroad were learned, and the actual situations for pelvic trauma rescue in Hunan Province were considered. The database for pelvic trauma was established based on the PostgreSQL and the advanced programming language Java 1.6.
 Results: The complex procedure for pelvic trauma rescue was described structurally. The contents for the database included general patient information, injurious condition, prehospital rescue, conditions in admission, treatment in hospital, status on discharge, diagnosis, classification, complication, trauma scoring and therapeutic effect. The database can be accessed through the internet by browser/servicer. The functions for the database include patient information management, data export, history query, progress report, video-image management and personal information management.
 Conclusion: The database with whole life cycle pelvic trauma is successfully established for the first time in China. It is scientific, functional, practical, and user-friendly.

Applications of GIS and database technologies to manage a Karst Feature Database

USGS Publications Warehouse

Gao, Y.; Tipping, R.G.; Alexander, E.C.

2006-01-01

This paper describes the management of a Karst Feature Database (KFD) in Minnesota. Two sets of applications in both GIS and Database Management System (DBMS) have been developed for the KFD of Minnesota. These applications were used to manage and to enhance the usability of the KFD. Structured Query Language (SQL) was used to manipulate transactions of the database and to facilitate the functionality of the user interfaces. The Database Administrator (DBA) authorized users with different access permissions to enhance the security of the database. Database consistency and recovery are accomplished by creating data logs and maintaining backups on a regular basis. The working database provides guidelines and management tools for future studies of karst features in Minnesota. The methodology of designing this DBMS is applicable to develop GIS-based databases to analyze and manage geomorphic and hydrologic datasets at both regional and local scales. The short-term goal of this research is to develop a regional KFD for the Upper Mississippi Valley Karst and the long-term goal is to expand this database to manage and study karst features at national and global scales.

Read Code quality assurance: from simple syntax to semantic stability.

PubMed

Schulz, E B; Barrett, J W; Price, C

1998-01-01

As controlled clinical vocabularies assume an increasing role in modern clinical information systems, so the issue of their quality demands greater attention. In order to meet the resulting stringent criteria for completeness and correctness, a quality assurance system comprising a database of more than 500 rules is being developed and applied to the Read Thesaurus. The authors discuss the requirement to apply quality assurance processes to their dynamic editing database in order to ensure the quality of exported products. Sources of errors include human, hardware, and software factors as well as new rules and transactions. The overall quality strategy includes prevention, detection, and correction of errors. The quality assurance process encompasses simple data specification, internal consistency, inspection procedures and, eventually, field testing. The quality assurance system is driven by a small number of tables and UNIX scripts, with "business rules" declared explicitly as Structured Query Language (SQL) statements. Concurrent authorship, client-server technology, and an initial failure to implement robust transaction control have all provided valuable lessons. The feedback loop for error management needs to be short.

An adaptable architecture for patient cohort identification from diverse data sources.

PubMed

Bache, Richard; Miles, Simon; Taweel, Adel

2013-12-01

We define and validate an architecture for systems that identify patient cohorts for clinical trials from multiple heterogeneous data sources. This architecture has an explicit query model capable of supporting temporal reasoning and expressing eligibility criteria independently of the representation of the data used to evaluate them. The architecture has the key feature that queries defined according to the query model are both pre and post-processed and this is used to address both structural and semantic heterogeneity. The process of extracting the relevant clinical facts is separated from the process of reasoning about them. A specific instance of the query model is then defined and implemented. We show that the specific instance of the query model has wide applicability. We then describe how it is used to access three diverse data warehouses to determine patient counts. Although the proposed architecture requires greater effort to implement the query model than would be the case for using just SQL and accessing a data-based management system directly, this effort is justified because it supports both temporal reasoning and heterogeneous data sources. The query model only needs to be implemented once no matter how many data sources are accessed. Each additional source requires only the implementation of a lightweight adaptor. The architecture has been used to implement a specific query model that can express complex eligibility criteria and access three diverse data warehouses thus demonstrating the feasibility of this approach in dealing with temporal reasoning and data heterogeneity.

PACSY, a relational database management system for protein structure and chemical shift analysis.

PubMed

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

An Expert System for Diagnosing Eye Diseases using Forward Chaining Method

NASA Astrophysics Data System (ADS)

Munaiseche, C. P. C.; Kaparang, D. R.; Rompas, P. T. D.

2018-02-01

Expert System is a system that seeks to adopt human knowledge to the computer, so that the computer can solve problems which are usually done by experts. The purpose of medical expert system is to support the diagnosis process of physicians. It considers facts and symptoms to provide diagnosis. This implies that a medical expert system uses knowledge about diseases and facts about the patients to suggest diagnosis. The aim of this research is to design an expert system application for diagnosing eye diseases using forward chaining method and to figure out user acceptance to this application through usability testing. Eye is selected because it is one of the five senses which is very sensitive and important. The scope of the work is extended to 16 types of eye diseases with 41 symptoms of the disease, arranged in 16 rules. The computer programming language employed was the PHP programming language and MySQL as the Relational Database Management System (RDBMS). The results obtained showed that the expert system was able to successfully diagnose eye diseases corresponding to the selected symptoms entered as query and the system evaluation through usability testing showed the expert system for diagnosis eye diseases had very good rate of usability, which includes learnability, efficiency, memorability, errors, and satisfaction so that the system can be received in the operational environment.

Experiments with Cross-Language Information Retrieval on a Health Portal for Psychology and Psychotherapy.

PubMed

Andrenucci, Andrea

2016-01-01

Few studies have been performed within cross-language information retrieval (CLIR) in the field of psychology and psychotherapy. The aim of this paper is to to analyze and assess the quality of available query translation methods for CLIR on a health portal for psychology. A test base of 100 user queries, 50 Multi Word Units (WUs) and 50 Single WUs, was used. Swedish was the source language and English the target language. Query translation methods based on machine translation (MT) and dictionary look-up were utilized in order to submit query translations to two search engines: Google Site Search and Quick Ask. Standard IR evaluation measures and a qualitative analysis were utilized to assess the results. The lexicon extracted with word alignment of the portal's parallel corpus provided better statistical results among dictionary look-ups. Google Translate provided more linguistically correct translations overall and also delivered better retrieval results in MT.

Interactive DataBase of Cosmic Ray Anisotropy (DB A10)

NASA Astrophysics Data System (ADS)

Asipenka, A.S.; Belov, A.V.; Eroshenko, E.F.; Klepach, E.G.; Oleneva, V.A.; Yake, V.G.

Data on the hourly means of cosmic ray density and anisotropy derived by the GSM method over the 1957-2006 are introduced in to MySQL database. This format allowed an access to data both in local and in the Internet. Using the realized combination of script-language Php and My SQL database the Internet project was created on the access for users data on the CR anisotropy in different formats (http://cr20.izmiran.ru/AnisotropyCR/main.htm/). Usage the sheaf Php and MySQL provides fast receiving data even in the Internet since a request and following process of data are accomplished on the project server. Usage of MySQL basis for the storing data on cosmic ray variations give a possibility to construct requests of different structures, extends the variety of data reflection, makes it possible the conformity data to other systems and usage them in other projects.

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.

Querying Event Sequences by Exact Match or Similarity Search: Design and Empirical Evaluation

PubMed Central

Wongsuphasawat, Krist; Plaisant, Catherine; Taieb-Maimon, Meirav; Shneiderman, Ben

2012-01-01

Specifying event sequence queries is challenging even for skilled computer professionals familiar with SQL. Most graphical user interfaces for database search use an exact match approach, which is often effective, but near misses may also be of interest. We describe a new similarity search interface, in which users specify a query by simply placing events on a blank timeline and retrieve a similarity-ranked list of results. Behind this user interface is a new similarity measure for event sequences which the users can customize by four decision criteria, enabling them to adjust the impact of missing, extra, or swapped events or the impact of time shifts. We describe a use case with Electronic Health Records based on our ongoing collaboration with hospital physicians. A controlled experiment with 18 participants compared exact match and similarity search interfaces. We report on the advantages and disadvantages of each interface and suggest a hybrid interface combining the best of both. PMID:22379286

STARS 2.0: 2nd-generation open-source archiving and query software

NASA Astrophysics Data System (ADS)

Winegar, Tom

2008-07-01

The Subaru Telescope is in process of developing an open-source alternative to the 1st-generation software and databases (STARS 1) used for archiving and query. For STARS 2, we have chosen PHP and Python for scripting and MySQL as the database software. We have collected feedback from staff and observers, and used this feedback to significantly improve the design and functionality of our future archiving and query software. Archiving - We identified two weaknesses in 1st-generation STARS archiving software: a complex and inflexible table structure and uncoordinated system administration for our business model: taking pictures from the summit and archiving them in both Hawaii and Japan. We adopted a simplified and normalized table structure with passive keyword collection, and we are designing an archive-to-archive file transfer system that automatically reports real-time status and error conditions and permits error recovery. Query - We identified several weaknesses in 1st-generation STARS query software: inflexible query tools, poor sharing of calibration data, and no automatic file transfer mechanisms to observers. We are developing improved query tools and sharing of calibration data, and multi-protocol unassisted file transfer mechanisms for observers. In the process, we have redefined a 'query': from an invisible search result that can only transfer once in-house right now, with little status and error reporting and no error recovery - to a stored search result that can be monitored, transferred to different locations with multiple protocols, reporting status and error conditions and permitting recovery from errors.

An adaptable architecture for patient cohort identification from diverse data sources

PubMed Central

Bache, Richard; Miles, Simon; Taweel, Adel

2013-01-01

Objective We define and validate an architecture for systems that identify patient cohorts for clinical trials from multiple heterogeneous data sources. This architecture has an explicit query model capable of supporting temporal reasoning and expressing eligibility criteria independently of the representation of the data used to evaluate them. Method The architecture has the key feature that queries defined according to the query model are both pre and post-processed and this is used to address both structural and semantic heterogeneity. The process of extracting the relevant clinical facts is separated from the process of reasoning about them. A specific instance of the query model is then defined and implemented. Results We show that the specific instance of the query model has wide applicability. We then describe how it is used to access three diverse data warehouses to determine patient counts. Discussion Although the proposed architecture requires greater effort to implement the query model than would be the case for using just SQL and accessing a data-based management system directly, this effort is justified because it supports both temporal reasoning and heterogeneous data sources. The query model only needs to be implemented once no matter how many data sources are accessed. Each additional source requires only the implementation of a lightweight adaptor. Conclusions The architecture has been used to implement a specific query model that can express complex eligibility criteria and access three diverse data warehouses thus demonstrating the feasibility of this approach in dealing with temporal reasoning and data heterogeneity. PMID:24064442

Efficient Queries of Stand-off Annotations for Natural Language Processing on Electronic Medical Records.

PubMed

Luo, Yuan; Szolovits, Peter

2016-01-01

In natural language processing, stand-off annotation uses the starting and ending positions of an annotation to anchor it to the text and stores the annotation content separately from the text. We address the fundamental problem of efficiently storing stand-off annotations when applying natural language processing on narrative clinical notes in electronic medical records (EMRs) and efficiently retrieving such annotations that satisfy position constraints. Efficient storage and retrieval of stand-off annotations can facilitate tasks such as mapping unstructured text to electronic medical record ontologies. We first formulate this problem into the interval query problem, for which optimal query/update time is in general logarithm. We next perform a tight time complexity analysis on the basic interval tree query algorithm and show its nonoptimality when being applied to a collection of 13 query types from Allen's interval algebra. We then study two closely related state-of-the-art interval query algorithms, proposed query reformulations, and augmentations to the second algorithm. Our proposed algorithm achieves logarithmic time stabbing-max query time complexity and solves the stabbing-interval query tasks on all of Allen's relations in logarithmic time, attaining the theoretic lower bound. Updating time is kept logarithmic and the space requirement is kept linear at the same time. We also discuss interval management in external memory models and higher dimensions.

Efficient Queries of Stand-off Annotations for Natural Language Processing on Electronic Medical Records

PubMed Central

Luo, Yuan; Szolovits, Peter

2016-01-01

In natural language processing, stand-off annotation uses the starting and ending positions of an annotation to anchor it to the text and stores the annotation content separately from the text. We address the fundamental problem of efficiently storing stand-off annotations when applying natural language processing on narrative clinical notes in electronic medical records (EMRs) and efficiently retrieving such annotations that satisfy position constraints. Efficient storage and retrieval of stand-off annotations can facilitate tasks such as mapping unstructured text to electronic medical record ontologies. We first formulate this problem into the interval query problem, for which optimal query/update time is in general logarithm. We next perform a tight time complexity analysis on the basic interval tree query algorithm and show its nonoptimality when being applied to a collection of 13 query types from Allen’s interval algebra. We then study two closely related state-of-the-art interval query algorithms, proposed query reformulations, and augmentations to the second algorithm. Our proposed algorithm achieves logarithmic time stabbing-max query time complexity and solves the stabbing-interval query tasks on all of Allen’s relations in logarithmic time, attaining the theoretic lower bound. Updating time is kept logarithmic and the space requirement is kept linear at the same time. We also discuss interval management in external memory models and higher dimensions. PMID:27478379

GraQL: A Query Language for High-Performance Attributed Graph Databases

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

Chavarría-Miranda, Daniel; Castellana, Vito G.; Morari, Alessandro

Graph databases have gained increasing interest in the last few years due to the emergence of data sources which are not easily analyzable in traditional relational models or for which a graph data model is the natural representation. In order to understand the design and implementation choices for an attributed graph database backend and query language, we have started to design our infrastructure for attributed graph databases. In this paper, we describe the design considerations of our in-memory attributed graph database system with a particular focus on the data definition and query language components.

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.

Connecting Provenance with Semantic Descriptions in the NASA Earth Exchange (NEX)

NASA Astrophysics Data System (ADS)

Votava, P.; Michaelis, A.; Nemani, R. R.

2012-12-01

NASA Earth Exchange (NEX) is a data, modeling and knowledge collaboratory that houses NASA satellite data, climate data and ancillary data where a focused community may come together to share modeling and analysis codes, scientific results, knowledge and expertise on a centralized platform. Some of the main goals of NEX are transparency and repeatability and to that extent we have been adding components that enable tracking of provenance of both scientific processes and datasets produced by these processes. As scientific processes become more complex, they are often developed collaboratively and it becomes increasingly important for the research team to be able to track the development of the process and the datasets that are produced along the way. Additionally, we want to be able to link the processes and the datasets developed on NEX to an existing information and knowledge, so that the users can query and compare the provenance of any dataset or process with regard to the component-specific attributes such as data quality, geographic location, related publications, user comments and annotations etc. We have developed several ontologies that describe datasets and workflow components available on NEX using the OWL ontology language as well as a simple ontology that provides linking mechanism to the collected provenance information. The provenance is captured in two ways - we utilize existing provenance infrastructure of VisTrails, which is used as a workflow engine on NEX, and we extend the captured provenance using the PROV data model expressed through the PROV-O ontology. We do this in order to link and query the provenance easier in the context of the existing NEX information and knowledge. The captured provenance graph is processed and stored using RDFlib with MySQL backend that can be queried using either RDFLib or SPARQL. As a concrete example, we show how this information is captured during anomaly detection process in large satellite datasets.

XGI: a graphical interface for XQuery creation.

PubMed

Li, Xiang; Gennari, John H; Brinkley, James F

2007-10-11

XML has become the default standard for data exchange among heterogeneous data sources, and in January 2007 XQuery (XML Query language) was recommended by the World Wide Web Consortium as the query language for XML. However, XQuery is a complex language that is difficult for non-programmers to learn. We have therefore developed XGI (XQuery Graphical Interface), a visual interface for graphically generating XQuery. In this paper we demonstrate the functionality of XGI through its application to a biomedical XML dataset. We describe the system architecture and the features of XGI in relation to several existing querying systems, we demonstrate the system's usability through a sample query construction, and we discuss a preliminary evaluation of XGI. Finally, we describe some limitations of the system, and our plans for future improvements.

PACSY, a relational database management system for protein structure and chemical shift analysis

PubMed Central

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

Hosting and pulishing astronomical data in SQL databases

NASA Astrophysics Data System (ADS)

Galkin, Anastasia; Klar, Jochen; Riebe, Kristin; Matokevic, Gal; Enke, Harry

2017-04-01

In astronomy, terabytes and petabytes of data are produced by ground instruments, satellite missions and simulations. At Leibniz-Institute for Astrophysics Potsdam (AIP) we host and publish terabytes of cosmological simulation and observational data. The public archive at AIP has now reached a size of 60TB and growing and helps to produce numerous scientific papers. The web framework Daiquiri offers a dedicated web interface for each of the hosted scientific databases. Scientists all around the world run SQL queries which include specific astrophysical functions and get their desired data in reasonable time. Daiquiri supports the scientific projects by offering a number of administration tools such as database and user management, contact messages to the staff and support for organization of meetings and workshops. The webpages can be customized and the Wordpress integration supports the participating scientists in maintaining the documentation and the projects' news sections.

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

An XML-Based Manipulation and Query Language for Rule-Based Information

NASA Astrophysics Data System (ADS)

Mansour, Essam; Höpfner, Hagen

Rules are utilized to assist in the monitoring process that is required in activities, such as disease management and customer relationship management. These rules are specified according to the application best practices. Most of research efforts emphasize on the specification and execution of these rules. Few research efforts focus on managing these rules as one object that has a management life-cycle. This paper presents our manipulation and query language that is developed to facilitate the maintenance of this object during its life-cycle and to query the information contained in this object. This language is based on an XML-based model. Furthermore, we evaluate the model and language using a prototype system applied to a clinical case study.

Photo-z-SQL: Integrated, flexible photometric redshift computation in a database

NASA Astrophysics Data System (ADS)

Beck, R.; Dobos, L.; Budavári, T.; Szalay, A. S.; Csabai, I.

2017-04-01

We present a flexible template-based photometric redshift estimation framework, implemented in C#, that can be seamlessly integrated into a SQL database (or DB) server and executed on-demand in SQL. The DB integration eliminates the need to move large photometric datasets outside a database for redshift estimation, and utilizes the computational capabilities of DB hardware. The code is able to perform both maximum likelihood and Bayesian estimation, and can handle inputs of variable photometric filter sets and corresponding broad-band magnitudes. It is possible to take into account the full covariance matrix between filters, and filter zero points can be empirically calibrated using measurements with given redshifts. The list of spectral templates and the prior can be specified flexibly, and the expensive synthetic magnitude computations are done via lazy evaluation, coupled with a caching of results. Parallel execution is fully supported. For large upcoming photometric surveys such as the LSST, the ability to perform in-place photo-z calculation would be a significant advantage. Also, the efficient handling of variable filter sets is a necessity for heterogeneous databases, for example the Hubble Source Catalog, and for cross-match services such as SkyQuery. We illustrate the performance of our code on two reference photo-z estimation testing datasets, and provide an analysis of execution time and scalability with respect to different configurations. The code is available for download at https://github.com/beckrob/Photo-z-SQL.

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.

Selecting the Best Mobile Information Service with Natural Language User Input

NASA Astrophysics Data System (ADS)

Feng, Qiangze; Qi, Hongwei; Fukushima, Toshikazu

Information services accessed via mobile phones provide information directly relevant to subscribers’ daily lives and are an area of dynamic market growth worldwide. Although many information services are currently offered by mobile operators, many of the existing solutions require a unique gateway for each service, and it is inconvenient for users to have to remember a large number of such gateways. Furthermore, the Short Message Service (SMS) is very popular in China and Chinese users would prefer to access these services in natural language via SMS. This chapter describes a Natural Language Based Service Selection System (NL3S) for use with a large number of mobile information services. The system can accept user queries in natural language and navigate it to the required service. Since it is difficult for existing methods to achieve high accuracy and high coverage and anticipate which other services a user might want to query, the NL3S is developed based on a Multi-service Ontology (MO) and Multi-service Query Language (MQL). The MO and MQL provide semantic and linguistic knowledge, respectively, to facilitate service selection for a user query and to provide adaptive service recommendations. Experiments show that the NL3S can achieve 75-95% accuracies and 85-95% satisfactions for processing various styles of natural language queries. A trial involving navigation of 30 different mobile services shows that the NL3S can provide a viable commercial solution for mobile operators.

Manchester visual query language

NASA Astrophysics Data System (ADS)

Oakley, John P.; Davis, Darryl N.; Shann, Richard T.

1993-04-01

We report a database language for visual retrieval which allows queries on image feature information which has been computed and stored along with images. The language is novel in that it provides facilities for dealing with feature data which has actually been obtained from image analysis. Each line in the Manchester Visual Query Language (MVQL) takes a set of objects as input and produces another, usually smaller, set as output. The MVQL constructs are mainly based on proven operators from the field of digital image analysis. An example is the Hough-group operator which takes as input a specification for the objects to be grouped, a specification for the relevant Hough space, and a definition of the voting rule. The output is a ranked list of high scoring bins. The query could be directed towards one particular image or an entire image database, in the latter case the bins in the output list would in general be associated with different images. We have implemented MVQL in two layers. The command interpreter is a Lisp program which maps each MVQL line to a sequence of commands which are used to control a specialized database engine. The latter is a hybrid graph/relational system which provides low-level support for inheritance and schema evolution. In the paper we outline the language and provide examples of useful queries. We also describe our solution to the engineering problems associated with the implementation of MVQL.

A New Publicly Available Chemical Query Language, CSRML ...

EPA Pesticide Factsheets

A new XML-based query language, CSRML, has been developed for representing chemical substructures, molecules, reaction rules, and reactions. CSRML queries are capable of integrating additional forms of information beyond the simple substructure (e.g., SMARTS) or reaction transformation (e.g., SMIRKS, reaction SMILES) queries currently in use. Chemotypes, a term used to represent advanced CSRML queries for repeated application can be encoded not only with connectivity and topology, but also with properties of atoms, bonds, electronic systems, or molecules. The CSRML language has been developed in parallel with a public set of chemotypes, i.e., the ToxPrint chemotypes, which are designed to provide excellent coverage of environmental, regulatory and commercial use chemical space, as well as to represent features and frameworks believed to be especially relevant to toxicity concerns. A software application, ChemoTyper, has also been developed and made publicly available to enable chemotype searching and fingerprinting against a target structure set. The public ChemoTyper houses the ToxPrint chemotype CSRML dictionary, as well as reference implementation so that the query specifications may be adopted by other chemical structure knowledge systems. The full specifications of the XML standard used in CSRML-based chemotypes are publicly available to facilitate and encourage the exchange of structural knowledge. Paper details specifications for a new XML-based query lan

Efficiently Distributing Component-Based Applications Across Wide-Area Environments

DTIC Science & Technology

2002-01-01

Oracle 8.1.7 Enterprise Edition), each running on a dedicated 1GHz dual-processor Pentium III workstation. For the RUBiS tests, we used a MySQL 4.0.12...a variety of sophisticated network-accessible services such as e-mail, banking, on-line shopping, entertainment, and serv - ing as a data exchange...Beans Catalog Handles read-only queries to product database Customer Serves as a façade to Order and Account Stateful Session Beans ShoppingCart

Auxiliary Library Explorer (ALEX) Development

DTIC Science & Technology

2016-02-01

non-empty cells. This is a laborious manual task and could probably have been avoided by using Java code to read the data directly from Excel. In fact...it might be even easier to leave the data as a comma separated variables (CSV) file and read the data in with Java , although this could create other...This is first implemented using the MakeFullDatabaseapp Java project, which performs an SQL query on the DSpace data to return a list of items for which

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

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.…

A Text Knowledge Base from the AI Handbook.

ERIC Educational Resources Information Center

Simmons, Robert F.

1987-01-01

Describes a prototype natural language text knowledge system (TKS) that was used to organize 50 pages of a handbook on artificial intelligence as an inferential knowledge base with natural language query and command capabilities. Representation of text, database navigation, query systems, discourse structuring, and future research needs are…

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

Assembling proteomics data as a prerequisite for the analysis of large scale experiments

PubMed Central

Schmidt, Frank; Schmid, Monika; Thiede, Bernd; Pleißner, Klaus-Peter; Böhme, Martina; Jungblut, Peter R

2009-01-01

Background Despite the complete determination of the genome sequence of a huge number of bacteria, their proteomes remain relatively poorly defined. Beside new methods to increase the number of identified proteins new database applications are necessary to store and present results of large- scale proteomics experiments. Results In the present study, a database concept has been developed to address these issues and to offer complete information via a web interface. In our concept, the Oracle based data repository system SQL-LIMS plays the central role in the proteomics workflow and was applied to the proteomes of Mycobacterium tuberculosis, Helicobacter pylori, Salmonella typhimurium and protein complexes such as 20S proteasome. Technical operations of our proteomics labs were used as the standard for SQL-LIMS template creation. By means of a Java based data parser, post-processed data of different approaches, such as LC/ESI-MS, MALDI-MS and 2-D gel electrophoresis (2-DE), were stored in SQL-LIMS. A minimum set of the proteomics data were transferred in our public 2D-PAGE database using a Java based interface (Data Transfer Tool) with the requirements of the PEDRo standardization. Furthermore, the stored proteomics data were extractable out of SQL-LIMS via XML. Conclusion The Oracle based data repository system SQL-LIMS played the central role in the proteomics workflow concept. Technical operations of our proteomics labs were used as standards for SQL-LIMS templates. Using a Java based parser, post-processed data of different approaches such as LC/ESI-MS, MALDI-MS and 1-DE and 2-DE were stored in SQL-LIMS. Thus, unique data formats of different instruments were unified and stored in SQL-LIMS tables. Moreover, a unique submission identifier allowed fast access to all experimental data. This was the main advantage compared to multi software solutions, especially if personnel fluctuations are high. Moreover, large scale and high-throughput experiments must be managed in a comprehensive repository system such as SQL-LIMS, to query results in a systematic manner. On the other hand, these database systems are expensive and require at least one full time administrator and specialized lab manager. Moreover, the high technical dynamics in proteomics may cause problems to adjust new data formats. To summarize, SQL-LIMS met the requirements of proteomics data handling especially in skilled processes such as gel-electrophoresis or mass spectrometry and fulfilled the PSI standardization criteria. The data transfer into a public domain via DTT facilitated validation of proteomics data. Additionally, evaluation of mass spectra by post-processing using MS-Screener improved the reliability of mass analysis and prevented storage of data junk. PMID:19166578

Path querying system on mobile devices

NASA Astrophysics Data System (ADS)

Lin, Xing; Wang, Yifei; Tian, Yuan; Wu, Lun

2006-01-01

Traditional approaches to path querying problems are not efficient and convenient under most circumstances. A more convenient and reliable approach to this problem has to be found. This paper is devoted to a path querying solution on mobile devices. By using an improved Dijkstra's shortest path algorithm and a natural language translating module, this system can help people find the shortest path between two places through their cell phones or other mobile devices. The chosen path is prompted in text of natural language, as well as a map picture. This system would be useful in solving best path querying problems and have potential to be a profitable business system.

mantisGRID: a grid platform for DICOM medical images management in Colombia and Latin America.

PubMed

Garcia Ruiz, Manuel; Garcia Chaves, Alvin; Ruiz Ibañez, Carlos; Gutierrez Mazo, Jorge Mario; Ramirez Giraldo, Juan Carlos; Pelaez Echavarria, Alejandro; Valencia Diaz, Edison; Pelaez Restrepo, Gustavo; Montoya Munera, Edwin Nelson; Garcia Loaiza, Bernardo; Gomez Gonzalez, Sebastian

2011-04-01

This paper presents the mantisGRID project, an interinstitutional initiative from Colombian medical and academic centers aiming to provide medical grid services for Colombia and Latin America. The mantisGRID is a GRID platform, based on open source grid infrastructure that provides the necessary services to access and exchange medical images and associated information following digital imaging and communications in medicine (DICOM) and health level 7 standards. The paper focuses first on the data abstraction architecture, which is achieved via Open Grid Services Architecture Data Access and Integration (OGSA-DAI) services and supported by the Globus Toolkit. The grid currently uses a 30-Mb bandwidth of the Colombian High Technology Academic Network, RENATA, connected to Internet 2. It also includes a discussion on the relational database created to handle the DICOM objects that were represented using Extensible Markup Language Schema documents, as well as other features implemented such as data security, user authentication, and patient confidentiality. Grid performance was tested using the three current operative nodes and the results demonstrated comparable query times between the mantisGRID (OGSA-DAI) and Distributed mySQL databases, especially for a large number of records.

Naturally Occurring Human Urinary Peptides for Use in Diagnosis of Chronic Kidney Disease*

PubMed Central

Good, David M.; Zürbig, Petra; Argilés, Àngel; Bauer, Hartwig W.; Behrens, Georg; Coon, Joshua J.; Dakna, Mohammed; Decramer, Stéphane; Delles, Christian; Dominiczak, Anna F.; Ehrich, Jochen H. H.; Eitner, Frank; Fliser, Danilo; Frommberger, Moritz; Ganser, Arnold; Girolami, Mark A.; Golovko, Igor; Gwinner, Wilfried; Haubitz, Marion; Herget-Rosenthal, Stefan; Jankowski, Joachim; Jahn, Holger; Jerums, George; Julian, Bruce A.; Kellmann, Markus; Kliem, Volker; Kolch, Walter; Krolewski, Andrzej S.; Luppi, Mario; Massy, Ziad; Melter, Michael; Neusüss, Christian; Novak, Jan; Peter, Karlheinz; Rossing, Kasper; Rupprecht, Harald; Schanstra, Joost P.; Schiffer, Eric; Stolzenburg, Jens-Uwe; Tarnow, Lise; Theodorescu, Dan; Thongboonkerd, Visith; Vanholder, Raymond; Weissinger, Eva M.; Mischak, Harald; Schmitt-Kopplin, Philippe

2010-01-01

Because of its availability, ease of collection, and correlation with physiology and pathology, urine is an attractive source for clinical proteomics/peptidomics. However, the lack of comparable data sets from large cohorts has greatly hindered the development of clinical proteomics. Here, we report the establishment of a reproducible, high resolution method for peptidome analysis of naturally occurring human urinary peptides and proteins, ranging from 800 to 17,000 Da, using samples from 3,600 individuals analyzed by capillary electrophoresis coupled to MS. All processed data were deposited in an Structured Query Language (SQL) database. This database currently contains 5,010 relevant unique urinary peptides that serve as a pool of potential classifiers for diagnosis and monitoring of various diseases. As an example, by using this source of information, we were able to define urinary peptide biomarkers for chronic kidney diseases, allowing diagnosis of these diseases with high accuracy. Application of the chronic kidney disease-specific biomarker set to an independent test cohort in the subsequent replication phase resulted in 85.5% sensitivity and 100% specificity. These results indicate the potential usefulness of capillary electrophoresis coupled to MS for clinical applications in the analysis of naturally occurring urinary peptides. PMID:20616184

Domain fusion analysis by applying relational algebra to protein sequence and domain databases

PubMed Central

Truong, Kevin; Ikura, Mitsuhiko

2003-01-01

Background Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. Results This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at . Conclusion As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time. PMID:12734020

[OISO, automatic treatment of patients management in oncogenetics].

PubMed

Guien, Céline; Fabre, Aurélie; Lagarde, Arnaud; Salgado, David; Gensollen-Thiriez, Catherine; Zattara, Hélène; Beroud, Christophe; Olschwang, Sylviane

Oncogenetics is a long-term process, which requires a close relation between patients and medical teams, good familial links allowing lifetime follow-up. Numerous documents are exchanged in between the medical team, which has to frequently interact. We present here a new tool that has been conceived specifically for this management. The tool has been developed according to a model-view-controler approach with the relational system PostgreSQL 9.3. The web site used PHP 5.3, HTML5 and CSS3 languages, completed with JavaScript and jQuery-AJAX functions and two additional modules, FPDF and PHPMailer. The tool allows multiple interactions, clinical data management, mailing and emailing, follow-up plannings. Requests are able to follow all patients and planning automatically, to send information to a large number of patients or physicians, and to report activity. The tool has been designed for oncogenetics and adapted to its different aspects. The CNIL delivered an authorization for use. Secured web access allows the management at a regional level. Its simple concept makes it evolutive according to the constant updates of genetic and clinical management of patients. Copyright © 2017 Société Française du Cancer. Published by Elsevier Masson SAS. All rights reserved.

Salary Management System for Small and Medium-sized Enterprises

NASA Astrophysics Data System (ADS)

Hao, Zhang; Guangli, Xu; Yuhuan, Zhang; Yilong, Lei

Small and Medium-sized Enterprises (SMEs) in the process of wage entry, calculation, the total number are needed to be done manually in the past, the data volume is quite large, processing speed is low, and it is easy to make error, which is resulting in low efficiency. The main purpose of writing this paper is to present the basis of salary management system, establish a scientific database, the computer payroll system, using the computer instead of a lot of past manual work in order to reduce duplication of staff labor, it will improve working efficiency.This system combines the actual needs of SMEs, through in-depth study and practice of the C/S mode, PowerBuilder10.0 development tools, databases and SQL language, Completed a payroll system needs analysis, database design, application design and development work. Wages, departments, units and personnel database file are included in this system, and have data management, department management, personnel management and other functions, through the control and management of the database query, add, delete, modify, and other functions can be realized. This system is reasonable design, a more complete function, stable operation has been tested to meet the basic needs of the work.

Extending the Query Language of a Data Warehouse for Patient Recruitment.

PubMed

Dietrich, Georg; Ertl, Maximilian; Fette, Georg; Kaspar, Mathias; Krebs, Jonathan; Mackenrodt, Daniel; Störk, Stefan; Puppe, Frank

2017-01-01

Patient recruitment for clinical trials is a laborious task, as many texts have to be screened. Usually, this work is done manually and takes a lot of time. We have developed a system that automates the screening process. Besides standard keyword queries, the query language supports extraction of numbers, time-spans and negations. In a feasibility study for patient recruitment from a stroke unit with 40 patients, we achieved encouraging extraction rates above 95% for numbers and negations and ca. 86% for time spans.

OnlineTED.com--a novel web-based audience response system for higher education. A pilot study to evaluate user acceptance.

PubMed

Kühbeck, Felizian; Engelhardt, Stefan; Sarikas, Antonio

2014-01-01

Audience response (AR) systems are increasingly used in undergraduate medical education. However, high costs and complexity of conventional AR systems often limit their use. Here we present a novel AR system that is platform independent and does not require hardware clickers or additional software to be installed. "OnlineTED" was developed at Technische Universität München (TUM) based on Hypertext Preprocessor (PHP) with a My Structured Query Language (MySQL)-database as server- and Javascript as client-side programming languages. "OnlineTED" enables lecturers to create and manage question sets online and start polls in-class via a web-browser. Students can participate in the polls with any internet-enabled device (smartphones, tablet-PCs or laptops). A paper-based survey was conducted with undergraduate medical students and lecturers at TUM to compare "OnlineTED" with conventional AR systems using clickers. "OnlineTED" received above-average evaluation results by both students and lecturers at TUM and was seen on par or superior to conventional AR systems. The survey results indicated that up to 80% of students at TUM own an internet-enabled device (smartphone or tablet-PC) for participation in web-based AR technologies. "OnlineTED" is a novel web-based and platform-independent AR system for higher education that was well received by students and lecturers. As a non-commercial alternative to conventional AR systems it may foster interactive teaching in undergraduate education, in particular with large audiences.

Regular paths in SparQL: querying the NCI Thesaurus.

PubMed

Detwiler, Landon T; Suciu, Dan; Brinkley, James F

2008-11-06

OWL, the Web Ontology Language, provides syntax and semantics for representing knowledge for the semantic web. Many of the constructs of OWL have a basis in the field of description logics. While the formal underpinnings of description logics have lead to a highly computable language, it has come at a cognitive cost. OWL ontologies are often unintuitive to readers lacking a strong logic background. In this work we describe GLEEN, a regular path expression library, which extends the RDF query language SparQL to support complex path expressions over OWL and other RDF-based ontologies. We illustrate the utility of GLEEN by showing how it can be used in a query-based approach to defining simpler, more intuitive views of OWL ontologies. In particular we show how relatively simple GLEEN-enhanced SparQL queries can create views of the OWL version of the NCI Thesaurus that match the views generated by the web-based NCI browser.

The NOAO Data Lab PHAT Photometry Database

NASA Astrophysics Data System (ADS)

Olsen, Knut; Williams, Ben; Fitzpatrick, Michael; PHAT Team

2018-01-01

We present a database containing both the combined photometric object catalog and the single epoch measurements from the Panchromatic Hubble Andromeda Treasury (PHAT). This database is hosted by the NOAO Data Lab (http://datalab.noao.edu), and as such exposes a number of data services to the PHAT photometry, including access through a Table Access Protocol (TAP) service, direct PostgreSQL queries, web-based and programmatic query interfaces, remote storage space for personal database tables and files, and a JupyterHub-based Notebook analysis environment, as well as image access through a Simple Image Access (SIA) service. We show how the Data Lab database and Jupyter Notebook environment allow for straightforward and efficient analyses of PHAT catalog data, including maps of object density, depth, and color, extraction of light curves of variable objects, and proper motion exploration.

A natural language query system for Hubble Space Telescope proposal selection

NASA Technical Reports Server (NTRS)

Hornick, Thomas; Cohen, William; Miller, Glenn

1987-01-01

The proposal selection process for the Hubble Space Telescope is assisted by a robust and easy to use query program (TACOS). The system parses an English subset language sentence regardless of the order of the keyword phases, allowing the user a greater flexibility than a standard command query language. Capabilities for macro and procedure definition are also integrated. The system was designed for flexibility in both use and maintenance. In addition, TACOS can be applied to any knowledge domain that can be expressed in terms of a single reaction. The system was implemented mostly in Common LISP. The TACOS design is described in detail, with particular attention given to the implementation methods of sentence processing.

Find the fish: using PROC SQL to build a relational database

USGS Publications Warehouse

Fabrizio, Mary C.; Nelson, Scott N.

1995-01-01

Reliable estimates of abundance and survival, gained through mark-recapture studies, are necessary to better understand how to manage and restore lake trout populations in the Great Lakes. Working with a 24-year data set from a mark-recapture study conducted in Lake Superior, we attempted to disclose information on tag shedding by examining recaptures of double-tagged fish. The data set consisted of 64,288 observations on fish which had been marked with one or more tags; a subset of these fish had been marked with two tags at initial capture. Although DATA and PROC statements could be used to obtain some of the information we sought, these statements could not be used to extract a complete set of results from the double-tagging experiments. We therefore used SQL processing to create three tables representing the same information but in a fully normalized relational structure. In addition, we created indices to efficiently examine complex relationships among the individual capture records. This approach allowed us to obtain all the information necessary to estimate tag retention through subsequent modeling. We believe that our success with SQL was due in large part to its ability to simultaneosly scan the same table more than once and to permit consideration of other tables in sub-queries.

Design of an On-Line Query Language for Full Text Patent Search.

ERIC Educational Resources Information Center

Glantz, Richard S.

The design of an English-like query language and an interactive computer environment for searching the full text of the U.S. patent collection are discussed. Special attention is paid to achieving a transparent user interface, to providing extremely broad search capabilities (including nested substitution classes, Kleene star events, and domain…

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.

Querying clinical data in HL7 RIM based relational model with morph-RDB.

PubMed

Priyatna, Freddy; Alonso-Calvo, Raul; Paraiso-Medina, Sergio; Corcho, Oscar

2017-10-05

Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to heterogeneous data sources. One possible approach to accommodate this need is to use RDB2RDF systems that provide RDF datasets as the unified view. These RDF datasets may be materialized and stored in a triple store, or transformed into RDF in real time, as virtual RDF data sources. Our previous efforts involved materialized RDF datasets, hence losing data freshness. In this paper we present a solution that uses an ontology based on the HL7 v3 Reference Information Model and a set of R2RML mappings that relate this ontology to an underlying relational database implementation, and where morph-RDB is used to expose a virtual, non-materialized SPARQL endpoint over the data. By applying a set of optimization techniques on the SPARQL-to-SQL query translation algorithm, we can now issue SPARQL queries to the underlying relational data with generally acceptable performance.

Prototype of Multifunctional Full-text Library in the Architecture Web-browser / Web-server / SQL-server

NASA Astrophysics Data System (ADS)

Lyapin, Sergey; Kukovyakin, Alexey

Within the framework of the research program "Textaurus" an operational prototype of multifunctional library T-Libra v.4.1. has been created which makes it possible to carry out flexible parametrizable search within a full-text database. The information system is realized in the architecture Web-browser / Web-server / SQL-server. This allows to achieve an optimal combination of universality and efficiency of text processing, on the one hand, and convenience and minimization of expenses for an end user (due to applying of a standard Web-browser as a client application), on the other one. The following principles underlie the information system: a) multifunctionality, b) intelligence, c) multilingual primary texts and full-text searching, d) development of digital library (DL) by a user ("administrative client"), e) multi-platform working. A "library of concepts", i.e. a block of functional models of semantic (concept-oriented) searching, as well as a subsystem of parametrizable queries to a full-text database, which is closely connected with the "library", serve as a conceptual basis of multifunctionality and "intelligence" of the DL T-Libra v.4.1. An author's paragraph is a unit of full-text searching in the suggested technology. At that, the "logic" of an educational / scientific topic or a problem can be built in a multilevel flexible structure of a query and the "library of concepts", replenishable by the developers and experts. About 10 queries of various level of complexity and conceptuality are realized in the suggested version of the information system: from simple terminological searching (taking into account lexical and grammatical paradigms of Russian) to several kinds of explication of terminological fields and adjustable two-parameter thematic searching (a [set of terms] and a [distance between terms] within the limits of an author's paragraph are such parameters correspondingly).

WE-E-BRB-11: Riview a Web-Based Viewer for Radiotherapy.

PubMed

Apte, A; Wang, Y; Deasy, J

2012-06-01

Collaborations involving radiotherapy data collection, such as the recently proposed international radiogenomics consortium, require robust, web-based tools to facilitate reviewing treatment planning information. We present the architecture and prototype characteristics for a web-based radiotherapy viewer. The web-based environment developed in this work consists of the following components: 1) Import of DICOM/RTOG data: CERR was leveraged to import DICOM/RTOG data and to convert to database friendly RT objects. 2) Extraction and Storage of RT objects: The scan and dose distributions were stored as .png files per slice and view plane. The file locations were written to the MySQL database. Structure contours and DVH curves were written to the database as numeric data. 3) Web interfaces to query, retrieve and visualize the RT objects: The Web application was developed using HTML 5 and Ruby on Rails (RoR) technology following the MVC philosophy. The open source ImageMagick library was utilized to overlay scan, dose and structures. The application allows users to (i) QA the treatment plans associated with a study, (ii) Query and Retrieve patients matching anonymized ID and study, (iii) Review up to 4 plans simultaneously in 4 window panes (iv) Plot DVH curves for the selected structures and dose distributions. A subset of data for lung cancer patients was used to prototype the system. Five user accounts were created to have access to this study. The scans, doses, structures and DVHs for 10 patients were made available via the web application. A web-based system to facilitate QA, and support Query, Retrieve and the Visualization of RT data was prototyped. The RIVIEW system was developed using open source and free technology like MySQL and RoR. We plan to extend the RIVIEW system further to be useful in clinical trial data collection, outcomes research, cohort plan review and evaluation. © 2012 American Association of Physicists in Medicine.

SP2Bench: A SPARQL Performance Benchmark

NASA Astrophysics Data System (ADS)

Schmidt, Michael; Hornung, Thomas; Meier, Michael; Pinkel, Christoph; Lausen, Georg

A meaningful analysis and comparison of both existing storage schemes for RDF data and evaluation approaches for SPARQL queries necessitates a comprehensive and universal benchmark platform. We present SP2Bench, a publicly available, language-specific performance benchmark for the SPARQL query language. SP2Bench is settled in the DBLP scenario and comprises a data generator for creating arbitrarily large DBLP-like documents and a set of carefully designed benchmark queries. The generated documents mirror vital key characteristics and social-world distributions encountered in the original DBLP data set, while the queries implement meaningful requests on top of this data, covering a variety of SPARQL operator constellations and RDF access patterns. In this chapter, we discuss requirements and desiderata for SPARQL benchmarks and present the SP2Bench framework, including its data generator, benchmark queries and performance metrics.

EpiGeNet: A Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer.

PubMed

Balaur, Irina; Saqi, Mansoor; Barat, Ana; Lysenko, Artem; Mazein, Alexander; Rawlings, Christopher J; Ruskin, Heather J; Auffray, Charles

2017-10-01

The development of colorectal cancer (CRC)-the third most common cancer type-has been associated with deregulations of cellular mechanisms stimulated by both genetic and epigenetic events. StatEpigen is a manually curated and annotated database, containing information on interdependencies between genetic and epigenetic signals, and specialized currently for CRC research. Although StatEpigen provides a well-developed graphical user interface for information retrieval, advanced queries involving associations between multiple concepts can benefit from more detailed graph representation of the integrated data. This can be achieved by using a graph database (NoSQL) approach. Data were extracted from StatEpigen and imported to our newly developed EpiGeNet, a graph database for storage and querying of conditional relationships between molecular (genetic and epigenetic) events observed at different stages of colorectal oncogenesis. We illustrate the enhanced capability of EpiGeNet for exploration of different queries related to colorectal tumor progression; specifically, we demonstrate the query process for (i) stage-specific molecular events, (ii) most frequently observed genetic and epigenetic interdependencies in colon adenoma, and (iii) paths connecting key genes reported in CRC and associated events. The EpiGeNet framework offers improved capability for management and visualization of data on molecular events specific to CRC initiation and progression.

Omicseq: a web-based search engine for exploring omics datasets

PubMed Central

Sun, Xiaobo; Pittard, William S.; Xu, Tianlei; Chen, Li; Zwick, Michael E.; Jiang, Xiaoqian; Wang, Fusheng

2017-01-01

Abstract The development and application of high-throughput genomics technologies has resulted in massive quantities of diverse omics data that continue to accumulate rapidly. These rich datasets offer unprecedented and exciting opportunities to address long standing questions in biomedical research. However, our ability to explore and query the content of diverse omics data is very limited. Existing dataset search tools rely almost exclusively on the metadata. A text-based query for gene name(s) does not work well on datasets wherein the vast majority of their content is numeric. To overcome this barrier, we have developed Omicseq, a novel web-based platform that facilitates the easy interrogation of omics datasets holistically to improve ‘findability’ of relevant data. The core component of Omicseq is trackRank, a novel algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. The Omicseq system is supported by a scalable and elastic, NoSQL database that hosts a large collection of processed omics datasets. In the front end, a simple, web-based interface allows users to enter queries and instantly receive search results as a list of ranked datasets deemed to be the most relevant. Omicseq is freely available at http://www.omicseq.org. PMID:28402462

Recent Evolution of the CDS Services - SIMBAD, VizieR and Aladin

NASA Astrophysics Data System (ADS)

Genova, F.; Allen, M. G.; Bienayme, O.; Boch, T.; Bonnarel, F.; Cambresy, L.; Derriere, S.; Dubois, P.; Fernique, P.; Lesteven, S.; Loup, C.; Ochsenbein, F.; Schaaff, A.; Vollmer, B.; Wenger, M.; Louys, M.; Jasniewicz, G.; Davoust, E.

2005-12-01

The Centre de Donnees astronomiques de Strasbourg (CDS) maintains several widely used databases and services. Among significant recent evolutions: - a new version of SIMBAD (SIMBAD 4), based on the PostgreSQL database system, has been developed, to replace the current version which has been operational since 1990. It allows new query and sampling possibilities. For accessing SIMBAD from other applications, a full Web Service will be made available in addition to the client-server program which is presently used as name resolver by many services. - VizieR, which gives access to major surveys, observation logs and tables published in journals, is continuously updated in collaboration with journals and ground- and space-based observatories. The diversity of information in VizieR makes it an excellent test-bed for the Virtual Observatory, in particular for the definition of astronomy semantics and of query language, and the implementation of registries. - a major update of Aladin (Aladin V3 Multiview) was released in April 2005. It integrates in particular a multiview display, image resampling, blinking, access to real pixel values (not only 8 bits), compatibility with common image formats such as GIF, JPEG and PNG, scaling functions for better pixel contrasts, a 'Region of Interest Generator' which automatically builds small views around catalog objects, a cross-match function, the possibility to compute new catalog colums via algebraic expressions, extended script commands for batch mode use, and access to additional data such as SDSS. Aladin is routinely used as a portal to the Virtual Observatory. Many of the new functions have been prototyped in the frame of the European Astrophysical Virtual Observatory project, and other are tested for the VO-TECH project.

An expression database for roots of the model legume Medicago truncatula under salt stress

PubMed Central

2009-01-01

Background Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes. Description The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database. Conclusion MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/. PMID:19906315

An expression database for roots of the model legume Medicago truncatula under salt stress.

PubMed

Li, Daofeng; Su, Zhen; Dong, Jiangli; Wang, Tao

2009-11-11

Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes. The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database. MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/.

Working with HITRAN Database Using Hapi: HITRAN Application Programming Interface

NASA Astrophysics Data System (ADS)

Kochanov, Roman V.; Hill, Christian; Wcislo, Piotr; Gordon, Iouli E.; Rothman, Laurence S.; Wilzewski, Jonas

2015-06-01

A HITRAN Application Programing Interface (HAPI) has been developed to allow users on their local machines much more flexibility and power. HAPI is a programming interface for the main data-searching capabilities of the new "HITRANonline" web service (http://www.hitran.org). It provides the possibility to query spectroscopic data from the HITRAN database in a flexible manner using either functions or query language. Some of the prominent current features of HAPI are: a) Downloading line-by-line data from the HITRANonline site to a local machine b) Filtering and processing the data in SQL-like fashion c) Conventional Python structures (lists, tuples, and dictionaries) for representing spectroscopic data d) Possibility to use a large set of third-party Python libraries to work with the data e) Python implementation of the HT lineshape which can be reduced to a number of conventional line profiles f) Python implementation of total internal partition sums (TIPS-2011) for spectra simulations g) High-resolution spectra calculation accounting for pressure, temperature and optical path length h) Providing instrumental functions to simulate experimental spectra i) Possibility to extend HAPI's functionality by custom line profiles, partitions sums and instrumental functions Currently the API is a module written in Python and uses Numpy library providing fast array operations. The API is designed to deal with data in multiple formats such as ASCII, CSV, HDF5 and XSAMS. This work has been supported by NASA Aura Science Team Grant NNX14AI55G and NASA Planetary Atmospheres Grant NNX13AI59G. L.S. Rothman et al. JQSRT, Volume 130, 2013, Pages 4-50 N.H. Ngo et al. JQSRT, Volume 129, November 2013, Pages 89-100 A. L. Laraia at al. Icarus, Volume 215, Issue 1, September 2011, Pages 391-400

Regional Differences in Thrombectomy Rates : Secondary use of Billing Codes in the MIRACUM (Medical Informatics for Research and Care in University Medicine) Consortium.

PubMed

Haverkamp, Christian; Ganslandt, Thomas; Horki, Petar; Boeker, Martin; Dörfler, Arnd; Schwab, Stefan; Berkefeld, Joachim; Pfeilschifter, Waltraud; Niesen, Wolf-Dirk; Egger, Karl; Kaps, Manfred; Brockmann, Marc A; Neumaier-Probst, Eva; Szabo, Kristina; Skalej, Martin; Bien, Siegfried; Best, Christoph; Prokosch, Hans-Ulrich; Urbach, Horst

2018-01-08

Mechanical thrombectomy, in addition to intravenous (i.v.) thrombolysis is recommended for treatment of acute stroke in patients with large vessel occlusions (LVO) in the anterior circulation up to 6 h after symptom onset. We compared thrombectomy rates of eight university hospitals of the MIRACUM consortium to analyze the implementation of this guideline in clinical routine. Anonymized billing data in a standardized format were loaded into a local i2b2 data warehouse by applying already existing extract, transform and load (ETL) routines. A locally executed uniform SQL (structured query language) query delivered aggregated site data for all inpatients with a discharge diagnosis of ischemic stroke (ICD-10 I63) containing counts for type of acute treatment, type of admission and age groups, which were centrally analyzed with R. From 2014 to 2016, the thrombectomy rate almost doubled from a mean of 4.7% to 9.6%, although significant differences between centers exist (range in 2016: 5.8-17%). The number of drip-and-ship procedures increased in 3 out of 8 centers. There was no evidence for a decrease in thrombectomy rates during weekends/holiday or among patients older than 80 years, but this age group is more likely to receive i.v. recombinant tissue plasminogen activator (rtPA). The observed increase of thrombectomy rates and drip-and-ship procedures without a significant difference between weekdays and weekends or patients of different ages is substantiating a rapid implementation of stroke guidelines within the analyzed neurovascular centers. The prototype of the MIRACUM Data Integration Center already contributes to health services research in Germany.

Natural language query system design for interactive information storage and retrieval systems. Presentation visuals. M.S. Thesis Final Report, 1 Jul. 1985 - 31 Dec. 1987

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Liu, I-Hsiung

1985-01-01

This Working Paper Series entry represents a collection of presentation visuals associated with the companion report entitled Natural Language Query System Design for Interactive Information Storage and Retrieval Systems, USL/DBMS NASA/RECON Working Paper Series report number DBMS.NASA/RECON-17.

The Effectiveness of Stemming for Natural-Language Access to Slovene Textual Data.

ERIC Educational Resources Information Center

Popovic, Mirko; Willett, Peter

1992-01-01

Reports on the use of stemming for Slovene language documents and queries in free-text retrieval systems and demonstrates that an appropriate stemming algorithm results in an increase in retrieval effectiveness when compared with nonstemming processing. A comparison is made with stemming of English versions of the same documents and queries. (24…

A Role Calculus for ORM

NASA Astrophysics Data System (ADS)

Curland, Matthew; Halpin, Terry; Stirewalt, Kurt

A conceptual schema of an information system specifies the fact structures of interest as well as related business rules that are either constraints or derivation rules. Constraints restrict the possible or permitted states or state transitions, while derivation rules enable some facts to be derived from others. Graphical languages are commonly used to specify conceptual schemas, but often need to be supplemented by more expressive textual languages to capture additional business rules, as well as conceptual queries that enable conceptual models to be queried directly. This paper describes research to provide a role calculus to underpin textual languages for Object-Role Modeling (ORM), to enable business rules and queries to be formulated in a language intelligible to business users. The role-based nature of this calculus, which exploits the attribute-free nature of ORM, appears to offer significant advantages over other proposed approaches, especially in the area of semantic stability.

A JEE RESTful service to access Conditions Data in ATLAS

NASA Astrophysics Data System (ADS)

Formica, Andrea; Gallas, E. J.

2015-12-01

Usage of condition data in ATLAS is extensive for offline reconstruction and analysis (e.g. alignment, calibration, data quality). The system is based on the LCG Conditions Database infrastructure, with read and write access via an ad hoc C++ API (COOL), a system which was developed before Run 1 data taking began. The infrastructure dictates that the data is organized into separate schemas (assigned to subsystems/groups storing distinct and independent sets of conditions), making it difficult to access information from several schemas at the same time. We have thus created PL/SQL functions containing queries to provide content extraction at multi-schema level. The PL/SQL API has been exposed to external clients by means of a Java application providing DB access via REST services, deployed inside an application server (JBoss WildFly). The services allow navigation over multiple schemas via simple URLs. The data can be retrieved either in XML or JSON formats, via simple clients (like curl or Web browsers).

A Web-based Tool for SDSS and 2MASS Database Searches

NASA Astrophysics Data System (ADS)

Hendrickson, M. A.; Uomoto, A.; Golimowski, D. A.

We have developed a web site using HTML, Php, Python, and MySQL that extracts, processes, and displays data from the Sloan Digital Sky Survey (SDSS) and the Two-Micron All-Sky Survey (2MASS). The goal is to locate brown dwarf candidates in the SDSS database by looking at color cuts; however, this site could also be useful for targeted searches of other databases as well. MySQL databases are created from broad searches of SDSS and 2MASS data. Broad queries on the SDSS and 2MASS database servers are run weekly so that observers have the most up-to-date information from which to select candidates for observation. Observers can look at detailed information about specific objects including finding charts, images, and available spectra. In addition, updates from previous observations can be added by any collaborators; this format makes observational collaboration simple. Observers can also restrict the database search, just before or during an observing run, to select objects of special interest.

Profile-IQ: Web-based data query system for local health department infrastructure and activities.

PubMed

Shah, Gulzar H; Leep, Carolyn J; Alexander, Dayna

2014-01-01

To demonstrate the use of National Association of County & City Health Officials' Profile-IQ, a Web-based data query system, and how policy makers, researchers, the general public, and public health professionals can use the system to generate descriptive statistics on local health departments. This article is a descriptive account of an important health informatics tool based on information from the project charter for Profile-IQ and the authors' experience and knowledge in design and use of this query system. Profile-IQ is a Web-based data query system that is based on open-source software: MySQL 5.5, Google Web Toolkit 2.2.0, Apache Commons Math library, Google Chart API, and Tomcat 6.0 Web server deployed on an Amazon EC2 server. It supports dynamic queries of National Profile of Local Health Departments data on local health department finances, workforce, and activities. Profile-IQ's customizable queries provide a variety of statistics not available in published reports and support the growing information needs of users who do not wish to work directly with data files for lack of staff skills or time, or to avoid a data use agreement. Profile-IQ also meets the growing demand of public health practitioners and policy makers for data to support quality improvement, community health assessment, and other processes associated with voluntary public health accreditation. It represents a step forward in the recent health informatics movement of data liberation and use of open source information technology solutions to promote public health.

Searching for cancer information on the internet: analyzing natural language search queries.

PubMed

Bader, Judith L; Theofanos, Mary Frances

2003-12-11

Searching for health information is one of the most-common tasks performed by Internet users. Many users begin searching on popular search engines rather than on prominent health information sites. We know that many visitors to our (National Cancer Institute) Web site, cancer.gov, arrive via links in search engine result. To learn more about the specific needs of our general-public users, we wanted to understand what lay users really wanted to know about cancer, how they phrased their questions, and how much detail they used. The National Cancer Institute partnered with AskJeeves, Inc to develop a methodology to capture, sample, and analyze 3 months of cancer-related queries on the Ask.com Web site, a prominent United States consumer search engine, which receives over 35 million queries per week. Using a benchmark set of 500 terms and word roots supplied by the National Cancer Institute, AskJeeves identified a test sample of cancer queries for 1 week in August 2001. From these 500 terms only 37 appeared >or= 5 times/day over the trial test week in 17208 queries. Using these 37 terms, 204165 instances of cancer queries were found in the Ask.com query logs for the actual test period of June-August 2001. Of these, 7500 individual user questions were randomly selected for detailed analysis and assigned to appropriate categories. The exact language of sample queries is presented. Considering multiples of the same questions, the sample of 7500 individual user queries represented 76077 queries (37% of the total 3-month pool). Overall 78.37% of sampled Cancer queries asked about 14 specific cancer types. Within each cancer type, queries were sorted into appropriate subcategories including at least the following: General Information, Symptoms, Diagnosis and Testing, Treatment, Statistics, Definition, and Cause/Risk/Link. The most-common specific cancer types mentioned in queries were Digestive/Gastrointestinal/Bowel (15.0%), Breast (11.7%), Skin (11.3%), and Genitourinary (10.5%). Additional subcategories of queries about specific cancer types varied, depending on user input. Queries that were not specific to a cancer type were also tracked and categorized. Natural-language searching affords users the opportunity to fully express their information needs and can aid users naïve to the content and vocabulary. The specific queries analyzed for this study reflect news and research studies reported during the study dates and would surely change with different study dates. Analyzing queries from search engines represents one way of knowing what kinds of content to provide to users of a given Web site. Users ask questions using whole sentences and keywords, often misspelling words. Providing the option for natural-language searching does not obviate the need for good information architecture, usability engineering, and user testing in order to optimize user experience.

Searching for Cancer Information on the Internet: Analyzing Natural Language Search Queries

PubMed Central

Theofanos, Mary Frances

2003-01-01

Background Searching for health information is one of the most-common tasks performed by Internet users. Many users begin searching on popular search engines rather than on prominent health information sites. We know that many visitors to our (National Cancer Institute) Web site, cancer.gov, arrive via links in search engine result. Objective To learn more about the specific needs of our general-public users, we wanted to understand what lay users really wanted to know about cancer, how they phrased their questions, and how much detail they used. Methods The National Cancer Institute partnered with AskJeeves, Inc to develop a methodology to capture, sample, and analyze 3 months of cancer-related queries on the Ask.com Web site, a prominent United States consumer search engine, which receives over 35 million queries per week. Using a benchmark set of 500 terms and word roots supplied by the National Cancer Institute, AskJeeves identified a test sample of cancer queries for 1 week in August 2001. From these 500 terms only 37 appeared ≥ 5 times/day over the trial test week in 17208 queries. Using these 37 terms, 204165 instances of cancer queries were found in the Ask.com query logs for the actual test period of June-August 2001. Of these, 7500 individual user questions were randomly selected for detailed analysis and assigned to appropriate categories. The exact language of sample queries is presented. Results Considering multiples of the same questions, the sample of 7500 individual user queries represented 76077 queries (37% of the total 3-month pool). Overall 78.37% of sampled Cancer queries asked about 14 specific cancer types. Within each cancer type, queries were sorted into appropriate subcategories including at least the following: General Information, Symptoms, Diagnosis and Testing, Treatment, Statistics, Definition, and Cause/Risk/Link. The most-common specific cancer types mentioned in queries were Digestive/Gastrointestinal/Bowel (15.0%), Breast (11.7%), Skin (11.3%), and Genitourinary (10.5%). Additional subcategories of queries about specific cancer types varied, depending on user input. Queries that were not specific to a cancer type were also tracked and categorized. Conclusions Natural-language searching affords users the opportunity to fully express their information needs and can aid users naïve to the content and vocabulary. The specific queries analyzed for this study reflect news and research studies reported during the study dates and would surely change with different study dates. Analyzing queries from search engines represents one way of knowing what kinds of content to provide to users of a given Web site. Users ask questions using whole sentences and keywords, often misspelling words. Providing the option for natural-language searching does not obviate the need for good information architecture, usability engineering, and user testing in order to optimize user experience. PMID:14713659

Development of a medical module for disaster information systems.

PubMed

Calik, Elif; Atilla, Rıdvan; Kaya, Hilal; Aribaş, Alirıza; Cengiz, Hakan; Dicle, Oğuz

2014-01-01

This study aims to improve a medical module which provides a real-time medical information flow about pre-hospital processes that gives health care in disasters; transferring, storing and processing the records that are in electronic media and over internet as a part of disaster information systems. In this study which is handled within the frame of providing information flow among professionals in a disaster case, to supply the coordination of healthcare team and transferring complete information to specified people at real time, Microsoft Access database and SQL query language were used to inform database applications. System was prepared on Microsoft .Net platform using C# language. Disaster information system-medical module was designed to be used in disaster area, field hospital, nearby hospitals, temporary inhabiting areas like tent city, vehicles that are used for dispatch, and providing information flow between medical officials and data centres. For fast recording of the disaster victim data, accessing to database which was used by health care professionals was provided (or granted) among analysing process steps and creating minimal datasets. Database fields were created in the manner of giving opportunity to enter new data and search old data which is recorded before disaster. Web application which provides access such as data entry to the database and searching towards the designed interfaces according to the login credentials access level. In this study, homepage and users' interfaces which were built on database in consequence of system analyses were provided with www.afmedinfo.com web site to the user access. With this study, a recommendation was made about how to use disaster-based information systems in the field of health. Awareness has been developed about the fact that disaster information system should not be perceived only as an early warning system. Contents and the differences of the health care practices of disaster information systems were revealed. A web application was developed supplying a link between the user and the database to make date entry and data query practices by the help of the developed interfaces.

Performance analysis of different database in new internet mapping system

NASA Astrophysics Data System (ADS)

Yao, Xing; Su, Wei; Gao, Shuai

2017-03-01

In the Mapping System of New Internet, Massive mapping entries between AID and RID need to be stored, added, updated, and deleted. In order to better deal with the problem when facing a large number of mapping entries update and query request, the Mapping System of New Internet must use high-performance database. In this paper, we focus on the performance of Redis, SQLite, and MySQL these three typical databases, and the results show that the Mapping System based on different databases can adapt to different needs according to the actual situation.

Saying What You're Looking For: Linguistics Meets Video Search.

PubMed

Barrett, Daniel Paul; Barbu, Andrei; Siddharth, N; Siskind, Jeffrey Mark

2016-10-01

We present an approach to searching large video corpora for clips which depict a natural-language query in the form of a sentence. Compositional semantics is used to encode subtle meaning differences lost in other approaches, such as the difference between two sentences which have identical words but entirely different meaning: The person rode the horse versus The horse rode the person. Given a sentential query and a natural-language parser, we produce a score indicating how well a video clip depicts that sentence for each clip in a corpus and return a ranked list of clips. Two fundamental problems are addressed simultaneously: detecting and tracking objects, and recognizing whether those tracks depict the query. Because both tracking and object detection are unreliable, our approach uses the sentential query to focus the tracker on the relevant participants and ensures that the resulting tracks are described by the sentential query. While most earlier work was limited to single-word queries which correspond to either verbs or nouns, we search for complex queries which contain multiple phrases, such as prepositional phrases, and modifiers, such as adverbs. We demonstrate this approach by searching for 2,627 naturally elicited sentential queries in 10 Hollywood movies.

vSPARQL: A View Definition Language for the Semantic Web

PubMed Central

Shaw, Marianne; Detwiler, Landon T.; Noy, Natalya; Brinkley, James; Suciu, Dan

2010-01-01

Translational medicine applications would like to leverage the biological and biomedical ontologies, vocabularies, and data sets available on the semantic web. We present a general solution for RDF information set reuse inspired by database views. Our view definition language, vSPARQL, allows applications to specify the exact content that they are interested in and how that content should be restructured or modified. Applications can access relevant content by querying against these view definitions. We evaluate the expressivity of our approach by defining views for practical use cases and comparing our view definition language to existing query languages. PMID:20800106

Concepts and implementations of natural language query systems

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Liu, I-Hsiung

1984-01-01

The currently developed user language interfaces of information systems are generally intended for serious users. These interfaces commonly ignore potentially the largest user group, i.e., casual users. This project discusses the concepts and implementations of a natural query language system which satisfy the nature and information needs of casual users by allowing them to communicate with the system in the form of their native (natural) language. In addition, a framework for the development of such an interface is also introduced for the MADAM (Multics Approach to Data Access and Management) system at the University of Southwestern Louisiana.

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease

PubMed Central

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Availability and implementation: Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. Database URL: http://rged.wall-eva.net PMID:25252782

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease.

PubMed

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. http://rged.wall-eva.net. © The Author(s) 2014. Published by Oxford University Press.

A UML Profile for Developing Databases that Conform to the Third Manifesto

NASA Astrophysics Data System (ADS)

Eessaar, Erki

The Third Manifesto (TTM) presents the principles of a relational database language that is free of deficiencies and ambiguities of SQL. There are database management systems that are created according to TTM. Developers need tools that support the development of databases by using these database management systems. UML is a widely used visual modeling language. It provides built-in extension mechanism that makes it possible to extend UML by creating profiles. In this paper, we introduce a UML profile for designing databases that correspond to the rules of TTM. We created the first version of the profile by translating existing profiles of SQL database design. After that, we extended and improved the profile. We implemented the profile by using UML CASE system StarUML™. We present an example of using the new profile. In addition, we describe problems that occurred during the profile development.

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…

Quality assessment of structure and language elements of written responses given by seven Scandinavian drug information centres.

PubMed

Reppe, Linda Amundstuen; Spigset, Olav; Kampmann, Jens Peter; Damkier, Per; Christensen, Hanne Rolighed; Böttiger, Ylva; Schjøtt, Jan

2017-05-01

The aim of this study was to identify structure and language elements affecting the quality of responses from Scandinavian drug information centres (DICs). Six different fictitious drug-related queries were sent to each of seven Scandinavian DICs. The centres were blinded for which queries were part of the study. The responses were assessed qualitatively by six clinical pharmacologists (internal experts) and six general practitioners (GPs, external experts). In addition, linguistic aspects of the responses were evaluated by a plain language expert. The quality of responses was generally judged as satisfactory to good. Presenting specific advice and conclusions were considered to improve the quality of the responses. However, small nuances in language formulations could affect the individual judgments of the experts, e.g. on whether or not advice was given. Some experts preferred the use of primary sources to the use of secondary and tertiary sources. Both internal and external experts criticised the use of abbreviations, professional terminology and study findings that was left unexplained. The plain language expert emphasised the importance of defining and explaining pharmacological terms to ensure that enquirers understand the response as intended. In addition, more use of active voice and less compressed text structure would be desirable. This evaluation of responses to DIC queries may give some indications on how to improve written responses on drug-related queries with respect to language and text structure. Giving specific advice and precise conclusions and avoiding too compressed language and non-standard abbreviations may aid to reach this goal.

searchSCF: Using MongoDB to Enable Richer Searches of Locally Hosted Science Data Repositories

NASA Astrophysics Data System (ADS)

Knosp, B.

2016-12-01

Science teams today are in the unusual position of almost having too much data available to them. Modern sensors and models are capable of outputting terabytes of data per day, which can make it difficult to find specific subsets of data. The sheer size of files can also make it time consuming to retrieve this big data from national data archive centers. Thus, many science teams choose to store what data they can on their local systems, but they are not always equipped with tools to help them intelligently organize and search their data. In its local data repository, the Aura Microwave Limb Sounder (MLS) science team at NASA's Jet Propulsion Laboratory has collected over 300TB of atmospheric science data from 71 missions/models that aid in validation, algorithm development, and research activities. When the project began, the team developed a MySQL database to aid in data queries, but this database was only designed to keep track of MLS and a few ancillary data sets, leving much of the data uncatalogued. The team has also seen database query time rise over the life of the mission. Even though the MLS science team's data holdings are not the size of a national data center's, team members still need tools to help them discover and utilize the data that they have on-hand. Over the past year, members of the science team have been looking for solutions to (1) store information on all the data sets they have collected in a single database, (2) store more metadata about each data file, (3) develop queries that can find relationships among these disparate data types, and (4) plug any new functions developed around this database into existing analysis, visualization, and web tools, transparently to users. In this presentation, I will discuss the searchSCF package that is currently under development. This package includes a NoSQL database management system (MongoDB) and a set of Python tools that both ingests data into the database and supports user queries. I will also highlight case studies of how this system could be used by the MLS science team, and how it could be implemented by other science teams with local data repositories.

Agent-Based Computing Integration and Testing

DTIC Science & Technology

2006-12-01

Query Language (DQL). Regrettably, DQL never became a W3C Member Submission itself, but likely had some influence on the SPARQL Protocol And RDF... Query Language ( SPARQL ) subsequently produced by the W3C Data Access Working Group (DAWG) as that working group also contained members from the DAML...Sponsored by Defense Advanced Research Projects Agency DARPA Order No. K536 APPROVED FOR PUBLIC RELEASE

Employing computers for the recruitment into clinical trials: a comprehensive systematic review.

PubMed

Köpcke, Felix; Prokosch, Hans-Ulrich

2014-07-01

Medical progress depends on the evaluation of new diagnostic and therapeutic interventions within clinical trials. Clinical trial recruitment support systems (CTRSS) aim to improve the recruitment process in terms of effectiveness and efficiency. The goals were to (1) create an overview of all CTRSS reported until the end of 2013, (2) find and describe similarities in design, (3) theorize on the reasons for different approaches, and (4) examine whether projects were able to illustrate the impact of CTRSS. We searched PubMed titles, abstracts, and keywords for terms related to CTRSS research. Query results were classified according to clinical context, workflow integration, knowledge and data sources, reasoning algorithm, and outcome. A total of 101 papers on 79 different systems were found. Most lacked details in one or more categories. There were 3 different CTRSS that dominated: (1) systems for the retrospective identification of trial participants based on existing clinical data, typically through Structured Query Language (SQL) queries on relational databases, (2) systems that monitored the appearance of a key event of an existing health information technology component in which the occurrence of the event caused a comprehensive eligibility test for a patient or was directly communicated to the researcher, and (3) independent systems that required a user to enter patient data into an interface to trigger an eligibility assessment. Although the treating physician was required to act for the patient in older systems, it is now becoming increasingly popular to offer this possibility directly to the patient. Many CTRSS are designed to fit the existing infrastructure of a clinical care provider or the particularities of a trial. We conclude that the success of a CTRSS depends more on its successful workflow integration than on sophisticated reasoning and data processing algorithms. Furthermore, some of the most recent literature suggest that an increase in recruited patients and improvements in recruitment efficiency can be expected, although the former will depend on the error rate of the recruitment process being replaced. Finally, to increase the quality of future CTRSS reports, we propose a checklist of items that should be included.

Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences

PubMed Central

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

2006-01-01

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

OnlineTED.com − a novel web-based audience response system for higher education. A pilot study to evaluate user acceptance

PubMed Central

Kühbeck, Felizian; Engelhardt, Stefan; Sarikas, Antonio

2014-01-01

Background and aim: Audience response (AR) systems are increasingly used in undergraduate medical education. However, high costs and complexity of conventional AR systems often limit their use. Here we present a novel AR system that is platform independent and does not require hardware clickers or additional software to be installed. Methods and results: “OnlineTED” was developed at Technische Universität München (TUM) based on Hypertext Preprocessor (PHP) with a My Structured Query Language (MySQL)-database as server- and Javascript as client-side programming languages. “OnlineTED” enables lecturers to create and manage question sets online and start polls in-class via a web-browser. Students can participate in the polls with any internet-enabled device (smartphones, tablet-PCs or laptops). A paper-based survey was conducted with undergraduate medical students and lecturers at TUM to compare "OnlineTED" with conventional AR systems using clickers. "OnlineTED" received above-average evaluation results by both students and lecturers at TUM and was seen on par or superior to conventional AR systems. The survey results indicated that up to 80% of students at TUM own an internet-enabled device (smartphone or tablet-PC) for participation in web-based AR technologies. Summary and Conclusion: “OnlineTED” is a novel web-based and platform-independent AR system for higher education that was well received by students and lecturers. As a non-commercial alternative to conventional AR systems it may foster interactive teaching in undergraduate education, in particular with large audiences. PMID:24575156

vSPARQL: a view definition language for the semantic web.

PubMed

Shaw, Marianne; Detwiler, Landon T; Noy, Natalya; Brinkley, James; Suciu, Dan

2011-02-01

Translational medicine applications would like to leverage the biological and biomedical ontologies, vocabularies, and data sets available on the semantic web. We present a general solution for RDF information set reuse inspired by database views. Our view definition language, vSPARQL, allows applications to specify the exact content that they are interested in and how that content should be restructured or modified. Applications can access relevant content by querying against these view definitions. We evaluate the expressivity of our approach by defining views for practical use cases and comparing our view definition language to existing query languages. Copyright © 2010 Elsevier Inc. All rights reserved.

QATT: a Natural Language Interface for QPE. M.S. Thesis

NASA Technical Reports Server (NTRS)

White, Douglas Robert-Graham

1989-01-01

QATT, a natural language interface developed for the Qualitative Process Engine (QPE) system is presented. The major goal was to evaluate the use of a preexisting natural language understanding system designed to be tailored for query processing in multiple domains of application. The other goal of QATT is to provide a comfortable environment in which to query envisionments in order to gain insight into the qualitative behavior of physical systems. It is shown that the use of the preexisting system made possible the development of a reasonably useful interface in a few months.

Query Expansion Using SNOMED-CT and Weighing Schemes

DTIC Science & Technology

2014-11-01

For this research, we have used SNOMED-CT along with UMLS Methathesaurus as our ontology in medical domain to expand the queries. General Terms...CT along with UMLS Methathesaurus as our ontology in medical domain to expand the queries. 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17...University of the Basque country discuss their finding on query expansion using external sources headlined by Unified Medical Language System ( UMLS

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.

SeqWare Query Engine: storing and searching sequence data in the cloud.

PubMed

O'Connor, Brian D; Merriman, Barry; Nelson, Stanley F

2010-12-21

Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the last few years. These efforts are merely a prelude for a future in which genome resequencing will be commonplace for both biomedical research and clinical applications. The dramatic increase in sequencer output strains all facets of computational infrastructure, especially databases and query interfaces. The advent of cloud computing, and a variety of powerful tools designed to process petascale datasets, provide a compelling solution to these ever increasing demands. In this work, we present the SeqWare Query Engine which has been created using modern cloud computing technologies and designed to support databasing information from thousands of genomes. Our backend implementation was built using the highly scalable, NoSQL HBase database from the Hadoop project. We also created a web-based frontend that provides both a programmatic and interactive query interface and integrates with widely used genome browsers and tools. Using the query engine, users can load and query variants (SNVs, indels, translocations, etc) with a rich level of annotations including coverage and functional consequences. As a proof of concept we loaded several whole genome datasets including the U87MG cell line. We also used a glioblastoma multiforme tumor/normal pair to both profile performance and provide an example of using the Hadoop MapReduce framework within the query engine. This software is open source and freely available from the SeqWare project (http://seqware.sourceforge.net). The SeqWare Query Engine provided an easy way to make the U87MG genome accessible to programmers and non-programmers alike. This enabled a faster and more open exploration of results, quicker tuning of parameters for heuristic variant calling filters, and a common data interface to simplify development of analytical tools. The range of data types supported, the ease of querying and integrating with existing tools, and the robust scalability of the underlying cloud-based technologies make SeqWare Query Engine a nature fit for storing and searching ever-growing genome sequence datasets.

SeqWare Query Engine: storing and searching sequence data in the cloud

PubMed Central

2010-01-01

Background Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the last few years. These efforts are merely a prelude for a future in which genome resequencing will be commonplace for both biomedical research and clinical applications. The dramatic increase in sequencer output strains all facets of computational infrastructure, especially databases and query interfaces. The advent of cloud computing, and a variety of powerful tools designed to process petascale datasets, provide a compelling solution to these ever increasing demands. Results In this work, we present the SeqWare Query Engine which has been created using modern cloud computing technologies and designed to support databasing information from thousands of genomes. Our backend implementation was built using the highly scalable, NoSQL HBase database from the Hadoop project. We also created a web-based frontend that provides both a programmatic and interactive query interface and integrates with widely used genome browsers and tools. Using the query engine, users can load and query variants (SNVs, indels, translocations, etc) with a rich level of annotations including coverage and functional consequences. As a proof of concept we loaded several whole genome datasets including the U87MG cell line. We also used a glioblastoma multiforme tumor/normal pair to both profile performance and provide an example of using the Hadoop MapReduce framework within the query engine. This software is open source and freely available from the SeqWare project (http://seqware.sourceforge.net). Conclusions The SeqWare Query Engine provided an easy way to make the U87MG genome accessible to programmers and non-programmers alike. This enabled a faster and more open exploration of results, quicker tuning of parameters for heuristic variant calling filters, and a common data interface to simplify development of analytical tools. The range of data types supported, the ease of querying and integrating with existing tools, and the robust scalability of the underlying cloud-based technologies make SeqWare Query Engine a nature fit for storing and searching ever-growing genome sequence datasets. PMID:21210981

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

Performance enhancement of a web-based picture archiving and communication system using commercial off-the-shelf server clusters.

PubMed

Liu, Yan-Lin; Shih, Cheng-Ting; Chang, Yuan-Jen; Chang, Shu-Jun; Wu, Jay

2014-01-01

The rapid development of picture archiving and communication systems (PACSs) thoroughly changes the way of medical informatics communication and management. However, as the scale of a hospital's operations increases, the large amount of digital images transferred in the network inevitably decreases system efficiency. In this study, a server cluster consisting of two server nodes was constructed. Network load balancing (NLB), distributed file system (DFS), and structured query language (SQL) duplication services were installed. A total of 1 to 16 workstations were used to transfer computed radiography (CR), computed tomography (CT), and magnetic resonance (MR) images simultaneously to simulate the clinical situation. The average transmission rate (ATR) was analyzed between the cluster and noncluster servers. In the download scenario, the ATRs of CR, CT, and MR images increased by 44.3%, 56.6%, and 100.9%, respectively, when using the server cluster, whereas the ATRs increased by 23.0%, 39.2%, and 24.9% in the upload scenario. In the mix scenario, the transmission performance increased by 45.2% when using eight computer units. The fault tolerance mechanisms of the server cluster maintained the system availability and image integrity. The server cluster can improve the transmission efficiency while maintaining high reliability and continuous availability in a healthcare environment.

Domain fusion analysis by applying relational algebra to protein sequence and domain databases.

PubMed

Truong, Kevin; Ikura, Mitsuhiko

2003-05-06

Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at http://calcium.uhnres.utoronto.ca/pi. As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time.

Implementation of remote monitoring and managing switches

NASA Astrophysics Data System (ADS)

Leng, Junmin; Fu, Guo

2010-12-01

In order to strengthen the safety performance of the network and provide the big convenience and efficiency for the operator and the manager, the system of remote monitoring and managing switches has been designed and achieved using the advanced network technology and present network resources. The fast speed Internet Protocol Cameras (FS IP Camera) is selected, which has 32-bit RSIC embedded processor and can support a number of protocols. An Optimal image compress algorithm Motion-JPEG is adopted so that high resolution images can be transmitted by narrow network bandwidth. The architecture of the whole monitoring and managing system is designed and implemented according to the current infrastructure of the network and switches. The control and administrative software is projected. The dynamical webpage Java Server Pages (JSP) development platform is utilized in the system. SQL (Structured Query Language) Server database is applied to save and access images information, network messages and users' data. The reliability and security of the system is further strengthened by the access control. The software in the system is made to be cross-platform so that multiple operating systems (UNIX, Linux and Windows operating systems) are supported. The application of the system can greatly reduce manpower cost, and can quickly find and solve problems.

Updates to the Virtual Atomic and Molecular Data Centre

NASA Astrophysics Data System (ADS)

Hill, Christian; Tennyson, Jonathan; Gordon, Iouli E.; Rothman, Laurence S.; Dubernet, Marie-Lise

2014-06-01

The Virtual Atomic and Molecular Data Centre (VAMDC) has established a set of standards for the storage and transmission of atomic and molecular data and an SQL-based query language (VSS2) for searching online databases, known as nodes. The project has also created an online service, the VAMDC Portal, through which all of these databases may be searched and their results compared and aggregated. Since its inception four years ago, the VAMDC e-infrastructure has grown to encompass over 40 databases, including HITRAN, in more than 20 countries and engages actively with scientists in six continents. Associated with the portal are a growing suite of software tools for the transformation of data from its native, XML-based, XSAMS format, to a range of more convenient human-readable (such as HTML) and machinereadable (such as CSV) formats. The relational database for HITRAN1, created as part of the VAMDC project is a flexible and extensible data model which is able to represent a wider range of parameters than the current fixed-format text-based one. Over the next year, a new online interface to this database will be tested, released and fully documented - this web application, HITRANonline2, will fully replace the ageing and incomplete JavaHAWKS software suite.

Performance Enhancement of a Web-Based Picture Archiving and Communication System Using Commercial Off-the-Shelf Server Clusters

PubMed Central

Chang, Shu-Jun; Wu, Jay

2014-01-01

The rapid development of picture archiving and communication systems (PACSs) thoroughly changes the way of medical informatics communication and management. However, as the scale of a hospital's operations increases, the large amount of digital images transferred in the network inevitably decreases system efficiency. In this study, a server cluster consisting of two server nodes was constructed. Network load balancing (NLB), distributed file system (DFS), and structured query language (SQL) duplication services were installed. A total of 1 to 16 workstations were used to transfer computed radiography (CR), computed tomography (CT), and magnetic resonance (MR) images simultaneously to simulate the clinical situation. The average transmission rate (ATR) was analyzed between the cluster and noncluster servers. In the download scenario, the ATRs of CR, CT, and MR images increased by 44.3%, 56.6%, and 100.9%, respectively, when using the server cluster, whereas the ATRs increased by 23.0%, 39.2%, and 24.9% in the upload scenario. In the mix scenario, the transmission performance increased by 45.2% when using eight computer units. The fault tolerance mechanisms of the server cluster maintained the system availability and image integrity. The server cluster can improve the transmission efficiency while maintaining high reliability and continuous availability in a healthcare environment. PMID:24701580

Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database.

PubMed

Arita, Masanori; Suwa, Kazuhiro

2008-09-17

In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database

PubMed Central

Arita, Masanori; Suwa, Kazuhiro

2008-01-01

Background In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. Results To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. Conclusion This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated. PMID:18822113

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

PubMed

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

2011-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2007-12-01

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

ExpTreeDB: web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO.

PubMed

Ni, Ming; Ye, Fuqiang; Zhu, Juanjuan; Li, Zongwei; Yang, Shuai; Yang, Bite; Han, Lu; Wu, Yongge; Chen, Ying; Li, Fei; Wang, Shengqi; Bo, Xiaochen

2014-12-01

Numerous public microarray datasets are valuable resources for the scientific communities. Several online tools have made great steps to use these data by querying related datasets with users' own gene signatures or expression profiles. However, dataset annotation and result exhibition still need to be improved. ExpTreeDB is a database that allows for queries on human and mouse microarray experiments from Gene Expression Omnibus with gene signatures or profiles. Compared with similar applications, ExpTreeDB pays more attention to dataset annotations and result visualization. We introduced a multiple-level annotation system to depict and organize original experiments. For example, a tamoxifen-treated cell line experiment is hierarchically annotated as 'agent→drug→estrogen receptor antagonist→tamoxifen'. Consequently, retrieved results are exhibited by an interactive tree-structured graphics, which provide an overview for related experiments and might enlighten users on key items of interest. The database is freely available at http://biotech.bmi.ac.cn/ExpTreeDB. Web site is implemented in Perl, PHP, R, MySQL and Apache. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Omicseq: a web-based search engine for exploring omics datasets.

PubMed

Sun, Xiaobo; Pittard, William S; Xu, Tianlei; Chen, Li; Zwick, Michael E; Jiang, Xiaoqian; Wang, Fusheng; Qin, Zhaohui S

2017-07-03

The development and application of high-throughput genomics technologies has resulted in massive quantities of diverse omics data that continue to accumulate rapidly. These rich datasets offer unprecedented and exciting opportunities to address long standing questions in biomedical research. However, our ability to explore and query the content of diverse omics data is very limited. Existing dataset search tools rely almost exclusively on the metadata. A text-based query for gene name(s) does not work well on datasets wherein the vast majority of their content is numeric. To overcome this barrier, we have developed Omicseq, a novel web-based platform that facilitates the easy interrogation of omics datasets holistically to improve 'findability' of relevant data. The core component of Omicseq is trackRank, a novel algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. The Omicseq system is supported by a scalable and elastic, NoSQL database that hosts a large collection of processed omics datasets. In the front end, a simple, web-based interface allows users to enter queries and instantly receive search results as a list of ranked datasets deemed to be the most relevant. Omicseq is freely available at http://www.omicseq.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

The contribution of morphological knowledge to French MeSH mapping for information retrieval.

PubMed Central

Zweigenbaum, P.; Darmoni, S. J.; Grabar, N.

2001-01-01

MeSH-indexed Internet health directories must provide a mapping from natural language queries to MeSH terms so that both health professionals and the general public can query their contents. We describe here the design of lexical knowledge bases for mapping French expressions to MeSH terms, and the initial evaluation of their contribution to Doc'CISMeF, the search tool of a MeSH-indexed directory of French-language medical Internet resources. The observed trend is in favor of the use of morphological knowledge as a moderate (approximately 5%) but effective factor for improving query to term mapping capabilities. PMID:11825295

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.

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.

A Query System Implementation Case Study.

ERIC Educational Resources Information Center

Hiser, Judith N.; Neil, M. Elizabeth

1985-01-01

The Department of Administrative Programming Services of Clemson University investigated products available in user-friendly retrieval systems. The test of INTELLECT, a natural language query system written by Artifical Intelligence Corporation, is described. (Author/MLW)

The Limitations of Term Co-Occurrence Data for Query Expansion in Document Retrieval Systems.

ERIC Educational Resources Information Center

Peat, Helen J.; Willett, Peter

1991-01-01

Identifies limitations in the use of term co-occurrence data as a basis for automatic query expansion in natural language document retrieval systems. The use of similarity coefficients to calculate the degree of similarity between pairs of terms is explained, and frequency and discriminatory characteristics for nearest neighbors of query terms are…

Portal to the GALEX Data Archive

NASA Astrophysics Data System (ADS)

Smith, M. A.; Conti, A.; Shiao, B.; Volpicelli, C. A.

2004-05-01

In early February MAST began its hosting of the GALEX public "Early Release Observations" images (40,000 objects) and spectra (1000 objects). MAST will host a much larger "first release," the GALEX DR1, in October, 2004. In this poster we describe features of our on-line website at http://galex.stsci.edu for researchers interested in downloading and browsing GALEX UV image and spectral data. The site, is based on MS .NET technology and user queries are entered for classes of objects or sky regions on a "MAST-like" query forms or with detailed queries written in SQL. In the latter case examples are provided to tailor a query to a user's specifications. The site provides novel features, such as tooltips that return keyword definitions, "active images" that return object classification and coordinate information in a 2.5 arcmin radius around the selected object, self-documentation of terms and tables, and of course a tutorial for new navigators. The GALEX database employs a Hierarchial Triangular Mesh system for rapid data discovery, neighbor searches, and cross correlations with other catalogs. Our "GMAX" tool allows a coplotting of object positions for objects observed by GALEX and other US-NVO compliant mission websites such as Sloan, 2MASS, FIRST.... As a member of the new Skynode network, GALEX has reported its web services to the US-NVO registry. This permits users to generate queries from other sites to cross-correlate, compare, and plot GALEX data using US-NVO protocols. Future plans for limited on-line data analysis and footprint services are described.

EURISWEB – Web-based epidemiological surveillance of antibiotic-resistant pneumococci in Day Care Centers

PubMed Central

Silva, Sara; Gouveia-Oliveira, Rodrigo; Maretzek, António; Carriço, João; Gudnason, Thorolfur; Kristinsson, Karl G; Ekdahl, Karl; Brito-Avô, António; Tomasz, Alexander; Sanches, Ilda Santos; Lencastre, Hermínia de; Almeida, Jonas

2003-01-01

Background EURIS (European Resistance Intervention Study) was launched as a multinational study in September of 2000 to identify the multitude of complex risk factors that contribute to the high carriage rate of drug resistant Streptococcus pneumoniae strains in children attending Day Care Centers in several European countries. Access to the very large number of data required the development of a web-based infrastructure – EURISWEB – that includes a relational online database, coupled with a query system for data retrieval, and allows integrative storage of demographic, clinical and molecular biology data generated in EURIS. Methods All components of the system were developed using open source programming tools: data storage management was supported by PostgreSQL, and the hypertext preprocessor to generate the web pages was implemented using PHP. The query system is based on a software agent running in the background specifically developed for EURIS. Results The website currently contains data related to 13,500 nasopharyngeal samples and over one million measures taken from 5,250 individual children, as well as over one thousand pre-made and user-made queries aggregated into several reports, approximately. It is presently in use by participating researchers from three countries (Iceland, Portugal and Sweden). Conclusion An operational model centered on a PHP engine builds the interface between the user and the database automatically, allowing an easy maintenance of the system. The query system is also sufficiently adaptable to allow the integration of several advanced data analysis procedures far more demanding than simple queries, eventually including artificial intelligence predictive models. PMID:12846930

Data management with a landslide inventory of the Franconian Alb (Germany) using a spatial database and GIS tools

NASA Astrophysics Data System (ADS)

Bemm, Stefan; Sandmeier, Christine; Wilde, Martina; Jaeger, Daniel; Schwindt, Daniel; Terhorst, Birgit

2014-05-01

The area of the Swabian-Franconian cuesta landscape (Southern Germany) is highly prone to landslides. This was apparent in the late spring of 2013, when numerous landslides occurred as a consequence of heavy and long-lasting rainfalls. The specific climatic situation caused numerous damages with serious impact on settlements and infrastructure. Knowledge on spatial distribution of landslides, processes and characteristics are important to evaluate the potential risk that can occur from mass movements in those areas. In the frame of two projects about 400 landslides were mapped and detailed data sets were compiled during years 2011 to 2014 at the Franconian Alb. The studies are related to the project "Slope stability and hazard zones in the northern Bavarian cuesta" (DFG, German Research Foundation) as well as to the LfU (The Bavarian Environment Agency) within the project "Georisks and climate change - hazard indication map Jura". The central goal of the present study is to create a spatial database for landslides. The database should contain all fundamental parameters to characterize the mass movements and should provide the potential for secure data storage and data management, as well as statistical evaluations. The spatial database was created with PostgreSQL, an object-relational database management system and PostGIS, a spatial database extender for PostgreSQL, which provides the possibility to store spatial and geographic objects and to connect to several GIS applications, like GRASS GIS, SAGA GIS, QGIS and GDAL, a geospatial library (Obe et al. 2011). Database access for querying, importing, and exporting spatial and non-spatial data is ensured by using GUI or non-GUI connections. The database allows the use of procedural languages for writing advanced functions in the R, Python or Perl programming languages. It is possible to work directly with the (spatial) data entirety of the database in R. The inventory of the database includes (amongst others), informations on location, landslide types and causes, geomorphological positions, geometries, hazards and damages, as well as assessments related to the activity of landslides. Furthermore, there are stored spatial objects, which represent the components of a landslide, in particular the scarps and the accumulation areas. Besides, waterways, map sheets, contour lines, detailed infrastructure data, digital elevation models, aspect and slope data are included. Examples of spatial queries to the database are intersections of raster and vector data for calculating values for slope gradients or aspects of landslide areas and for creating multiple, overlaying sections for the comparison of slopes, as well as distances to the infrastructure or to the next receiving drainage. Furthermore, getting informations on landslide magnitudes, distribution and clustering, as well as potential correlations concerning geomorphological or geological conditions. The data management concept in this study can be implemented for any academic, public or private use, because it is independent from any obligatory licenses. The created spatial database offers a platform for interdisciplinary research and socio-economic questions, as well as for landslide susceptibility and hazard indication mapping. Obe, R.O., Hsu, L.S. 2011. PostGIS in action. - pp 492, Manning Publications, Stamford

A data analysis expert system for large established distributed databases

NASA Technical Reports Server (NTRS)

Gnacek, Anne-Marie; An, Y. Kim; Ryan, J. Patrick

1987-01-01

A design for a natural language database interface system, called the Deductively Augmented NASA Management Decision support System (DANMDS), is presented. The DANMDS system components have been chosen on the basis of the following considerations: maximal employment of the existing NASA IBM-PC computers and supporting software; local structuring and storing of external data via the entity-relationship model; a natural easy-to-use error-free database query language; user ability to alter query language vocabulary and data analysis heuristic; and significant artificial intelligence data analysis heuristic techniques that allow the system to become progressively and automatically more useful.

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.

Machine Translation-Supported Cross-Language Information Retrieval for a Consumer Health Resource

PubMed Central

Rosemblat, Graciela; Gemoets, Darren; Browne, Allen C.; Tse, Tony

2003-01-01

The U.S. National Institutes of Health, through its National Library of Medicine, developed ClinicalTrials.gov to provide the public with easy access to information on clinical trials on a wide range of conditions or diseases. Only English language information retrieval is currently supported. Given the growing number of Spanish speakers in the U.S. and their increasing use of the Web, we anticipate a significant increase in Spanish-speaking users. This study compares the effectiveness of two common cross-language information retrieval methods using machine translation, query translation versus document translation, using a subset of genuine user queries from ClinicalTrials.gov. Preliminary results conducted with the ClinicalTrials.gov search engine show that in our environment, query translation is statistically significantly better than document translation. We discuss possible reasons for this result and we conclude with suggestions for future work. PMID:14728236

Development of noSQL data storage for the ATLAS PanDA Monitoring System

NASA Astrophysics Data System (ADS)

Ito, H.; Potekhin, M.; Wenaus, T.

2012-12-01

For several years the PanDA Workload Management System has been the basis for distributed production and analysis for the ATLAS experiment at the LHC. Since the start of data taking PanDA usage has ramped up steadily, typically exceeding 500k completed jobs/day by June 2011. The associated monitoring data volume has been rising as well, to levels that present a new set of challenges in the areas of database scalability and monitoring system performance and efficiency. These challenges are being met with an R&D effort aimed at implementing a scalable and efficient monitoring data storage based on a noSQL solution (Cassandra). We present our motivations for using this technology, as well as data design and the techniques used for efficient indexing of the data. We also discuss the hardware requirements as they were determined by testing with actual data and realistic rate of queries. In conclusion, we present our experience with operating a Cassandra cluster over an extended period of time and with data load adequate for planned application.

EarthServer - an FP7 project to enable the web delivery and analysis of 3D/4D models

NASA Astrophysics Data System (ADS)

Laxton, John; Sen, Marcus; Passmore, James

2013-04-01

EarthServer aims at open access and ad-hoc analytics on big Earth Science data, based on the OGC geoservice standards Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS). The WCS model defines "coverages" as a unifying paradigm for multi-dimensional raster data, point clouds, meshes, etc., thereby addressing a wide range of Earth Science data including 3D/4D models. WCPS allows declarative SQL-style queries on coverages. The project is developing a pilot implementing these standards, and will also investigate the use of GeoSciML to describe coverages. Integration of WCPS with XQuery will in turn allow coverages to be queried in combination with their metadata and GeoSciML description. The unified service will support navigation, extraction, aggregation, and ad-hoc analysis on coverage data from SQL. Clients will range from mobile devices to high-end immersive virtual reality, and will enable 3D model visualisation using web browser technology coupled with developing web standards. EarthServer is establishing open-source client and server technology intended to be scalable to Petabyte/Exabyte volumes, based on distributed processing, supercomputing, and cloud virtualization. Implementation will be based on the existing rasdaman server technology developed. Services using rasdaman technology are being installed serving the atmospheric, oceanographic, geological, cryospheric, planetary and general earth observation communities. The geology service (http://earthserver.bgs.ac.uk/) is being provided by BGS and at present includes satellite imagery, superficial thickness data, onshore DTMs and 3D models for the Glasgow area. It is intended to extend the data sets available to include 3D voxel models. Use of the WCPS standard allows queries to be constructed against single or multiple coverages. For example on a single coverage data for a particular area can be selected or data with a particular range of pixel values. Queries on multiple surfaces can be constructed to calculate, for example, the thickness between two surfaces in a 3D model or the depth from ground surface to the top of a particular geologic unit. In the first version of the service a simple interface showing some example queries has been implemented in order to show the potential of the technologies. The project aims to develop the services available in light of user feedback, both in terms of the data available, the functionality and the interface. User feedback on the services guides the software and standards development aspects of the project, leading to enhanced versions of the software which will be implemented in upgraded versions of the services during the lifetime of the project.

Monitoring of IaaS and scientific applications on the Cloud using the Elasticsearch ecosystem

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Berzano, D.; Guarise, A.; Lusso, S.; Masera, M.; Vallero, S.

2015-05-01

The private Cloud at the Torino INFN computing centre offers IaaS services to different scientific computing applications. The infrastructure is managed with the OpenNebula cloud controller. The main stakeholders of the facility are a grid Tier-2 site for the ALICE collaboration at LHC, an interactive analysis facility for the same experiment and a grid Tier-2 site for the BES-III collaboration, plus an increasing number of other small tenants. Besides keeping track of the usage, the automation of dynamic allocation of resources to tenants requires detailed monitoring and accounting of the resource usage. As a first investigation towards this, we set up a monitoring system to inspect the site activities both in terms of IaaS and applications running on the hosted virtual instances. For this purpose we used the Elasticsearch, Logstash and Kibana stack. In the current implementation, the heterogeneous accounting information is fed to different MySQL databases and sent to Elasticsearch via a custom Logstash plugin. For the IaaS metering, we developed sensors for the OpenNebula API. The IaaS level information gathered through the API is sent to the MySQL database through an ad-hoc developed RESTful web service, which is also used for other accounting purposes. Concerning the application level, we used the Root plugin TProofMonSenderSQL to collect accounting data from the interactive analysis facility. The BES-III virtual instances used to be monitored with Zabbix, as a proof of concept we also retrieve the information contained in the Zabbix database. Each of these three cases is indexed separately in Elasticsearch. We are now starting to consider dismissing the intermediate level provided by the SQL database and evaluating a NoSQL option as a unique central database for all the monitoring information. We setup a set of Kibana dashboards with pre-defined queries in order to monitor the relevant information in each case. In this way we have achieved a uniform monitoring interface for both the IaaS and the scientific applications, mostly leveraging off-the-shelf tools.

Learning for Semantic Parsing and Natural Language Generation Using Statistical Machine Translation Techniques

DTIC Science & Technology

2007-08-01

In this domain, queries typically show a deeply nested structure, which makes the semantic parsing task rather challenging , e.g.: What states border...only 80% of the GEOQUERY queries are semantically tractable, which shows that GEOQUERY is indeed a more challenging domain than ATIS. Note that none...a particularly challenging task, because of the inherent ambiguity of natural languages on both sides. It has inspired a large body of research. In

FPGA-based prototype storage system with phase change memory

NASA Astrophysics Data System (ADS)

Li, Gezi; Chen, Xiaogang; Chen, Bomy; Li, Shunfen; Zhou, Mi; Han, Wenbing; Song, Zhitang

2016-10-01

With the ever-increasing amount of data being stored via social media, mobile telephony base stations, and network devices etc. the database systems face severe bandwidth bottlenecks when moving vast amounts of data from storage to the processing nodes. At the same time, Storage Class Memory (SCM) technologies such as Phase Change Memory (PCM) with unique features like fast read access, high density, non-volatility, byte-addressability, positive response to increasing temperature, superior scalability, and zero standby leakage have changed the landscape of modern computing and storage systems. In such a scenario, we present a storage system called FLEET which can off-load partial or whole SQL queries to the storage engine from CPU. FLEET uses an FPGA rather than conventional CPUs to implement the off-load engine due to its highly parallel nature. We have implemented an initial prototype of FLEET with PCM-based storage. The results demonstrate that significant performance and CPU utilization gains can be achieved by pushing selected query processing components inside in PCM-based storage.

Easily configured real-time CPOE Pick Off Tool supporting focused clinical research and quality improvement.

PubMed

Rosenbaum, Benjamin P; Silkin, Nikolay; Miller, Randolph A

2014-01-01

Real-time alerting systems typically warn providers about abnormal laboratory results or medication interactions. For more complex tasks, institutions create site-wide 'data warehouses' to support quality audits and longitudinal research. Sophisticated systems like i2b2 or Stanford's STRIDE utilize data warehouses to identify cohorts for research and quality monitoring. However, substantial resources are required to install and maintain such systems. For more modest goals, an organization desiring merely to identify patients with 'isolation' orders, or to determine patients' eligibility for clinical trials, may adopt a simpler, limited approach based on processing the output of one clinical system, and not a data warehouse. We describe a limited, order-entry-based, real-time 'pick off' tool, utilizing public domain software (PHP, MySQL). Through a web interface the tool assists users in constructing complex order-related queries and auto-generates corresponding database queries that can be executed at recurring intervals. We describe successful application of the tool for research and quality monitoring.

Building a Diabetes Registry from the Veterans Health Administration's Computerized Patient Record System

PubMed Central

F. O. Kern, Elizabeth; Beischel, Scott; Stalnaker, Randal; Aron, David C.; Kirsh, Susan R.; Watts, Sharon A.

2008-01-01

Background Little information is available describing how to implement a disease registry from an electronic patient record system. The aim of this report is to describe the technology, methods, and utility of a diabetes registry populated by the Veterans Health Information Systems Architecture (VistA), which underlies the computerized patient record system of the Veterans Health Administration (VHA) in Veteran Affairs Integrated Service Network 10 (VISN 10). Methods VISN 10 data from VistA were mapped to a relational SQL-based data system using KB_SQL software. Operational definitions for diabetes, active clinical management, and responsible providers were used to create views of patient-level data in the diabetes registry. Query Analyzer was used to access the data views directly. Semicustomizable reports were created by linking the diabetes registry to a Web page using Microsoft asp.net2. A retrospective observational study design was used to analyze trends in the process of care and outcomes. Results Since October 2001, 81,227 patients with diabetes have enrolled in VISN 10: approximately 42,000 are currently under active management by VISN 10 providers. By tracking primary care visits, we assigned 91% to a clinic group responsible for diabetes care. In the Cleveland Veterans Affairs Medical Center (VAMC), the frequency of mean annual hemoglobin A1c levels ≥9% has declined significantly over 5 years. Almost 4000 patients have been seen in diabetes intervention programs in the Cleveland VAMC over the past 4 years. Conclusions A diabetes registry can be populated from the database underlying the VHA electronic patient record database system and linked to Web-based and ad hoc queries useful for quality improvement. PMID:19885172

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.

TEQUEL: The query language of SADDLE

NASA Technical Reports Server (NTRS)

Rajan, S. D.

1984-01-01

A relational database management system is presented that is tailored for engineering applications. A wide variety of engineering data types are supported and the data definition language (DDL) and data manipulation language (DML) are extended to handle matrices. The system can be used either in the standalone mode or through a FORTRAN or PASCAL application program. The query language is of the relational calculus type and allows the user to store, retrieve, update and delete tuples from relations. The relational operations including union, intersect and differ facilitate creation of temporary relations that can be used for manipulating information in a powerful manner. Sample applications are shown to illustrate the creation of data through a FORTRAN program and data manipulation using the TEQUEL DML.

Depth-area-duration characteristics of storm rainfall in Texas using Multi-Sensor Precipitation Estimates

NASA Astrophysics Data System (ADS)

McEnery, J. A.; Jitkajornwanich, K.

2012-12-01

This presentation will describe the methodology and overall system development by which a benchmark dataset of precipitation information has been used to characterize the depth-area-duration relations in heavy rain storms occurring over regions of Texas. Over the past two years project investigators along with the National Weather Service (NWS) West Gulf River Forecast Center (WGRFC) have developed and operated a gateway data system to ingest, store, and disseminate NWS multi-sensor precipitation estimates (MPE). As a pilot project of the Integrated Water Resources Science and Services (IWRSS) initiative, this testbed uses a Standard Query Language (SQL) server to maintain a full archive of current and historic MPE values within the WGRFC service area. These time series values are made available for public access as web services in the standard WaterML format. Having this volume of information maintained in a comprehensive database now allows the use of relational analysis capabilities within SQL to leverage these multi-sensor precipitation values and produce a valuable derivative product. The area of focus for this study is North Texas and will utilize values that originated from the West Gulf River Forecast Center (WGRFC); one of three River Forecast Centers currently represented in the holdings of this data system. Over the past two decades, NEXRAD radar has dramatically improved the ability to record rainfall. The resulting hourly MPE values, distributed over an approximate 4 km by 4 km grid, are considered by the NWS to be the "best estimate" of rainfall. The data server provides an accepted standard interface for internet access to the largest time-series dataset of NEXRAD based MPE values ever assembled. An automated script has been written to search and extract storms over the 18 year period of record from the contents of this massive historical precipitation database. Not only can it extract site-specific storms, but also duration-specific storms and storms separated by user defined inter-event periods. A separate storm database has been created to store the selected output. By storing output within tables in a separate database, we can make use of powerful SQL capabilities to perform flexible pattern analysis. Previous efforts have made use of historic data from limited clusters of irregularly spaced physical gauges. Spatial extent of the observational network has been a limiting factor. The relatively dense distribution of MPE provides a virtual mesh of observations stretched over the landscape. This work combines a unique hydrologic data resource with programming and database analysis to characterize storm depth-area-duration relationships.

Building a semi-automatic ontology learning and construction system for geosciences

NASA Astrophysics Data System (ADS)

Babaie, H. A.; Sunderraman, R.; Zhu, Y.

2013-12-01

We are developing an ontology learning and construction framework that allows continuous, semi-automatic knowledge extraction, verification, validation, and maintenance by potentially a very large group of collaborating domain experts in any geosciences field. The system brings geoscientists from the side-lines to the center stage of ontology building, allowing them to collaboratively construct and enrich new ontologies, and merge, align, and integrate existing ontologies and tools. These constantly evolving ontologies can more effectively address community's interests, purposes, tools, and change. The goal is to minimize the cost and time of building ontologies, and maximize the quality, usability, and adoption of ontologies by the community. Our system will be a domain-independent ontology learning framework that applies natural language processing, allowing users to enter their ontology in a semi-structured form, and a combined Semantic Web and Social Web approach that lets direct participation of geoscientists who have no skill in the design and development of their domain ontologies. A controlled natural language (CNL) interface and an integrated authoring and editing tool automatically convert syntactically correct CNL text into formal OWL constructs. The WebProtege-based system will allow a potentially large group of geoscientists, from multiple domains, to crowd source and participate in the structuring of their knowledge model by sharing their knowledge through critiquing, testing, verifying, adopting, and updating of the concept models (ontologies). We will use cloud storage for all data and knowledge base components of the system, such as users, domain ontologies, discussion forums, and semantic wikis that can be accessed and queried by geoscientists in each domain. We will use NoSQL databases such as MongoDB as a service in the cloud environment. MongoDB uses the lightweight JSON format, which makes it convenient and easy to build Web applications using just HTML5 and Javascript, thereby avoiding cumbersome server side coding present in the traditional approaches. The JSON format used in MongoDB is also suitable for storing and querying RDF data. We will store the domain ontologies and associated linked data in JSON/RDF formats. Our Web interface will be built upon the open source and configurable WebProtege ontology editor. We will develop a simplified mobile version of our user interface which will automatically detect the hosting device and adjust the user interface layout to accommodate different screen sizes. We will also use the Semantic Media Wiki that allows the user to store and query the data within the wiki pages. By using HTML 5, JavaScript, and WebGL, we aim to create an interactive, dynamic, and multi-dimensional user interface that presents various geosciences data sets in a natural and intuitive way.

An Analysis of Application Generators.

DTIC Science & Technology

1983-03-01

query language OUEL in the programming language C, THESEUS [20], which embeds relational operators in the language Euclid. Schmidt [21] reports some...34The Design and Implementation of INGRES," ACM-TODS, Vol. 1. No. 3, 1976,. 33 £ 20. Shopiro,J.E., " THESEUS -A Programming Language for Relational

On the Semantics of SPARQL

NASA Astrophysics Data System (ADS)

Arenas, Marcelo; Gutierrez, Claudio; Pérez, Jorge

The Resource Description Framework (RDF) is the standard data model for representing information about World Wide Web resources. In January 2008, it was released the recommendation of the W3C for querying RDF data, a query language called SPARQL. In this chapter, we give a detailed description of the semantics of this language. We start by focusing on the definition of a formal semantics for the core part of SPARQL, and then move to the definition for the entire language, including all the features in the specification of SPARQL by the W3C such as blank nodes in graph patterns and bag semantics for solutions.

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.

Active Wiki Knowledge Repository

DTIC Science & Technology

2012-10-01

data using SPARQL queries or RESTful web-services; ‘gardening’ tools for examining the semantically tagged content in the wiki; high-level language tool...Tagging & RDF triple-store Fusion and inferences for collaboration Tools for Consuming Data SPARQL queries or RESTful WS Inference & Gardening tools...other stores using AW SPARQL queries and rendering templates; and 4) Interactively share maps and other content using annotation tools to post notes

A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language

PubMed Central

2011-01-01

Shotgun lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform. PMID:21247462

Cross-Language Information Retrieval: An Analysis of Errors.

ERIC Educational Resources Information Center

Ruiz, Miguel E.; Srinivasan, Padmini

1998-01-01

Investigates an automatic method for Cross Language Information Retrieval (CLIR) that utilizes the multilingual Unified Medical Language System (UMLS) Metathesaurus to translate Spanish natural-language queries into English. Results indicate that for Spanish, the UMLS Metathesaurus-based CLIR method is at least equivalent to if not better than…

The Binding Database: data management and interface design.

PubMed

Chen, Xi; Lin, Yuhmei; Liu, Ming; Gilson, Michael K

2002-01-01

The large and growing body of experimental data on biomolecular binding is of enormous value in developing a deeper understanding of molecular biology, in developing new therapeutics, and in various molecular design applications. However, most of these data are found only in the published literature and are therefore difficult to access and use. No existing public database has focused on measured binding affinities and has provided query capabilities that include chemical structure and sequence homology searches. We have created Binding DataBase (BindingDB), a public, web-accessible database of measured binding affinities. BindingDB is based upon a relational data specification for describing binding measurements via Isothermal Titration Calorimetry (ITC) and enzyme inhibition. A corresponding XML Document Type Definition (DTD) is used to create and parse intermediate files during the on-line deposition process and will also be used for data interchange, including collection of data from other sources. The on-line query interface, which is constructed with Java Servlet technology, supports standard SQL queries as well as searches for molecules by chemical structure and sequence homology. The on-line deposition interface uses Java Server Pages and JavaBean objects to generate dynamic HTML and to store intermediate results. The resulting data resource provides a range of functionality with brisk response-times, and lends itself well to continued development and enhancement.

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

PubMed Central

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

2011-01-01

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

A journey to Semantic Web query federation in the life sciences.

PubMed

Cheung, Kei-Hoi; Frost, H Robert; Marshall, M Scott; Prud'hommeaux, Eric; Samwald, Matthias; Zhao, Jun; Paschke, Adrian

2009-10-01

As interest in adopting the Semantic Web in the biomedical domain continues to grow, Semantic Web technology has been evolving and maturing. A variety of technological approaches including triplestore technologies, SPARQL endpoints, Linked Data, and Vocabulary of Interlinked Datasets have emerged in recent years. In addition to the data warehouse construction, these technological approaches can be used to support dynamic query federation. As a community effort, the BioRDF task force, within the Semantic Web for Health Care and Life Sciences Interest Group, is exploring how these emerging approaches can be utilized to execute distributed queries across different neuroscience data sources. We have created two health care and life science knowledge bases. We have explored a variety of Semantic Web approaches to describe, map, and dynamically query multiple datasets. We have demonstrated several federation approaches that integrate diverse types of information about neurons and receptors that play an important role in basic, clinical, and translational neuroscience research. Particularly, we have created a prototype receptor explorer which uses OWL mappings to provide an integrated list of receptors and executes individual queries against different SPARQL endpoints. We have also employed the AIDA Toolkit, which is directed at groups of knowledge workers who cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. We have explored a tool called "FeDeRate", which enables a global SPARQL query to be decomposed into subqueries against the remote databases offering either SPARQL or SQL query interfaces. Finally, we have explored how to use the vocabulary of interlinked Datasets (voiD) to create metadata for describing datasets exposed as Linked Data URIs or SPARQL endpoints. We have demonstrated the use of a set of novel and state-of-the-art Semantic Web technologies in support of a neuroscience query federation scenario. We have identified both the strengths and weaknesses of these technologies. While Semantic Web offers a global data model including the use of Uniform Resource Identifiers (URI's), the proliferation of semantically-equivalent URI's hinders large scale data integration. Our work helps direct research and tool development, which will be of benefit to this community.

A journey to Semantic Web query federation in the life sciences

PubMed Central

Cheung, Kei-Hoi; Frost, H Robert; Marshall, M Scott; Prud'hommeaux, Eric; Samwald, Matthias; Zhao, Jun; Paschke, Adrian

2009-01-01

Background As interest in adopting the Semantic Web in the biomedical domain continues to grow, Semantic Web technology has been evolving and maturing. A variety of technological approaches including triplestore technologies, SPARQL endpoints, Linked Data, and Vocabulary of Interlinked Datasets have emerged in recent years. In addition to the data warehouse construction, these technological approaches can be used to support dynamic query federation. As a community effort, the BioRDF task force, within the Semantic Web for Health Care and Life Sciences Interest Group, is exploring how these emerging approaches can be utilized to execute distributed queries across different neuroscience data sources. Methods and results We have created two health care and life science knowledge bases. We have explored a variety of Semantic Web approaches to describe, map, and dynamically query multiple datasets. We have demonstrated several federation approaches that integrate diverse types of information about neurons and receptors that play an important role in basic, clinical, and translational neuroscience research. Particularly, we have created a prototype receptor explorer which uses OWL mappings to provide an integrated list of receptors and executes individual queries against different SPARQL endpoints. We have also employed the AIDA Toolkit, which is directed at groups of knowledge workers who cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. We have explored a tool called "FeDeRate", which enables a global SPARQL query to be decomposed into subqueries against the remote databases offering either SPARQL or SQL query interfaces. Finally, we have explored how to use the vocabulary of interlinked Datasets (voiD) to create metadata for describing datasets exposed as Linked Data URIs or SPARQL endpoints. Conclusion We have demonstrated the use of a set of novel and state-of-the-art Semantic Web technologies in support of a neuroscience query federation scenario. We have identified both the strengths and weaknesses of these technologies. While Semantic Web offers a global data model including the use of Uniform Resource Identifiers (URI's), the proliferation of semantically-equivalent URI's hinders large scale data integration. Our work helps direct research and tool development, which will be of benefit to this community. PMID:19796394

Visually defining and querying consistent multi-granular clinical temporal abstractions.

PubMed

Combi, Carlo; Oliboni, Barbara

2012-02-01

The main goal of this work is to propose a framework for the visual specification and query of consistent multi-granular clinical temporal abstractions. We focus on the issue of querying patient clinical information by visually defining and composing temporal abstractions, i.e., high level patterns derived from several time-stamped raw data. In particular, we focus on the visual specification of consistent temporal abstractions with different granularities and on the visual composition of different temporal abstractions for querying clinical databases. Temporal abstractions on clinical data provide a concise and high-level description of temporal raw data, and a suitable way to support decision making. Granularities define partitions on the time line and allow one to represent time and, thus, temporal clinical information at different levels of detail, according to the requirements coming from the represented clinical domain. The visual representation of temporal information has been considered since several years in clinical domains. Proposed visualization techniques must be easy and quick to understand, and could benefit from visual metaphors that do not lead to ambiguous interpretations. Recently, physical metaphors such as strips, springs, weights, and wires have been proposed and evaluated on clinical users for the specification of temporal clinical abstractions. Visual approaches to boolean queries have been considered in the last years and confirmed that the visual support to the specification of complex boolean queries is both an important and difficult research topic. We propose and describe a visual language for the definition of temporal abstractions based on a set of intuitive metaphors (striped wall, plastered wall, brick wall), allowing the clinician to use different granularities. A new algorithm, underlying the visual language, allows the physician to specify only consistent abstractions, i.e., abstractions not containing contradictory conditions on the component abstractions. Moreover, we propose a visual query language where different temporal abstractions can be composed to build complex queries: temporal abstractions are visually connected through the usual logical connectives AND, OR, and NOT. The proposed visual language allows one to simply define temporal abstractions by using intuitive metaphors, and to specify temporal intervals related to abstractions by using different temporal granularities. The physician can interact with the designed and implemented tool by point-and-click selections, and can visually compose queries involving several temporal abstractions. The evaluation of the proposed granularity-related metaphors consisted in two parts: (i) solving 30 interpretation exercises by choosing the correct interpretation of a given screenshot representing a possible scenario, and (ii) solving a complex exercise, by visually specifying through the interface a scenario described only in natural language. The exercises were done by 13 subjects. The percentage of correct answers to the interpretation exercises were slightly different with respect to the considered metaphors (54.4--striped wall, 73.3--plastered wall, 61--brick wall, and 61--no wall), but post hoc statistical analysis on means confirmed that differences were not statistically significant. The result of the user's satisfaction questionnaire related to the evaluation of the proposed granularity-related metaphors ratified that there are no preferences for one of them. The evaluation of the proposed logical notation consisted in two parts: (i) solving five interpretation exercises provided by a screenshot representing a possible scenario and by three different possible interpretations, of which only one was correct, and (ii) solving five exercises, by visually defining through the interface a scenario described only in natural language. Exercises had an increasing difficulty. The evaluation involved a total of 31 subjects. Results related to this evaluation phase confirmed us about the soundness of the proposed solution even in comparison with a well known proposal based on a tabular query form (the only significant difference is that our proposal requires more time for the training phase: 21 min versus 14 min). In this work we have considered the issue of visually composing and querying temporal clinical patient data. In this context we have proposed a visual framework for the specification of consistent temporal abstractions with different granularities and for the visual composition of different temporal abstractions to build (possibly) complex queries on clinical databases. A new algorithm has been proposed to check the consistency of the specified granular abstraction. From the evaluation of the proposed metaphors and interfaces and from the comparison of the visual query language with a well known visual method for boolean queries, the soundness of the overall system has been confirmed; moreover, pros and cons and possible improvements emerged from the comparison of different visual metaphors and solutions. Copyright © 2011 Elsevier B.V. All rights reserved.

Automatic Query Formulations in Information Retrieval.

ERIC Educational Resources Information Center

Salton, G.; And Others

1983-01-01

Introduces methods designed to reduce role of search intermediaries by generating Boolean search formulations automatically using term frequency considerations from natural language statements provided by system patrons. Experimental results are supplied and methods are described for applying automatic query formulation process in practice.…

On-Demand Associative Cross-Language Information Retrieval

NASA Astrophysics Data System (ADS)

Geraldo, André Pinto; Moreira, Viviane P.; Gonçalves, Marcos A.

This paper proposes the use of algorithms for mining association rules as an approach for Cross-Language Information Retrieval. These algorithms have been widely used to analyse market basket data. The idea is to map the problem of finding associations between sales items to the problem of finding term translations over a parallel corpus. The proposal was validated by means of experiments using queries in two distinct languages: Portuguese and Finnish to retrieve documents in English. The results show that the performance of our proposed approach is comparable to the performance of the monolingual baseline and to query translation via machine translation, even though these systems employ more complex Natural Language Processing techniques. The combination between machine translation and our approach yielded the best results, even outperforming the monolingual baseline.

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

Semantic based man-machine interface for real-time communication

NASA Technical Reports Server (NTRS)

Ali, M.; Ai, C.-S.

1988-01-01

A flight expert system (FLES) was developed to assist pilots in monitoring, diagnosing and recovering from in-flight faults. To provide a communications interface between the flight crew and FLES, a natural language interface (NALI) was implemented. Input to NALI is processed by three processors: (1) the semantics parser; (2) the knowledge retriever; and (3) the response generator. First the semantic parser extracts meaningful words and phrases to generate an internal representation of the query. At this point, the semantic parser has the ability to map different input forms related to the same concept into the same internal representation. Then the knowledge retriever analyzes and stores the context of the query to aid in resolving ellipses and pronoun references. At the end of this process, a sequence of retrievel functions is created as a first step in generating the proper response. Finally, the response generator generates the natural language response to the query. The architecture of NALI was designed to process both temporal and nontemporal queries. The architecture and implementation of NALI are described.

Time-related patient data retrieval for the case studies from the pharmacogenomics research network

PubMed Central

Zhu, Qian; Tao, Cui; Ding, Ying; Chute, Christopher G.

2012-01-01

There are lots of question-based data elements from the pharmacogenomics research network (PGRN) studies. Many data elements contain temporal information. To semantically represent these elements so that they can be machine processiable is a challenging problem for the following reasons: (1) the designers of these studies usually do not have the knowledge of any computer modeling and query languages, so that the original data elements usually are represented in spreadsheets in human languages; and (2) the time aspects in these data elements can be too complex to be represented faithfully in a machine-understandable way. In this paper, we introduce our efforts on representing these data elements using semantic web technologies. We have developed an ontology, CNTRO, for representing clinical events and their temporal relations in the web ontology language (OWL). Here we use CNTRO to represent the time aspects in the data elements. We have evaluated 720 time-related data elements from PGRN studies. We adapted and extended the knowledge representation requirements for EliXR-TIME to categorize our data elements. A CNTRO-based SPARQL query builder has been developed to customize users’ own SPARQL queries for each knowledge representation requirement. The SPARQL query builder has been evaluated with a simulated EHR triple store to ensure its functionalities. PMID:23076712

Time-related patient data retrieval for the case studies from the pharmacogenomics research network.

PubMed

Zhu, Qian; Tao, Cui; Ding, Ying; Chute, Christopher G

2012-11-01

There are lots of question-based data elements from the pharmacogenomics research network (PGRN) studies. Many data elements contain temporal information. To semantically represent these elements so that they can be machine processiable is a challenging problem for the following reasons: (1) the designers of these studies usually do not have the knowledge of any computer modeling and query languages, so that the original data elements usually are represented in spreadsheets in human languages; and (2) the time aspects in these data elements can be too complex to be represented faithfully in a machine-understandable way. In this paper, we introduce our efforts on representing these data elements using semantic web technologies. We have developed an ontology, CNTRO, for representing clinical events and their temporal relations in the web ontology language (OWL). Here we use CNTRO to represent the time aspects in the data elements. We have evaluated 720 time-related data elements from PGRN studies. We adapted and extended the knowledge representation requirements for EliXR-TIME to categorize our data elements. A CNTRO-based SPARQL query builder has been developed to customize users' own SPARQL queries for each knowledge representation requirement. The SPARQL query builder has been evaluated with a simulated EHR triple store to ensure its functionalities.

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.

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

Enabling On-Demand Database Computing with MIT SuperCloud Database Management System

DTIC Science & Technology

2015-09-15

arc.liv.ac.uk/trac/SGE) provides these services and is independent of programming language (C, Fortran, Java , Matlab, etc) or parallel programming...a MySQL database to store DNS records. The DNS records are controlled via a simple web service interface that allows records to be created

GIS tool for California state legislature electoral history

NASA Astrophysics Data System (ADS)

Artham, Swathi

The California State Legislature contains two bodies consisting of the lower house, the California State Assembly, with eighty members, and the upper house, the California State Senate, with forty members. Elections are held for every two years for both Senate and Assembly. The terms of the Senators are staggered so that half the membership is elected every two years, whereas all the Assembly members are elected every two years. The electoral district boundaries vary after every 10-year census. My main objective is to provide a summary of both California State Senate and California State Assembly election results in a single GIS tool, from the years 1970 to 2012. This tool provides information about different trends in the California State Senate and State Assembly elections along the years. This tool was designed to help students, and teachers to interactively learn about the California State Legislature elections. Users can view the election results by selecting a particular year for Senate or Assembly, which results in adding a new layer on the map with a coloring scheme for better understanding of change of parties; red for Republicans, blue for Democrats and green for Independents. Users can click on any district shown on the map using a hotlink tool to see the electoral trends for the districts for the past years. This application provides a powerful Stored Query Language (SQL) query option to enter queries and get election results in the form of tables with various fields. This data can be further used to aid other analysis as per user requirements. This tool also provides various visual statistics using graphs and tables for voter turnout, number of candidates won by each party, number of seats changed from one party to another. It also features a color matrix table that helps users to see trends in California State Senate and Assembly. Every two-year election results are shown in the form of graphs and tables for better understanding by the user. The tool provides two quiz options for users who are willing to test the knowledge they gained using the tool. This tool was developed in JAVA swing and AWT, Map Objects Java Objects (MOJO), Apache Derby, DBF Explorer, HTML5, CSS3 and JavaScript.

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

Visualization of Vgi Data Through the New NASA Web World Wind Virtual Globe

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Kilsedar, C. E.; Zamboni, G.

2016-06-01

GeoWeb 2.0, laying the foundations of Volunteered Geographic Information (VGI) systems, has led to platforms where users can contribute to the geographic knowledge that is open to access. Moreover, as a result of the advancements in 3D visualization, virtual globes able to visualize geographic data even on browsers emerged. However the integration of VGI systems and virtual globes has not been fully realized. The study presented aims to visualize volunteered data in 3D, considering also the ease of use aspects for general public, using Free and Open Source Software (FOSS). The new Application Programming Interface (API) of NASA, Web World Wind, written in JavaScript and based on Web Graphics Library (WebGL) is cross-platform and cross-browser, so that the virtual globe created using this API can be accessible through any WebGL supported browser on different operating systems and devices, as a result not requiring any installation or configuration on the client-side, making the collected data more usable to users, which is not the case with the World Wind for Java as installation and configuration of the Java Virtual Machine (JVM) is required. Furthermore, the data collected through various VGI platforms might be in different formats, stored in a traditional relational database or in a NoSQL database. The project developed aims to visualize and query data collected through Open Data Kit (ODK) platform and a cross-platform application, where data is stored in a relational PostgreSQL and NoSQL CouchDB databases respectively.

Computer systems and methods for the query and visualization of multidimensional databases

DOEpatents

Stolte, Chris; Tang, Diane L.; Hanrahan, Patrick

2006-08-08

A method and system for producing graphics. A hierarchical structure of a database is determined. A visual table, comprising a plurality of panes, is constructed by providing a specification that is in a language based on the hierarchical structure of the database. In some cases, this language can include fields that are in the database schema. The database is queried to retrieve a set of tuples in accordance with the specification. A subset of the set of tuples is associated with a pane in the plurality of panes.

Computer systems and methods for the query and visualization of multidimensional database

DOEpatents

Stolte, Chris; Tang, Diane L.; Hanrahan, Patrick

2010-05-11

A method and system for producing graphics. A hierarchical structure of a database is determined. A visual table, comprising a plurality of panes, is constructed by providing a specification that is in a language based on the hierarchical structure of the database. In some cases, this language can include fields that are in the database schema. The database is queried to retrieve a set of tuples in accordance with the specification. A subset of the set of tuples is associated with a pane in the plurality of panes.

A database system to support image algorithm evaluation

NASA Technical Reports Server (NTRS)

Lien, Y. E.

1977-01-01

The design is given of an interactive image database system IMDB, which allows the user to create, retrieve, store, display, and manipulate images through the facility of a high-level, interactive image query (IQ) language. The query language IQ permits the user to define false color functions, pixel value transformations, overlay functions, zoom functions, and windows. The user manipulates the images through generic functions. The user can direct images to display devices for visual and qualitative analysis. Image histograms and pixel value distributions can also be computed to obtain a quantitative analysis of images.

CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages.

PubMed

Bot, Jan J; Reinders, Marcel J T

2011-09-01

CytoscapeRPC is a plugin for Cytoscape which allows users to create, query and modify Cytoscape networks from any programming language which supports XML-RPC. This enables them to access Cytoscape functionality and visualize their data interactively without leaving the programming environment with which they are familiar. Install through the Cytoscape plugin manager or visit the web page: http://wiki.nbic.nl/index.php/CytoscapeRPC for the user tutorial and download. j.j.bot@tudelft.nl; j.j.bot@tudelft.nl.

The Use of Dynamic Segment Scoring for Language-Independent Question Answering

DTIC Science & Technology

2001-01-01

initial window with one sentence is compared to scores corre- his/PRONOUN brother/ CONSANGUINITY like/SIMILARITY his/PRONOUN call/NOMENCLATURE he/PRONOUN...the query processing mod- ule. Using the differences between index numbers to specify phys- ical distance relationships among query keywords, we can

Exploring No-SQL alternatives for ALMA monitoring system

NASA Astrophysics Data System (ADS)

Shen, Tzu-Chiang; Soto, Ruben; Merino, Patricio; Peña, Leonel; Bartsch, Marcelo; Aguirre, Alvaro; Ibsen, Jorge

2014-07-01

The Atacama Large Millimeter /submillimeter Array (ALMA) will be a unique research instrument composed of at least 66 reconfigurable high-precision antennas, located at the Chajnantor plain in the Chilean Andes at an elevation of 5000 m. This paper describes the experience gained after several years working with the monitoring system, which has a strong requirement of collecting and storing up to 150K variables with a highest sampling rate of 20.8 kHz. The original design was built on top of a cluster of relational database server and network attached storage with fiber channel interface. As the number of monitoring points increases with the number of antennas included in the array, the current monitoring system demonstrated to be able to handle the increased data rate in the collection and storage area (only one month of data), but the data query interface showed serious performance degradation. A solution based on no-SQL platform was explored as an alternative to the current long-term storage system. Among several alternatives, mongoDB has been selected. In the data flow, intermediate cache servers based on Redis were introduced to allow faster streaming of the most recently acquired data to web based charts and applications for online data analysis.

Open-Source GIS

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

Vatsavai, Raju; Burk, Thomas E; Lime, Steve

2012-01-01

The components making up an Open Source GIS are explained in this chapter. A map server (Sect. 30.1) can broadly be defined as a software platform for dynamically generating spatially referenced digital map products. The University of Minnesota MapServer (UMN Map Server) is one such system. Its basic features are visualization, overlay, and query. Section 30.2 names and explains many of the geospatial open source libraries, such as GDAL and OGR. The other libraries are FDO, JTS, GEOS, JCS, MetaCRS, and GPSBabel. The application examples include derived GIS-software and data format conversions. Quantum GIS, its origin and its applications explainedmore » in detail in Sect. 30.3. The features include a rich GUI, attribute tables, vector symbols, labeling, editing functions, projections, georeferencing, GPS support, analysis, and Web Map Server functionality. Future developments will address mobile applications, 3-D, and multithreading. The origins of PostgreSQL are outlined and PostGIS discussed in detail in Sect. 30.4. It extends PostgreSQL by implementing the Simple Feature standard. Section 30.5 details the most important open source licenses such as the GPL, the LGPL, the MIT License, and the BSD License, as well as the role of the Creative Commons.« less

A Grid Metadata Service for Earth and Environmental Sciences

NASA Astrophysics Data System (ADS)

Fiore, Sandro; Negro, Alessandro; Aloisio, Giovanni

2010-05-01

Critical challenges for climate modeling researchers are strongly connected with the increasingly complex simulation models and the huge quantities of produced datasets. Future trends in climate modeling will only increase computational and storage requirements. For this reason the ability to transparently access to both computational and data resources for large-scale complex climate simulations must be considered as a key requirement for Earth Science and Environmental distributed systems. From the data management perspective (i) the quantity of data will continuously increases, (ii) data will become more and more distributed and widespread, (iii) data sharing/federation will represent a key challenging issue among different sites distributed worldwide, (iv) the potential community of users (large and heterogeneous) will be interested in discovery experimental results, searching of metadata, browsing collections of files, compare different results, display output, etc.; A key element to carry out data search and discovery, manage and access huge and distributed amount of data is the metadata handling framework. What we propose for the management of distributed datasets is the GRelC service (a data grid solution focusing on metadata management). Despite the classical approaches, the proposed data-grid solution is able to address scalability, transparency, security and efficiency and interoperability. The GRelC service we propose is able to provide access to metadata stored in different and widespread data sources (relational databases running on top of MySQL, Oracle, DB2, etc. leveraging SQL as query language, as well as XML databases - XIndice, eXist, and libxml2 based documents, adopting either XPath or XQuery) providing a strong data virtualization layer in a grid environment. Such a technological solution for distributed metadata management leverages on well known adopted standards (W3C, OASIS, etc.); (ii) supports role-based management (based on VOMS), which increases flexibility and scalability; (iii) provides full support for Grid Security Infrastructure, which means (authorization, mutual authentication, data integrity, data confidentiality and delegation); (iv) is compatible with existing grid middleware such as gLite and Globus and finally (v) is currently adopted at the Euro-Mediterranean Centre for Climate Change (CMCC - Italy) to manage the entire CMCC data production activity as well as in the international Climate-G testbed.

A Simple Blueprint for Automatic Boolean Query Processing.

ERIC Educational Resources Information Center

Salton, G.

1988-01-01

Describes a new Boolean retrieval environment in which an extended soft Boolean logic is used to automatically construct queries from original natural language formulations provided by users. Experimental results that compare the retrieval effectiveness of this method to conventional Boolean and vector processing are discussed. (27 references)…

Experiments in Multi-Lingual Information Retrieval.

ERIC Educational Resources Information Center

Salton, Gerard

A comparison was made of the performance in an automatic information retrieval environment of user queries and document abstracts available in natural language form in both English and French. The results obtained indicate that the automatic indexing and retrieval techniques actually used appear equally effective in handling the query and document…

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

KARL: A Knowledge-Assisted Retrieval Language. Presentation visuals. M.S. Thesis Final Report, 1 Jul. 1985 - 31 Dec. 1987

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Triantafyllopoulos, Spiros

1985-01-01

A collection of presentation visuals associated with the companion report entitled KARL: A Knowledge-Assisted Retrieval Language, is presented. Information is given on data retrieval, natural language database front ends, generic design objectives, processing capababilities and the query processing cycle.

Getting Answers to Natural Language Questions on the Web.

ERIC Educational Resources Information Center

Radev, Dragomir R.; Libner, Kelsey; Fan, Weiguo

2002-01-01

Describes a study that investigated the use of natural language questions on Web search engines. Highlights include query languages; differences in search engine syntax; and results of logistic regression and analysis of variance that showed aspects of questions that predicted significantly different performances, including the number of words,…

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

On describing human white matter anatomy: the white matter query language.

PubMed

Wassermann, Demian; Makris, Nikos; Rathi, Yogesh; Shenton, Martha; Kikinis, Ron; Kubicki, Marek; Westin, Carl-Fredrik

2013-01-01

The main contribution of this work is the careful syntactical definition of major white matter tracts in the human brain based on a neuroanatomist's expert knowledge. We present a technique to formally describe white matter tracts and to automatically extract them from diffusion MRI data. The framework is based on a novel query language with a near-to-English textual syntax. This query language allows us to construct a dictionary of anatomical definitions describing white matter tracts. The definitions include adjacent gray and white matter regions, and rules for spatial relations. This enables automated coherent labeling of white matter anatomy across subjects. We use our method to encode anatomical knowledge in human white matter describing 10 association and 8 projection tracts per hemisphere and 7 commissural tracts. The technique is shown to be comparable in accuracy to manual labeling. We present results applying this framework to create a white matter atlas from 77 healthy subjects, and we use this atlas in a proof-of-concept study to detect tract changes specific to schizophrenia.

FastBit: Interactively Searching Massive Data

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

Wu, Kesheng; Ahern, Sean; Bethel, E. Wes

2009-06-23

As scientific instruments and computer simulations produce more and more data, the task of locating the essential information to gain insight becomes increasingly difficult. FastBit is an efficient software tool to address this challenge. In this article, we present a summary of the key underlying technologies, namely bitmap compression, encoding, and binning. Together these techniques enable FastBit to answer structured (SQL) queries orders of magnitude faster than popular database systems. To illustrate how FastBit is used in applications, we present three examples involving a high-energy physics experiment, a combustion simulation, and an accelerator simulation. In each case, FastBit significantly reducesmore » the response time and enables interactive exploration on terabytes of data.« less

GOSSS-DR1: The First Data Release of the Galactic O-star Spectroscopic Survey

NASA Astrophysics Data System (ADS)

Sota, Alfredo; Maíz Apellániz, Jesús; Barbá, Rodolfo H.; Walborn, Nolan R.; Alfaro, Emilio J.; Gamen, Roberto C.; Morrell, Nidia I.; Arias, Julia I.; Gallego Calvente, A. T.

2013-06-01

Coinciding with this meeting, we are publishing the first data release of GOSSS. This release contains [a] revised spectral classifications and [b] blue-violet R~2500 spectra in FITS format for ~400 Galactic O stars, including all brighter than B=8. DR1 (and future releases) will take place through GOSC, the Galactic O-Star Catalog (http://gosc.iaa.es), which will be updated for the occasion. Since 2011 GOSC runs on a MySQL database and allows for queries based on coordinates, spectral class, photometry, and other parameters. Future data releases will include the rest of the stars observed in GOSSS (currently 1521 with ~1000 more planned in the next two years).

Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes.

PubMed

Hiscock, D; Upton, C

2000-05-01

The Viral Genome DataBase (VGDB) contains detailed information of the genes and predicted protein sequences from 15 completely sequenced genomes of large (&100 kb) viruses (2847 genes). The data that is stored includes DNA sequence, protein sequence, GenBank and user-entered notes, molecular weight (MW), isoelectric point (pI), amino acid content, A + T%, nucleotide frequency, dinucleotide frequency and codon use. The VGDB is a mySQL database with a user-friendly JAVA GUI. Results of queries can be easily sorted by any of the individual parameters. The software and additional figures and information are available at http://athena.bioc.uvic.ca/genomes/index.html .

Using CLIPS in a distributed system: The Network Control Center (NCC) expert system

NASA Technical Reports Server (NTRS)

Wannemacher, Tom

1990-01-01

This paper describes an intelligent troubleshooting system for the Help Desk domain. It was developed on an IBM-compatible 80286 PC using Microsoft C and CLIPS and an AT&T 3B2 minicomputer using the UNIFY database and a combination of shell script, C programs and SQL queries. The two computers are linked by a lan. The functions of this system are to help non-technical NCC personnel handle trouble calls, to keep a log of problem calls with complete, concise information, and to keep a historical database of problems. The database helps identify hardware and software problem areas and provides a source of new rules for the troubleshooting knowledge base.

An Examination of Job Skills Posted on Internet Databases: Implications for Information Systems Degree Programs.

ERIC Educational Resources Information Center

Liu, Xia; Liu, Lai C.; Koong, Kai S.; Lu, June

2003-01-01

Analysis of 300 information technology job postings in two Internet databases identified the following skill categories: programming languages (Java, C/C++, and Visual Basic were most frequent); website development (57% sought SQL and HTML skills); databases (nearly 50% required Oracle); networks (only Windows NT or wide-area/local-area networks);…

A Hybrid Spatio-Temporal Data Indexing Method for Trajectory Databases

PubMed Central

Ke, Shengnan; Gong, Jun; Li, Songnian; Zhu, Qing; Liu, Xintao; Zhang, Yeting

2014-01-01

In recent years, there has been tremendous growth in the field of indoor and outdoor positioning sensors continuously producing huge volumes of trajectory data that has been used in many fields such as location-based services or location intelligence. Trajectory data is massively increased and semantically complicated, which poses a great challenge on spatio-temporal data indexing. This paper proposes a spatio-temporal data indexing method, named HBSTR-tree, which is a hybrid index structure comprising spatio-temporal R-tree, B*-tree and Hash table. To improve the index generation efficiency, rather than directly inserting trajectory points, we group consecutive trajectory points as nodes according to their spatio-temporal semantics and then insert them into spatio-temporal R-tree as leaf nodes. Hash table is used to manage the latest leaf nodes to reduce the frequency of insertion. A new spatio-temporal interval criterion and a new node-choosing sub-algorithm are also proposed to optimize spatio-temporal R-tree structures. In addition, a B*-tree sub-index of leaf nodes is built to query the trajectories of targeted objects efficiently. Furthermore, a database storage scheme based on a NoSQL-type DBMS is also proposed for the purpose of cloud storage. Experimental results prove that HBSTR-tree outperforms TB*-tree in some aspects such as generation efficiency, query performance and query type. PMID:25051028

A hybrid spatio-temporal data indexing method for trajectory databases.

PubMed

Ke, Shengnan; Gong, Jun; Li, Songnian; Zhu, Qing; Liu, Xintao; Zhang, Yeting

2014-07-21

In recent years, there has been tremendous growth in the field of indoor and outdoor positioning sensors continuously producing huge volumes of trajectory data that has been used in many fields such as location-based services or location intelligence. Trajectory data is massively increased and semantically complicated, which poses a great challenge on spatio-temporal data indexing. This paper proposes a spatio-temporal data indexing method, named HBSTR-tree, which is a hybrid index structure comprising spatio-temporal R-tree, B*-tree and Hash table. To improve the index generation efficiency, rather than directly inserting trajectory points, we group consecutive trajectory points as nodes according to their spatio-temporal semantics and then insert them into spatio-temporal R-tree as leaf nodes. Hash table is used to manage the latest leaf nodes to reduce the frequency of insertion. A new spatio-temporal interval criterion and a new node-choosing sub-algorithm are also proposed to optimize spatio-temporal R-tree structures. In addition, a B*-tree sub-index of leaf nodes is built to query the trajectories of targeted objects efficiently. Furthermore, a database storage scheme based on a NoSQL-type DBMS is also proposed for the purpose of cloud storage. Experimental results prove that HBSTR-tree outperforms TB*-tree in some aspects such as generation efficiency, query performance and query type.

An ontology-driven tool for structured data acquisition using Web forms.

PubMed

Gonçalves, Rafael S; Tu, Samson W; Nyulas, Csongor I; Tierney, Michael J; Musen, Mark A

2017-08-01

Structured data acquisition is a common task that is widely performed in biomedicine. However, current solutions for this task are far from providing a means to structure data in such a way that it can be automatically employed in decision making (e.g., in our example application domain of clinical functional assessment, for determining eligibility for disability benefits) based on conclusions derived from acquired data (e.g., assessment of impaired motor function). To use data in these settings, we need it structured in a way that can be exploited by automated reasoning systems, for instance, in the Web Ontology Language (OWL); the de facto ontology language for the Web. We tackle the problem of generating Web-based assessment forms from OWL ontologies, and aggregating input gathered through these forms as an ontology of "semantically-enriched" form data that can be queried using an RDF query language, such as SPARQL. We developed an ontology-based structured data acquisition system, which we present through its specific application to the clinical functional assessment domain. We found that data gathered through our system is highly amenable to automatic analysis using queries. We demonstrated how ontologies can be used to help structuring Web-based forms and to semantically enrich the data elements of the acquired structured data. The ontologies associated with the enriched data elements enable automated inferences and provide a rich vocabulary for performing queries.

SPARQLog: SPARQL with Rules and Quantification

NASA Astrophysics Data System (ADS)

Bry, François; Furche, Tim; Marnette, Bruno; Ley, Clemens; Linse, Benedikt; Poppe, Olga

SPARQL has become the gold-standard for RDF query languages. Nevertheless, we believe there is further room for improving RDF query languages. In this chapter, we investigate the addition of rules and quantifier alternation to SPARQL. That extension, called SPARQLog, extends previous RDF query languages by arbitrary quantifier alternation: blank nodes may occur in the scope of all, some, or none of the universal variables of a rule. In addition, SPARQLog is aware of important RDF features such as the distinction between blank nodes, literals and IRIs or the RDFS vocabulary. The semantics of SPARQLog is closed (every answer is an RDF graph), but lifts RDF's restrictions on literal and blank node occurrences for intermediary data. We show how to define a sound and complete operational semantics that can be implemented using existing logic programming techniques. While SPARQLog is Turing complete, we identify a decidable (in fact, polynomial time) fragment SwARQLog ensuring polynomial data-complexity inspired from the notion of super-weak acyclicity in data exchange. Furthermore, we prove that SPARQLog with no universal quantifiers in the scope of existential ones (∀ ∃ fragment) is equivalent to full SPARQLog in presence of graph projection. Thus, the convenience of arbitrary quantifier alternation comes, in fact, for free. These results, though here presented in the context of RDF querying, apply similarly also in the more general setting of data exchange.

Querying XML Data with SPARQL

NASA Astrophysics Data System (ADS)

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

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

Vaccine-criticism on the internet: new insights based on French-speaking websites.

PubMed

Ward, Jeremy K; Peretti-Watel, Patrick; Larson, Heidi J; Raude, Jocelyn; Verger, Pierre

2015-02-18

The internet is playing an increasingly important part in fueling vaccine related controversies and in generating vaccine hesitant behaviors. English language Antivaccination websites have been thoroughly analyzed, however, little is known of the arguments presented in other languages on the internet. This study presents three types of results: (1) Authors apply a time tested content analysis methodology to describe the information diffused by French language vaccine critical websites in comparison with English speaking websites. The contents of French language vaccine critical websites are very similar to those of English language websites except for the relative absence of moral and religious arguments. (2) Authors evaluate the likelihood that internet users will find those websites through vaccine-related queries on a variety of French-language versions of google. Queries on controversial vaccines generated many more vaccine critical websites than queries on vaccination in general. (3) Authors propose a typology of vaccine critical websites. Authors distinguish between (a) websites that criticize all vaccines ("antivaccine" websites) and websites that criticize only some vaccines ("vaccine-selective" websites), and between (b) websites that focus on vaccines ("vaccine-focused" websites) and those for which vaccines were only a secondary topic of interest ("generalist" websites). The differences in stances by groups and websites affect the likelihood that they will be believed and by whom. This study therefore helps understand the different information landscapes that may contribute to the variety of forms of vaccine hesitancy. Public authorities should have better awareness and understanding of these stances to bring appropriate answers to the different controversies about vaccination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Functional Analysis of Language Interactions between Down Syndrome Children and Their Mothers.

ERIC Educational Resources Information Center

Hooshyar, Nahid T.

A 20-minute videotape sample was obtained of the language interactions between 20 Down syndrome children (ages 38 to 107 months) and their mothers during informal playtime. Linguistic utterances of mothers and children were coded according to the following language categories: query, declarative, imperative, performative, feedback, imitation,…

Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of Cerebrotendinous xanthomatosis.

PubMed

Taboada, María; Martínez, Diego; Pilo, Belén; Jiménez-Escrig, Adriano; Robinson, Peter N; Sobrido, María J

2012-07-31

Semantic Web technology can considerably catalyze translational genetics and genomics research in medicine, where the interchange of information between basic research and clinical levels becomes crucial. This exchange involves mapping abstract phenotype descriptions from research resources, such as knowledge databases and catalogs, to unstructured datasets produced through experimental methods and clinical practice. This is especially true for the construction of mutation databases. This paper presents a way of harmonizing abstract phenotype descriptions with patient data from clinical practice, and querying this dataset about relationships between phenotypes and genetic variants, at different levels of abstraction. Due to the current availability of ontological and terminological resources that have already reached some consensus in biomedicine, a reuse-based ontology engineering approach was followed. The proposed approach uses the Ontology Web Language (OWL) to represent the phenotype ontology and the patient model, the Semantic Web Rule Language (SWRL) to bridge the gap between phenotype descriptions and clinical data, and the Semantic Query Web Rule Language (SQWRL) to query relevant phenotype-genotype bidirectional relationships. The work tests the use of semantic web technology in the biomedical research domain named cerebrotendinous xanthomatosis (CTX), using a real dataset and ontologies. A framework to query relevant phenotype-genotype bidirectional relationships is provided. Phenotype descriptions and patient data were harmonized by defining 28 Horn-like rules in terms of the OWL concepts. In total, 24 patterns of SWQRL queries were designed following the initial list of competency questions. As the approach is based on OWL, the semantic of the framework adapts the standard logical model of an open world assumption. This work demonstrates how semantic web technologies can be used to support flexible representation and computational inference mechanisms required to query patient datasets at different levels of abstraction. The open world assumption is especially good for describing only partially known phenotype-genotype relationships, in a way that is easily extensible. In future, this type of approach could offer researchers a valuable resource to infer new data from patient data for statistical analysis in translational research. In conclusion, phenotype description formalization and mapping to clinical data are two key elements for interchanging knowledge between basic and clinical research.

The EPMI Malay Basin petroleum geology database: Design philosophy and keys to success

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

Low, H.E.; Creaney, S.; Fairchild, L.H.

1994-07-01

Esso Production Malaysia Inc. (EPMI) developed and populated a database containing information collected in the areas of basic well data: stratigraphy, lithology, facies; pressure, temperature, column/contacts; geochemistry, shows and stains, migration, fluid properties; maturation; seal; structure. Paradox was used as the database engine and query language, with links to ZYCOR ZMAP+ for mapping and SAS for data analysis. Paradox has a query language that is simple enough for users. The ability to link to good analytical packages was deemed more important than having the capability in the package. Important elements of design philosophy were included: (1) information on data qualitymore » had to be rigorously recorded; (2) raw and interpreted data were kept separate and clearly identified; (3) correlations between rock and chronostratigraphic surfaces were recorded; and (4) queries across technical boundaries had to be seamless.« less

WebDB Component Builder - Lessons Learned

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

Macedo, C.

2000-02-15

Oracle WebDB is the easiest way to produce web enabled lightweight and enterprise-centric applications. This concept from Oracle has tantalized our taste for simplistic web development by using a purely web based tool that lives nowhere else but in the database. The use of online wizards, templates, and query builders, which produces PL/SQL behind the curtains, can be used straight ''out of the box'' by both novice and seasoned developers. The topic of this presentation will introduce lessons learned by developing and deploying applications built using the WebDB Component Builder in conjunction with custom PL/SQL code to empower a hybridmore » application. There are two kinds of WebDB components: those that display data to end users via reporting, and those that let end users update data in the database via entry forms. The presentation will also discuss various methods within the Component Builder to enhance the applications pushed to the desktop. The demonstrated example is an application entitled HOME (Helping Other's More Effectively) that was built to manage a yearly United Way Campaign effort. Our task was to build an end to end application which could manage approximately 900 non-profit agencies, an average of 4,100 individual contributions, and $1.2 million dollars. Using WebDB, the shell of the application was put together in a matter of a few weeks. However, we did encounter some hurdles that WebDB, in it's stage of infancy (v2.0), could not solve for us directly. Together with custom PL/SQL, WebDB's Component Builder became a powerful tool that enabled us to produce a very flexible hybrid application.« less

My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing.

PubMed

Van Neste, Christophe; Vandewoestyne, Mado; Van Criekinge, Wim; Deforce, Dieter; Van Nieuwerburgh, Filip

2014-03-01

Forensic scientists are currently investigating how to transition from capillary electrophoresis (CE) to massive parallel sequencing (MPS) for analysis of forensic DNA profiles. MPS offers several advantages over CE such as virtually unlimited multiplexy of loci, combining both short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci, small amplicons without constraints of size separation, more discrimination power, deep mixture resolution and sample multiplexing. We present our bioinformatic framework My-Forensic-Loci-queries (MyFLq) for analysis of MPS forensic data. For allele calling, the framework uses a MySQL reference allele database with automatically determined regions of interest (ROIs) by a generic maximal flanking algorithm which makes it possible to use any STR or SNP forensic locus. Python scripts were designed to automatically make allele calls starting from raw MPS data. We also present a method to assess the usefulness and overall performance of a forensic locus with respect to MPS, as well as methods to estimate whether an unknown allele, which sequence is not present in the MySQL database, is in fact a new allele or a sequencing error. The MyFLq framework was applied to an Illumina MiSeq dataset of a forensic Illumina amplicon library, generated from multilocus STR polymerase chain reaction (PCR) on both single contributor samples and multiple person DNA mixtures. Although the multilocus PCR was not yet optimized for MPS in terms of amplicon length or locus selection, the results show excellent results for most loci. The results show a high signal-to-noise ratio, correct allele calls, and a low limit of detection for minor DNA contributors in mixed DNA samples. Technically, forensic MPS affords great promise for routine implementation in forensic genomics. The method is also applicable to adjacent disciplines such as molecular autopsy in legal medicine and in mitochondrial DNA research. Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

MO-F-CAMPUS-T-05: SQL Database Queries to Determine Treatment Planning Resource Usage

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

Fox, C; Gladstone, D

2015-06-15

Purpose: A radiation oncology clinic’s treatment capacity is traditionally thought to be limited by the number of machines in the clinic. As the number of fractions per course decrease and the number of adaptive plans increase, the question of how many treatment plans a clinic can plan becomes increasingly important. This work seeks to lay the ground work for assessing treatment planning resource usage. Methods: Care path templates were created using the Aria 11 care path interface. Care path tasks included key steps in the treatment planning process from the completion of CT simulation through the first radiation treatment. SQLmore » Server Management Studio was used to run SQL queries to extract task completion time stamps along with care path template information and diagnosis codes from the Aria database. 6 months of planning cycles were evaluated. Elapsed time was evaluated in terms of work hours within Monday – Friday, 7am to 5pm. Results: For the 195 validated treatment planning cycles, the average time for planning and MD review was 22.8 hours. Of those cases 33 were categorized as urgent. The average planning time for urgent plans was 5 hours. A strong correlation between diagnosis code and range of elapsed planning time was as well as between elapsed time and select diagnosis codes was observed. It was also observed that tasks were more likely to be completed on the date due than the time that they were due. Follow-up confirmed that most users did not look at the due time. Conclusion: Evaluation of elapsed planning time and other tasks suggest that care paths should be adjusted to allow for different contouring and planning times for certain diagnosis codes and urgent cases. Additional clinic training around task due times vs dates or a structuring of care paths around due dates is also needed.« less

A Fuzzy Query Mechanism for Human Resource Websites

NASA Astrophysics Data System (ADS)

Lai, Lien-Fu; Wu, Chao-Chin; Huang, Liang-Tsung; Kuo, Jung-Chih

Users' preferences often contain imprecision and uncertainty that are difficult for traditional human resource websites to deal with. In this paper, we apply the fuzzy logic theory to develop a fuzzy query mechanism for human resource websites. First, a storing mechanism is proposed to store fuzzy data into conventional database management systems without modifying DBMS models. Second, a fuzzy query language is proposed for users to make fuzzy queries on fuzzy databases. User's fuzzy requirement can be expressed by a fuzzy query which consists of a set of fuzzy conditions. Third, each fuzzy condition associates with a fuzzy importance to differentiate between fuzzy conditions according to their degrees of importance. Fourth, the fuzzy weighted average is utilized to aggregate all fuzzy conditions based on their degrees of importance and degrees of matching. Through the mutual compensation of all fuzzy conditions, the ordering of query results can be obtained according to user's preference.

A Semantic Basis for Proof Queries and Transformations

NASA Technical Reports Server (NTRS)

Aspinall, David; Denney, Ewen W.; Luth, Christoph

2013-01-01

We extend the query language PrQL, designed for inspecting machine representations of proofs, to also allow transformation of proofs. PrQL natively supports hiproofs which express proof structure using hierarchically nested labelled trees, which we claim is a natural way of taming the complexity of huge proofs. Query-driven transformations enable manipulation of this structure, in particular, to transform proofs produced by interactive theorem provers into forms that assist their understanding, or that could be consumed by other tools. In this paper we motivate and define basic transformation operations, using an abstract denotational semantics of hiproofs and queries. This extends our previous semantics for queries based on syntactic tree representations.We define update operations that add and remove sub-proofs, and manipulate the hierarchy to group and ungroup nodes. We show that

Spatiotemporal conceptual platform for querying archaeological information systems

NASA Astrophysics Data System (ADS)

Partsinevelos, Panagiotis; Sartzetaki, Mary; Sarris, Apostolos

2015-04-01

Spatial and temporal distribution of archaeological sites has been shown to associate with several attributes including marine, water, mineral and food resources, climate conditions, geomorphological features, etc. In this study, archeological settlement attributes are evaluated under various associations in order to provide a specialized query platform in a geographic information system (GIS). Towards this end, a spatial database is designed to include a series of archaeological findings for a secluded geographic area of Crete in Greece. The key categories of the geodatabase include the archaeological type (palace, burial site, village, etc.), temporal information of the habitation/usage period (pre Minoan, Minoan, Byzantine, etc.), and the extracted geographical attributes of the sites (distance to sea, altitude, resources, etc.). Most of the related spatial attributes are extracted with readily available GIS tools. Additionally, a series of conceptual data attributes are estimated, including: Temporal relation of an era to a future one in terms of alteration of the archaeological type, topologic relations of various types and attributes, spatial proximity relations between various types. These complex spatiotemporal relational measures reveal new attributes towards better understanding of site selection for prehistoric and/or historic cultures, yet their potential combinations can become numerous. Therefore, after the quantification of the above mentioned attributes, they are classified as of their importance for archaeological site location modeling. Under this new classification scheme, the user may select a geographic area of interest and extract only the important attributes for a specific archaeological type. These extracted attributes may then be queried against the entire spatial database and provide a location map of possible new archaeological sites. This novel type of querying is robust since the user does not have to type a standard SQL query but graphically select an area of interest. In addition, according to the application at hand, novel spatiotemporal attributes and relations can be supported, towards the understanding of historical settlement patterns.

[The design and implementation of the web typical surface object spectral information system in arid areas based on .NET and SuperMap].

PubMed

Xia, Jun; Tashpolat, Tiyip; Zhang, Fei; Ji, Hong-jiang

2011-07-01

The characteristic of object spectrum is not only the base of the quantification analysis of remote sensing, but also the main content of the basic research of remote sensing. The typical surface object spectral database in arid areas oasis is of great significance for applied research on remote sensing in soil salinization. In the present paper, the authors took the Ugan-Kuqa River Delta Oasis as an example, unified .NET and the SuperMap platform with SQL Server database stored data, used the B/S pattern and the C# language to design and develop the typical surface object spectral information system, and established the typical surface object spectral database according to the characteristics of arid areas oasis. The system implemented the classified storage and the management of typical surface object spectral information and the related attribute data of the study areas; this system also implemented visualized two-way query between the maps and attribute data, the drawings of the surface object spectral response curves and the processing of the derivative spectral data and its drawings. In addition, the system initially possessed a simple spectral data mining and analysis capabilities, and this advantage provided an efficient, reliable and convenient data management and application platform for the Ugan-Kuqa River Delta Oasis's follow-up study in soil salinization. Finally, It's easy to maintain, convinient for secondary development and practically operating in good condition.

Telemedicine: Development of a distance care system for pre-dialysis chronic kidney disease patients.

PubMed

Fernandes, Natália Maria da Silva; Bastos, Marcus Gomes; Oliveira, Nivalda A C de; Costa, Alex do Vale; Bernardino, Heder Soares

2015-01-01

The focus in the treatment of CKD is to prevent its progression through optimal medical control. The large number of patients with CKD has pressed nephrologists to assess more patients into ever-smaller periods of consultation. The use of light technologies as a promising form of health care. The internet offers the opportunity to manipulate the doctor in his professional contact with the user. To develop a web system to attend the patients with CKD not on dialysis and clinically stable stages at distance. Developed a system using the Java language, MySQL database and PrimeFaces framework; available on a Glassfish application server. The initial access is performed by the nephrologist, which registers the patients with their personal information and access data. After being registered, the patient (or family doctor) can enter the data of your query and these will be following, passed on to the nephrologist for evaluation. The form with the data of interest is pre-determined, but there is possibility to add free-form information. The system enables, in addition, there is exchange of messages between doctors and patients. In addition, users receive messages via e-mail alerting them of their duties. Confidentiality is guaranteed by individual passwords for doctors and patients. This tool will enable to increase the coverage area of nephrologists, reduce costs and bring the patient to the primary care physician, using the Family Health Program as an interface between the patient and the nephrology secondary care.

The HITRAN2016 molecular spectroscopic database

NASA Astrophysics Data System (ADS)

Gordon, I. E.; Rothman, L. S.; Hill, C.; Kochanov, R. V.; Tan, Y.; Bernath, P. F.; Birk, M.; Boudon, V.; Campargue, A.; Chance, K. V.; Drouin, B. J.; Flaud, J.-M.; Gamache, R. R.; Hodges, J. T.; Jacquemart, D.; Perevalov, V. I.; Perrin, A.; Shine, K. P.; Smith, M.-A. H.; Tennyson, J.; Toon, G. C.; Tran, H.; Tyuterev, V. G.; Barbe, A.; Császár, A. G.; Devi, V. M.; Furtenbacher, T.; Harrison, J. J.; Hartmann, J.-M.; Jolly, A.; Johnson, T. J.; Karman, T.; Kleiner, I.; Kyuberis, A. A.; Loos, J.; Lyulin, O. M.; Massie, S. T.; Mikhailenko, S. N.; Moazzen-Ahmadi, N.; Müller, H. S. P.; Naumenko, O. V.; Nikitin, A. V.; Polyansky, O. L.; Rey, M.; Rotger, M.; Sharpe, S. W.; Sung, K.; Starikova, E.; Tashkun, S. A.; Auwera, J. Vander; Wagner, G.; Wilzewski, J.; Wcisło, P.; Yu, S.; Zak, E. J.

2017-12-01

This paper 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, additional 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. A powerful application programming interface making use of structured query language (SQL) features for higher-level applications of HITRAN is also provided.

The USGS Earthquake Notification Service (ENS): Customizable notifications of earthquakes around the globe

USGS Publications Warehouse

Wald, Lisa A.; Wald, David J.; Schwarz, Stan; Presgrave, Bruce; Earle, Paul S.; Martinez, Eric; Oppenheimer, David

2008-01-01

At the beginning of 2006, the U.S. Geological Survey (USGS) Earthquake Hazards Program (EHP) introduced a new automated Earthquake Notification Service (ENS) to take the place of the National Earthquake Information Center (NEIC) "Bigquake" system and the various other individual EHP e-mail list-servers for separate regions in the United States. These included northern California, southern California, and the central and eastern United States. ENS is a "one-stop shopping" system that allows Internet users to subscribe to flexible and customizable notifications for earthquakes anywhere in the world. The customization capability allows users to define the what (magnitude threshold), the when (day and night thresholds), and the where (specific regions) for their notifications. Customization is achieved by employing a per-user based request profile, allowing the notifications to be tailored for each individual's requirements. Such earthquake-parameter-specific custom delivery was not possible with simple e-mail list-servers. Now that event and user profiles are in a structured query language (SQL) database, additional flexibility is possible. At the time of this writing, ENS had more than 114,000 subscribers, with more than 200,000 separate user profiles. On a typical day, more than 188,000 messages get sent to a variety of widely distributed users for a wide range of earthquake locations and magnitudes. The purpose of this article is to describe how ENS works, highlight the features it offers, and summarize plans for future developments.

Open Clients for Distributed Databases

NASA Astrophysics Data System (ADS)

Chayes, D. N.; Arko, R. A.

2001-12-01

We are actively developing a collection of open source example clients that demonstrate use of our "back end" data management infrastructure. The data management system is reported elsewhere at this meeting (Arko and Chayes: A Scaleable Database Infrastructure). In addition to their primary goal of being examples for others to build upon, some of these clients may have limited utility in them selves. More information about the clients and the data infrastructure is available on line at http://data.ldeo.columbia.edu. The available examples to be demonstrated include several web-based clients including those developed for the Community Review System of the Digital Library for Earth System Education, a real-time watch standers log book, an offline interface to use log book entries, a simple client to search on multibeam metadata and others are Internet enabled and generally web-based front ends that support searches against one or more relational databases using industry standard SQL queries. In addition to the web based clients, simple SQL searches from within Excel and similar applications will be demonstrated. By defining, documenting and publishing a clear interface to the fully searchable databases, it becomes relatively easy to construct client interfaces that are optimized for specific applications in comparison to building a monolithic data and user interface system.

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

NASA Astrophysics Data System (ADS)

Howe, B.; Halperin, D.

2014-12-01

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

Developing A Web-based User Interface for Semantic Information Retrieval

NASA Technical Reports Server (NTRS)

Berrios, Daniel C.; Keller, Richard M.

2003-01-01

While there are now a number of languages and frameworks that enable computer-based systems to search stored data semantically, the optimal design for effective user interfaces for such systems is still uncle ar. Such interfaces should mask unnecessary query detail from users, yet still allow them to build queries of arbitrary complexity without significant restrictions. We developed a user interface supporting s emantic query generation for Semanticorganizer, a tool used by scient ists and engineers at NASA to construct networks of knowledge and dat a. Through this interface users can select node types, node attribute s and node links to build ad-hoc semantic queries for searching the S emanticOrganizer network.

WebBio, a web-based management and analysis system for patient data of biological products in hospital.

PubMed

Lu, Ying-Hao; Kuo, Chen-Chun; Huang, Yaw-Bin

2011-08-01

We selected HTML, PHP and JavaScript as the programming languages to build "WebBio", a web-based system for patient data of biological products and used MySQL as database. WebBio is based on the PHP-MySQL suite and is run by Apache server on Linux machine. WebBio provides the functions of data management, searching function and data analysis for 20 kinds of biological products (plasma expanders, human immunoglobulin and hematological products). There are two particular features in WebBio: (1) pharmacists can rapidly find out whose patients used contaminated products for medication safety, and (2) the statistics charts for a specific product can be automatically generated to reduce pharmacist's work loading. WebBio has successfully turned traditional paper work into web-based data management.

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.

The BDNYC database of low-mass stars, brown dwarfs, and planetary mass companions

NASA Astrophysics Data System (ADS)

Cruz, Kelle; Rodriguez, David; Filippazzo, Joseph; Gonzales, Eileen; Faherty, Jacqueline K.; Rice, Emily; BDNYC

2018-01-01

We present a web-interface to a database of low-mass stars, brown dwarfs, and planetary mass companions. Users can send SELECT SQL queries to the database, perform searches by coordinates or name, check the database inventory on specified objects, and even plot spectra interactively. The initial version of this database contains information for 198 objects and version 2 will contain over 1000 objects. The database currently includes photometric data from 2MASS, WISE, and Spitzer and version 2 will include a significant portion of the publicly available optical and NIR spectra for brown dwarfs. The database is maintained and curated by the BDNYC research group and we welcome contributions from other researchers via GitHub.

The Data Acquisition System of the Stockholm Educational Air Shower Array

NASA Astrophysics Data System (ADS)

Hofverberg, P.; Johansson, H.; Pearce, M.; Rydstrom, S.; Wikstrom, C.

2005-12-01

The Stockholm Educational Air Shower Array (SEASA) project is deploying an array of plastic scintillator detector stations on school roofs in the Stockholm area. Signals from GPS satellites are used to time synchronise signals from the widely separated detector stations, allowing cosmic ray air showers to be identified and studied. A low-cost and highly scalable data acquisition system has been produced using embedded Linux processors which communicate station data to a central server running a MySQL database. Air shower data can be visualised in real-time using a Java-applet client. It is also possible to query the database and manage detector stations from the client. In this paper, the design and performance of the system are described

Analysis of web-related threats in ten years of logs from a scientific portal

NASA Astrophysics Data System (ADS)

Santos, Rafael D. C.; Grégio, André R. A.; Raddick, Jordan; Vattki, Vamsi; Szalay, Alex

2012-06-01

SkyServer is an Internet portal to data from the Sloan Digital Sky Survey, the largest online archive of astronomy data in the world. provides free access to hundreds of millions of celestial objects for science, education and outreach purposes. Logs of accesses to SkyServer comprise around 930 million hits, 140 million web services accesses and 170 million SQL submitted queries, collected over the past 10 years. These logs also contain indications of compromise attempts on the servers. In this paper, we show some threats that were detected in ten years of stored logs, and compare them with known threats in those years. Also, we present an analysis of the evolution of those threats over these years.

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.

Integrating unified medical language system and association mining techniques into relevance feedback for biomedical literature search.

PubMed

Ji, Yanqing; Ying, Hao; Tran, John; Dews, Peter; Massanari, R Michael

2016-07-19

Finding highly relevant articles from biomedical databases is challenging not only because it is often difficult to accurately express a user's underlying intention through keywords but also because a keyword-based query normally returns a long list of hits with many citations being unwanted by the user. This paper proposes a novel biomedical literature search system, called BiomedSearch, which supports complex queries and relevance feedback. The system employed association mining techniques to build a k-profile representing a user's relevance feedback. More specifically, we developed a weighted interest measure and an association mining algorithm to find the strength of association between a query and each concept in the article(s) selected by the user as feedback. The top concepts were utilized to form a k-profile used for the next-round search. BiomedSearch relies on Unified Medical Language System (UMLS) knowledge sources to map text files to standard biomedical concepts. It was designed to support queries with any levels of complexity. A prototype of BiomedSearch software was made and it was preliminarily evaluated using the Genomics data from TREC (Text Retrieval Conference) 2006 Genomics Track. Initial experiment results indicated that BiomedSearch increased the mean average precision (MAP) for a set of queries. With UMLS and association mining techniques, BiomedSearch can effectively utilize users' relevance feedback to improve the performance of biomedical literature search.

Improving Concept-Based Web Image Retrieval by Mixing Semantically Similar Greek Queries

ERIC Educational Resources Information Center

Lazarinis, Fotis

2008-01-01

Purpose: Image searching is a common activity for web users. Search engines offer image retrieval services based on textual queries. Previous studies have shown that web searching is more demanding when the search is not in English and does not use a Latin-based language. The aim of this paper is to explore the behaviour of the major search…

Design of a Low-Cost Adaptive Question Answering System for Closed Domain Factoid Queries

ERIC Educational Resources Information Center

Toh, Huey Ling

2010-01-01

Closed domain question answering (QA) systems achieve precision and recall at the cost of complex language processing techniques to parse the answer corpus. We propose a "query-based" model for indexing answers in a closed domain factoid QA system. Further, we use a phrase term inference method for improving the ranking order of related questions.…

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.

CITE NLM: Natural-Language Searching in an Online Catalog.

ERIC Educational Resources Information Center

Doszkocs, Tamas E.

1983-01-01

The National Library of Medicine's Current Information Transfer in English public access online catalog offers unique subject search capabilities--natural-language query input, automatic medical subject headings display, closest match search strategy, ranked document output, dynamic end user feedback for search refinement. References, description…

Interrogation: General vs. Local.

ERIC Educational Resources Information Center

Johnson, Jeannette

This paper proposes a set of hypotheses on the nature of interrogration as a possible language universal. Examples and phrase structure rules and diagrams are given. Examining Tamazight and English, genetically unrelated languages with almost no contact, the author distinguishes two types of interrogation: (1) general, querying acceptability to…

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.

Clinician-Oriented Access to Data - C.O.A.D.: A Natural Language Interface to a VA DHCP Database

PubMed Central

Levy, Christine; Rogers, Elizabeth

1995-01-01

Hospitals collect enormous amounts of data related to the on-going care of patients. Unfortunately, a clinicians access to the data is limited by complexities of the database structure and/or programming skills required to access the database. The COAD project attempts to bridge the gap between the clinical user's need for specific information from the database, and the wealth of data residing in the hospital information system. The project design includes a natural language interface to data contained in a VA DHCP database. We have developed a prototype which links natural language software to certain DHCP data elements, including, patient demographics, prescriptions, diagnoses, laboratory data, and provider information. English queries can by typed onto the system, and answers to the questions are returned. Future work includes refinement of natural language/DHCP connections to enable more sophisticated queries, and optimization of the system to reduce response time to user questions.

Spanish for Business: A Journey into Employability

ERIC Educational Resources Information Center

Lallana, Amparo; Pastor-González, Victoria

2016-01-01

As language lecturers, we believe that we equip our graduates with a range of key skills that give them an edge in the employment market. But, query final year students of a Business and Languages degree on the value of language learning for employability, and they are likely to mention a small number of functional abilities such as CV writing and…

Persistent Identifiers for Improved Accessibility for Linked Data Querying

NASA Astrophysics Data System (ADS)

Shepherd, A.; Chandler, C. L.; Arko, R. A.; Fils, D.; Jones, M. B.; Krisnadhi, A.; Mecum, B.

2016-12-01

The adoption of linked open data principles within the geosciences has increased the amount of accessible information available on the Web. However, this data is difficult to consume for those who are unfamiliar with Semantic Web technologies such as Web Ontology Language (OWL), Resource Description Framework (RDF) and SPARQL - the RDF query language. Consumers would need to understand the structure of the data and how to efficiently query it. Furthermore, understanding how to query doesn't solve problems of poor precision and recall in search results. For consumers unfamiliar with the data, full-text searches are most accessible, but not ideal as they arrest the advantages of data disambiguation and co-reference resolution efforts. Conversely, URI searches across linked data can deliver improved search results, but knowledge of these exact URIs may remain difficult to obtain. The increased adoption of Persistent Identifiers (PIDs) can lead to improved linked data querying by a wide variety of consumers. Because PIDs resolve to a single entity, they are an excellent data point for disambiguating content. At the same time, PIDs are more accessible and prominent than a single data provider's linked data URI. When present in linked open datasets, PIDs provide balance between the technical and social hurdles of linked data querying as evidenced by the NSF EarthCube GeoLink project. The GeoLink project, funded by NSF's EarthCube initiative, have brought together data repositories include content from field expeditions, laboratory analyses, journal publications, conference presentations, theses/reports, and funding awards that span scientific studies from marine geology to marine ecosystems and biogeochemistry to paleoclimatology.

Querying temporal clinical databases on granular trends.

PubMed

Combi, Carlo; Pozzi, Giuseppe; Rossato, Rosalba

2012-04-01

This paper focuses on the identification of temporal trends involving different granularities in clinical databases, where data are temporal in nature: for example, while follow-up visit data are usually stored at the granularity of working days, queries on these data could require to consider trends either at the granularity of months ("find patients who had an increase of systolic blood pressure within a single month") or at the granularity of weeks ("find patients who had steady states of diastolic blood pressure for more than 3 weeks"). Representing and reasoning properly on temporal clinical data at different granularities are important both to guarantee the efficacy and the quality of care processes and to detect emergency situations. Temporal sequences of data acquired during a care process provide a significant source of information not only to search for a particular value or an event at a specific time, but also to detect some clinically-relevant patterns for temporal data. We propose a general framework for the description and management of temporal trends by considering specific temporal features with respect to the chosen time granularity. Temporal aspects of data are considered within temporal relational databases, first formally by using a temporal extension of the relational calculus, and then by showing how to map these relational expressions to plain SQL queries. Throughout the paper we consider the clinical domain of hemodialysis, where several parameters are periodically sampled during every session. Copyright © 2011 Elsevier Inc. All rights reserved.

MP3C - the Minor Planet Physical Properties Catalogue: a New VO Service For Multi-database Query

NASA Astrophysics Data System (ADS)

Tanga, Paolo; Delbo, M.; Gerakis, J.

2013-10-01

In the last few years we witnessed a large growth in the number of asteroids for which we have physical properties. However, these data are dispersed in a multiplicity of catalogs. Extracting data and combining them for further analysis requires custom tools, a situation further complicated by the variety of data sources, some of them standardized (Planetary Data System) others not. With these problems in mind, we created a new Virtual Observatory service named “Minor Planet Physical Properties Catalogue” (abbreviated as MP3C - http://mp3c.oca.eu/). MP3C is not a new database, but rather a portal allowing the user to access selected properties of objects by easy SQL query, even from different sources. At present, such diverse data as orbital parameters, photometric and light curve parameters, sizes and albedos derived by IRAS, AKARI and WISE, SDSS colors, SMASS taxonomy, family membership, satellite data, stellar occultation results, are included. Other data sources will be added in the near future. The physical properties output of the MP3C can be tuned by the users by query criteria based upon ranges of values of the ingested quantities. The resulting list of object can be used for interactive plots through standard VO tools such as TOPCAT. Also, their ephemerids and visibilities from given sites can be computed. We are targeting full VO compliance for providing a new standardized service to the community.

UMass at TREC 2002: Cross Language and Novelty Tracks

DTIC Science & Technology

2002-01-01

resources – stemmers, dictionaries , machine translation, and an acronym database. We found that proper names were extremely important in this year’s queries...data by manually annotating 48 additional topics. 1. Cross Language Track We submitted one monolingual run and four cross-language runs. For the... monolingual run, the technology was essentially the same as the system we used for TREC 2001. For the cross-language run, we integrated some new

The Effect of Bilingual Term List Size on Dictionary-Based Cross-Language Information Retrieval

DTIC Science & Technology

2006-01-01

The Effect of Bilingual Term List Size on Dictionary -Based Cross-Language Information Retrieval Dina Demner-Fushman Department of Computer Science... dictionary -based Cross-Language Information Retrieval (CLIR), in which the goal is to find documents written in one natural language based on queries that...in which the documents are written. In dictionary -based CLIR techniques, the princi- pal source of translation knowledge is a translation lexicon

Collaboration-Centred Cities through Urban Apps Based on Open and User-Generated Data

PubMed Central

Aguilera, Unai; López-de-Ipiña, Diego; Pérez, Jorge

2016-01-01

This paper describes the IES Cities platform conceived to streamline the development of urban apps that combine heterogeneous datasets provided by diverse entities, namely, government, citizens, sensor infrastructure and other information data sources. This work pursues the challenge of achieving effective citizen collaboration by empowering them to prosume urban data across time. Particularly, this paper focuses on the query mapper; a key component of the IES Cities platform devised to democratize the development of open data-based mobile urban apps. This component allows developers not only to use available data, but also to contribute to existing datasets with the execution of SQL sentences. In addition, the component allows developers to create ad hoc storages for their applications, publishable as new datasets accessible by other consumers. As multiple users could be contributing and using a dataset, our solution also provides a data level permission mechanism to control how the platform manages the access to its datasets. We have evaluated the advantages brought forward by IES Cities from the developers’ perspective by describing an exemplary urban app created on top of it. In addition, we include an evaluation of the main functionalities of the query mapper. PMID:27376300

Collaboration-Centred Cities through Urban Apps Based on Open and User-Generated Data.

PubMed

Aguilera, Unai; López-de-Ipiña, Diego; Pérez, Jorge

2016-07-01

This paper describes the IES Cities platform conceived to streamline the development of urban apps that combine heterogeneous datasets provided by diverse entities, namely, government, citizens, sensor infrastructure and other information data sources. This work pursues the challenge of achieving effective citizen collaboration by empowering them to prosume urban data across time. Particularly, this paper focuses on the query mapper; a key component of the IES Cities platform devised to democratize the development of open data-based mobile urban apps. This component allows developers not only to use available data, but also to contribute to existing datasets with the execution of SQL sentences. In addition, the component allows developers to create ad hoc storages for their applications, publishable as new datasets accessible by other consumers. As multiple users could be contributing and using a dataset, our solution also provides a data level permission mechanism to control how the platform manages the access to its datasets. We have evaluated the advantages brought forward by IES Cities from the developers' perspective by describing an exemplary urban app created on top of it. In addition, we include an evaluation of the main functionalities of the query mapper.