New Path Based Index Structure for Processing CAS Queries over XML Database

Directory of Open Access Journals (Sweden)

Krishna Asawa

2017-01-01

Full Text Available Querying nested data has become one of the most challenging issues for retrieving desired information from the Web. Today diverse applications generate a tremendous amount of data in different formats. These data and information exchanged on the Web are commonly expressed as nested representation such as XML, JSON, etc. Unlike the traditional database system, they don't have a rigid schema. In general, the nested data is managed by storing data and its structures separately which significantly reduces the performance of data retrieving. Ensuring efficiency of processing queries which locates the exact positions of the elements has become a big challenging issue. There are different indexing structures which have been proposed in the literature to improve the performance of the query processing on the nested structure. Most of the past researches on nested structure concentrate on the structure alone. This paper proposes new index structure which combines siblings of the terminal nodes as one path which efficiently processes twig queries with less number of lookups and joins. The proposed approach is compared with some of the existing approaches. The results also show that they are processed with better performance compared to the existing ones.

StarDOM: From STAR format to XML

International Nuclear Information System (INIS)

Linge, Jens P.; Nilges, Michael; Ehrlich, Lutz

1999-01-01

StarDOM is a software package for the representation of STAR files as document object models and the conversion of STAR files into XML. This allows interactive navigation by using the Document Object Model representation of the data as well as easy access by XML query languages. As an example application, the entire BioMagResBank has been transformed into XML format. Using an XML query language, statistical queries on the collected NMR data sets can be constructed with very little effort. The BioMagResBank/XML data and the software can be obtained at http://www.nmr.embl-heidelberg.de/nmr/StarDOM/

Shuttle-Data-Tape XML Translator

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Intelligent Search on XML Data

NARCIS (Netherlands)

Blanken, Henk; Grabs, T.; Schek, H-J.; Schenkel, R.; Weikum, G.; Unknown, [Unknown

2003-01-01

Recently, we have seen a steep increase in the popularity and adoption of XML, in areas such as traditional databases, e-business, the scientific environment, and on the web. Querying XML documents and data efficiently is a challenging issue; this book approaches search on XML data by combining

Constraint-based query distribution framework for an integrated global schema

DEFF Research Database (Denmark)

Malik, Ahmad Kamran; Qadir, Muhammad Abdul; Iftikhar, Nadeem

2009-01-01

and replicated data sources. The provided system is all XML-based which poses query in XML form, transforms, and integrates local results in an XML document. Contributions include the use of constraints in our existing global schema which help in source selection and query optimization, and a global query...

XML: Ejemplos de uso

OpenAIRE

Luján Mora, Sergio

2011-01-01

XML (eXtensible Markup Language, Lenguaje de marcas extensible) - Aplicación XML = Lenguaje de marcado = Vocabulario - Ejemplos: DocBook, Chemical Markup Language, Keyhole Markup Language, Mathematical Markup Language, Open Document, Open XML Format, Scalable Vector Graphics, Systems Byology Markup Language.

Experience in Computer-Assisted XML-Based Modelling in the Context of Libraries

CERN Document Server

Niinimäki, M

2003-01-01

In this paper, we introduce a software called Meta Data Visualisation (MDV) that (i) assists the user with a graphical user interface in the creation of his specific document types, (ii) creates a database according to these document types, (iii) allows the user to browse the database, and (iv) uses native XML presentation of the data in order to allow queries or data to be exported to other XML-based systems. We illustrate the use of MDV and XML modelling using library-related examples to build a bibliographic database. In our opinion, creating document type descriptions corresponds to conceptual and logical database design in a database design process. We consider that this design can be supported with a suitable set of tools that help the designer concentrate on conceptual issues instead of implementation issues. Our hypothesis is that using the methodology presented in this paper we can create XML databases that are useful and relevant, and with which MDV works as a user interface.

A comparison of database systems for XML-type data.

Science.gov (United States)

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.

Securing XML Documents

Directory of Open Access Journals (Sweden)

Charles Shoniregun

2004-11-01

Full Text Available XML (extensible markup language is becoming the current standard for establishing interoperability on the Web. XML data are self-descriptive and syntax-extensible; this makes it very suitable for representation and exchange of semi-structured data, and allows users to define new elements for their specific applications. As a result, the number of documents incorporating this standard is continuously increasing over the Web. The processing of XML documents may require a traversal of all document structure and therefore, the cost could be very high. A strong demand for a means of efficient and effective XML processing has posed a new challenge for the database world. This paper discusses a fast and efficient indexing technique for XML documents, and introduces the XML graph numbering scheme. It can be used for indexing and securing graph structure of XML documents. This technique provides an efficient method to speed up XML data processing. Furthermore, the paper explores the classification of existing methods impact of query processing, and indexing.

TX-Kw: An Effective Temporal XML Keyword Search

OpenAIRE

Rasha Bin-Thalab; Neamat El-Tazi; Mohamed E.El-Sharkawi

2013-01-01

Inspired by the great success of information retrieval (IR) style keyword search on the web, keyword search on XML has emerged recently. Existing methods cannot resolve challenges addressed by using keyword search in Temporal XML documents. We propose a way to evaluate temporal keyword search queries over Temporal XML documents. Moreover, we propose a new ranking method based on the time-aware IR ranking methods to rank temporal keyword search queries results. Extensive experiments have been ...

Storing XML Documents in Databases

OpenAIRE

Schmidt, A.R.; Manegold, Stefan; Kersten, Martin; Rivero, L.C.; Doorn, J.H.; Ferraggine, V.E.

2005-01-01

textabstractThe authors introduce concepts for loading large amounts of XML documents into databases where the documents are stored and maintained. The goal is to make XML databases as unobtrusive in multi-tier systems as possible and at the same time provide as many services defined by the XML standards as possible. The ubiquity of XML has sparked great interest in deploying concepts known from Relational Database Management Systems such as declarative query languages, transactions, indexes ...

Statistical Language Models for Intelligent XML Retrieval

NARCIS (Netherlands)

Hiemstra, Djoerd; Blanken, Henk; Grabs, T.; Schek, H-J.; Schenkel, R.; Weikum, G.

2003-01-01

The XML standards that are currently emerging have a number of characteristics that can also be found in database management systems, like schemas (DTDs and XML schema) and query languages (XPath and XQuery). Following this line of reasoning, an XML database might resemble traditional database

Statistical language Models for Intelligent XML Retrieval

NARCIS (Netherlands)

Hiemstra, Djoerd; Blanken, H.M.; Grabs, T.; Schek, H-J.; Schenkel, R.; Weikum, G.

2003-01-01

The XML standards that are currently emerging have a number of characteristics that can also be found in database management systems, like schemas (DTDs and XML schema) and query languages (XPath and XQuery). Following this line of reasoning, an XML database might resemble traditional database

Labeling RDF Graphs for Linear Time and Space Querying

Science.gov (United States)

Furche, Tim; Weinzierl, Antonius; Bry, François

Indices and data structures for web querying have mostly considered tree shaped data, reflecting the view of XML documents as tree-shaped. However, for RDF (and when querying ID/IDREF constraints in XML) data is indisputably graph-shaped. In this chapter, we first study existing indexing and labeling schemes for RDF and other graph datawith focus on support for efficient adjacency and reachability queries. For XML, labeling schemes are an important part of the widespread adoption of XML, in particular for mapping XML to existing (relational) database technology. However, the existing indexing and labeling schemes for RDF (and graph data in general) sacrifice one of the most attractive properties of XML labeling schemes, the constant time (and per-node space) test for adjacency (child) and reachability (descendant). In the second part, we introduce the first labeling scheme for RDF data that retains this property and thus achieves linear time and space processing of acyclic RDF queries on a significantly larger class of graphs than previous approaches (which are mostly limited to tree-shaped data). Finally, we show how this labeling scheme can be applied to (acyclic) SPARQL queries to obtain an evaluation algorithm with time and space complexity linear in the number of resources in the queried RDF graph.

Integrating XML Data in the TARGIT OLAP System

DEFF Research Database (Denmark)

Pedersen, Dennis; Pedersen, Jesper; Pedersen, Torben Bach

2004-01-01

This paper presents work on logical integration of OLAP and XML data sources, carried out in cooperation between TARGIT, a Danish OLAP client vendor, and Aalborg University. A prototype has been developed that allows XML data on the WWW to be used as dimensions and measures in the OLAP system...... the ability to use XML data as measures, as well as a novel multigranular data model and query language that formalizes and extends the TARGIT data model and query language....

Domain XML semantic integration based on extraction rules and ontology mapping

Directory of Open Access Journals (Sweden)

Huayu LI

2016-08-01

Full Text Available A plenty of XML documents exist in petroleum engineering field, but traditional XML integration solution can’t provide semantic query, which leads to low data use efficiency. In light of WeXML(oil&gas well XML data semantic integration and query requirement, this paper proposes a semantic integration method based on extraction rules and ontology mapping. The method firstly defines a series of extraction rules with which elements and properties of WeXML Schema are mapped to classes and properties in WeOWL ontology, respectively; secondly, an algorithm is used to transform WeXML documents into WeOWL instances. Because WeOWL provides limited semantics, ontology mappings between two ontologies are then built to explain class and property of global ontology with terms of WeOWL, and semantic query based on global domain concepts model is provided. By constructing a WeXML data semantic integration prototype system, the proposed transformational rule, the transfer algorithm and the mapping rule are tested.

The OLAP-XML Federation System

DEFF Research Database (Denmark)

Yin, Xuepeng; Pedersen, Torben Bach

2006-01-01

We present the logical “OLAP-XML Federation System” that enables the external data available in XML format to be used as virtual dimensions. Unlike the complex and time-consuming physical integration of OLAP and external data in current OLAP systems, our system makes OLAP queries referencing fast...

A Survey in Indexing and Searching XML Documents.

Science.gov (United States)

Luk, Robert W. P.; Leong, H. V.; Dillon, Tharam S.; Chan, Alvin T. S.; Croft, W. Bruce; Allan, James

2002-01-01

Discussion of XML focuses on indexing techniques for XML documents, grouping them into flat-file, semistructured, and structured indexing paradigms. Highlights include searching techniques, including full text search and multistage search; search result presentations; database and information retrieval system integration; XML query languages; and…

An exponentiation method for XML element retrieval.

Science.gov (United States)

Wichaiwong, Tanakorn

2014-01-01

XML document is now widely used for modelling and storing structured documents. The structure is very rich and carries important information about contents and their relationships, for example, e-Commerce. XML data-centric collections require query terms allowing users to specify constraints on the document structure; mapping structure queries and assigning the weight are significant for the set of possibly relevant documents with respect to structural conditions. In this paper, we present an extension to the MEXIR search system that supports the combination of structural and content queries in the form of content-and-structure queries, which we call the Exponentiation function. It has been shown the structural information improve the effectiveness of the search system up to 52.60% over the baseline BM25 at MAP.

Assessing XML Data Management with XMark

OpenAIRE

Schmidt, A.R.; Waas, F.; Kersten, Martin; Carey, M.J.; Manolescu, I.; Busse, R.

2002-01-01

textabstractWe discuss some of the experiences we gathered during the development and deployment of XMark, a tool to assess the infrastructure and performance of XML Data Management Systems. Since the appearance of the first XML database prototypes in research institutions and development labs, topics like validation, performance evaluation and optimization of XML query processors have received significant interest. The XMark benchmark follows a tradition in database research and provides a f...

Utilizing Structural Knowledge for Information Retrieval in XML Databases

NARCIS (Netherlands)

Mihajlovic, V.; Hiemstra, Djoerd; Blok, H.E.; Apers, Peter M.G.

In this paper we address the problem of immediate translation of eXtensible Mark-up Language (XML) information retrieval (IR) queries to relational database expressions and stress the benefits of using an intermediate XML-specific algebra over relational algebra. We show how adding an XML-specific

An Exponentiation Method for XML Element Retrieval

Science.gov (United States)

2014-01-01

XML document is now widely used for modelling and storing structured documents. The structure is very rich and carries important information about contents and their relationships, for example, e-Commerce. XML data-centric collections require query terms allowing users to specify constraints on the document structure; mapping structure queries and assigning the weight are significant for the set of possibly relevant documents with respect to structural conditions. In this paper, we present an extension to the MEXIR search system that supports the combination of structural and content queries in the form of content-and-structure queries, which we call the Exponentiation function. It has been shown the structural information improve the effectiveness of the search system up to 52.60% over the baseline BM25 at MAP. PMID:24696643

XML: Ejemplos de uso (presentación)

OpenAIRE

Luján Mora, Sergio

2011-01-01

XML (eXtensible Markup Language, Lenguaje de marcas extensible) - Aplicación XML = Lenguaje de marcado = Vocabulario - Ejemplos: DocBook, Chemical Markup Language, Keyhole Markup Language, Mathematical Markup Language, Open Document, Open XML Format, Scalable Vector Graphics, Systems Byology Markup Language.

Integrity Based Access Control Model for Multilevel XML Document

Institute of Scientific and Technical Information of China (English)

HONG Fan; FENG Xue-bin; HUANO Zhi; ZHENG Ming-hui

2008-01-01

XML's increasing popularity highlights the security demand for XML documents. A mandatory access control model for XML document is presented on the basis of investigation of the function dependency of XML documents and discussion of the integrity properties of multilevel XML document. Then, the algorithms for decomposition/recovery multilevel XML document into/from single level document are given, and the manipulation rules for typical operations of XQuery and XUpdate: QUERY, INSERT,UPDATE, and REMOVE, are elaborated. The multilevel XML document access model can meet the requirement of sensitive information processing application.

XML schema matching: balancing efficiency and effectiveness by means of clustering

NARCIS (Netherlands)

Smiljanic, M.

2006-01-01

In this thesis we place our research in the scope of a tool which looks for information within XML data on the Internet. We envision a personal schema querying system which enables a user to express his information need by specifying a personal XML schema. The user can also ask queries over his

Graphical modeling and query language for hospitals.

Science.gov (United States)

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

Compression of Probabilistic XML Documents

Science.gov (United States)

Veldman, Irma; de Keijzer, Ander; van Keulen, Maurice

Database techniques to store, query and manipulate data that contains uncertainty receives increasing research interest. Such UDBMSs can be classified according to their underlying data model: relational, XML, or RDF. We focus on uncertain XML DBMS with as representative example the Probabilistic XML model (PXML) of [10,9]. The size of a PXML document is obviously a factor in performance. There are PXML-specific techniques to reduce the size, such as a push down mechanism, that produces equivalent but more compact PXML documents. It can only be applied, however, where possibilities are dependent. For normal XML documents there also exist several techniques for compressing a document. Since Probabilistic XML is (a special form of) normal XML, it might benefit from these methods even more. In this paper, we show that existing compression mechanisms can be combined with PXML-specific compression techniques. We also show that best compression rates are obtained with a combination of PXML-specific technique with a rather simple generic DAG-compression technique.

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

Science.gov (United States)

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

2018-05-11

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

XQOWL: An Extension of XQuery for OWL Querying and Reasoning

Directory of Open Access Journals (Sweden)

Jesús M. Almendros-Jiménez

2015-01-01

Full Text Available One of the main aims of the so-called Web of Data is to be able to handle heterogeneous resources where data can be expressed in either XML or RDF. The design of programming languages able to handle both XML and RDF data is a key target in this context. In this paper we present a framework called XQOWL that makes possible to handle XML and RDF/OWL data with XQuery. XQOWL can be considered as an extension of the XQuery language that connects XQuery with SPARQL and OWL reasoners. XQOWL embeds SPARQL queries (via Jena SPARQL engine in XQuery and enables to make calls to OWL reasoners (HermiT, Pellet and FaCT++ from XQuery. It permits to combine queries against XML and RDF/OWL resources as well as to reason with RDF/OWL data. Therefore input data can be either XML or RDF/OWL and output data can be formatted in XML (also using RDF/OWL XML serialization.

A Database Approach to Content-based XML retrieval

NARCIS (Netherlands)

Hiemstra, Djoerd

2003-01-01

This paper describes a rst prototype system for content-based retrieval from XML data. The system's design supports both XPath queries and complex information retrieval queries based on a language modelling approach to information retrieval. Evaluation using the INEX benchmark shows that it is

CIRQuL: Complex Information Retrieval Query Language

NARCIS (Netherlands)

Mihajlovic, V.; Hiemstra, Djoerd; Apers, Peter M.G.

In this paper we will present a new framework for the retrieval of XML documents. We will describe the extension for existing query languages (XPath and XQuery) geared toward ranked information retrieval and full-text search in XML documents. Furthermore we will present language models for ranked

An Evaluation of the Interactive Query Expansion in an Online Library Catalogue with a Graphical User Interface.

Science.gov (United States)

Hancock-Beaulieu, Micheline; And Others

1995-01-01

An online library catalog was used to evaluate an interactive query expansion facility based on relevance feedback for the Okapi, probabilistic, term weighting, retrieval system. A graphical user interface allowed searchers to select candidate terms extracted from relevant retrieved items to reformulate queries. Results suggested that the…

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

Science.gov (United States)

Mitri, Michel

2012-01-01

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

Vague element selection and query rewriting for XML retrieval

NARCIS (Netherlands)

Mihajlovic, V.; Hiemstra, Djoerd; Blok, H.E.; de Jong, Franciska M.G.; Kraaij, W.

In this paper we present the extension of our prototype three-level database system (TIJAH) developed for structured information retrieval. The extension is aimed at modeling vague search on XML elements. All three levels (conceptual, logical, and physical) of the TIJAH system are enhanced to

Managing XML Data to optimize Performance into Object-Relational Databases

Directory of Open Access Journals (Sweden)

Iuliana BOTHA

2011-06-01

Full Text Available This paper propose some possibilities for manage XML data in order to optimize performance into object-relational databases. It is detailed the possibility of storing XML data into such databases, using for exemplification an Oracle database and there are tested some optimizing techniques of the queries over XMLType tables, like indexing and partitioning tables.

Integrating personalized medical test contents with XML and XSL-FO.

Science.gov (United States)

Toddenroth, Dennis; Dugas, Martin; Frankewitsch, Thomas

2011-03-01

In 2004 the adoption of a modular curriculum at the medical faculty in Muenster led to the introduction of centralized examinations based on multiple-choice questions (MCQs). We report on how organizational challenges of realizing faculty-wide personalized tests were addressed by implementation of a specialized software module to automatically generate test sheets from individual test registrations and MCQ contents. Key steps of the presented method for preparing personalized test sheets are (1) the compilation of relevant item contents and graphical media from a relational database with database queries, (2) the creation of Extensible Markup Language (XML) intermediates, and (3) the transformation into paginated documents. The software module by use of an open source print formatter consistently produced high-quality test sheets, while the blending of vectorized textual contents and pixel graphics resulted in efficient output file sizes. Concomitantly the module permitted an individual randomization of item sequences to prevent illicit collusion. The automatic generation of personalized MCQ test sheets is feasible using freely available open source software libraries, and can be efficiently deployed on a faculty-wide scale.

Constructing an XML database of linguistics data

Directory of Open Access Journals (Sweden)

J H Kroeze

2010-04-01

Full Text Available A language-oriented, multi-dimensional database of the linguistic characteristics of the Hebrew text of the Old Testament can enable researchers to do ad hoc queries. XML is a suitable technology to transform free text into a database. A clause’s word order can be kept intact while other features such as syntactic and semantic functions can be marked as elements or attributes. The elements or attributes from the XML “database” can be accessed and proces sed by a 4th generation programming language, such as Visual Basic. XML is explored as an option to build an exploitable database of linguistic data by representing inherently multi-dimensional data, including syntactic and semantic analyses of free text.

IR and OLAP in XML document warehouses

DEFF Research Database (Denmark)

Perez, Juan Manuel; Pedersen, Torben Bach; Berlanga, Rafael

2005-01-01

In this paper we propose to combine IR and OLAP (On-Line Analytical Processing) technologies to exploit a warehouse of text-rich XML documents. In the system we plan to develop, a multidimensional implementation of a relevance modeling document model will be used for interactively querying...

Concept-based query language approach to enterprise information systems

Science.gov (United States)

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.

A structural query system for Han characters

DEFF Research Database (Denmark)

Skala, Matthew

2016-01-01

The IDSgrep structural query system for Han character dictionaries is presented. This dictionary search system represents the spatial structure of Han characters using Extended Ideographic Description Sequences (EIDSes), a data model and syntax based on the Unicode IDS concept. It includes a query...... language for EIDS databases, with a freely available implementation and format translation from popular third-party IDS and XML character databases. The system is designed to suit the needs of font developers and foreign language learners. The search algorithm includes a bit vector index inspired by Bloom...... filters to support faster query operations. Experimental results are presented, evaluating the effect of the indexing on query performance....

XML, Ontologies, and Their Clinical Applications.

Science.gov (United States)

Yu, Chunjiang; Shen, Bairong

2016-01-01

The development of information technology has resulted in its penetration into every area of clinical research. Various clinical systems have been developed, which produce increasing volumes of clinical data. However, saving, exchanging, querying, and exploiting these data are challenging issues. The development of Extensible Markup Language (XML) has allowed the generation of flexible information formats to facilitate the electronic sharing of structured data via networks, and it has been used widely for clinical data processing. In particular, XML is very useful in the fields of data standardization, data exchange, and data integration. Moreover, ontologies have been attracting increased attention in various clinical fields in recent years. An ontology is the basic level of a knowledge representation scheme, and various ontology repositories have been developed, such as Gene Ontology and BioPortal. The creation of these standardized repositories greatly facilitates clinical research in related fields. In this chapter, we discuss the basic concepts of XML and ontologies, as well as their clinical applications.

DICOM supported sofware configuration by XML files

International Nuclear Information System (INIS)

LucenaG, Bioing Fabian M; Valdez D, Andres E; Gomez, Maria E; Nasisi, Oscar H

2007-01-01

A method for the configuration of informatics systems that provide support to DICOM standards using XML files is proposed. The difference with other proposals is base on that this system does not code the information of a DICOM objects file, but codes the standard itself in an XML file. The development itself is the format for the XML files mentioned, in order that they can support what DICOM normalizes for multiple languages. In this way, the same configuration file (or files) can be use in different systems. Jointly the XML configuration file generated, we wrote also a set of CSS and XSL files. So the same file can be visualized in a standard browser, as a query system of DICOM standard, emerging use, that did not was a main objective but brings a great utility and versatility. We exposed also some uses examples of the configuration file mainly in relation with the load of DICOM information objects. Finally, at the conclusions we show the utility that the system has already provided when the edition of DICOM standard changes from 2006 to 2007

Supercharged JavaScript Graphics with HTML5 canvas, jQuery, and More

CERN Document Server

Cecco, Raffaele

2011-01-01

With HTML5 and improved web browser support, JavaScript has become the tool of choice for creating high-performance web graphics. This faced-paced book shows you how to use JavaScript, jQuery, DHTML, and HTML5's Canvas element to create rich web applications for computers and mobile devices. By following real-world examples, experienced web developers learn fun and useful approaches to arcade games, DHTML effects, business dashboards, and other applications. This book serves complex subjects in easily digestible pieces, and each topic acts as a foundation for the next. Tackle JavaScript opti

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

Science.gov (United States)

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.

CSchema: A Downgrading Policy Language for XML Access Control

Institute of Scientific and Technical Information of China (English)

Dong-Xi Liu

2007-01-01

The problem of regulating access to XML documents has attracted much attention from both academic and industry communities.In existing approaches, the XML elements specified by access policies are either accessible or inac-cessible according to their sensitivity.However, in some cases, the original XML elements are sensitive and inaccessible, but after being processed in some appropriate ways, the results become insensitive and thus accessible.This paper proposes a policy language to accommodate such cases, which can express the downgrading operations on sensitive data in XML documents through explicit calculations on them.The proposed policy language is called calculation-embedded schema (CSchema), which extends the ordinary schema languages with protection type for protecting sensitive data and specifying downgrading operations.CSchema language has a type system to guarantee the type correctness of the embedded calcula-tion expressions and moreover this type system also generates a security view after type checking a CSchema policy.Access policies specified by CSchema are enforced by a validation procedure, which produces the released documents containing only the accessible data by validating the protected documents against CSchema policies.These released documents are then ready tobe accessed by, for instance, XML query engines.By incorporating this validation procedure, other XML processing technologies can use CSchema as the access control module.

Defining the XML schema matching problem for a personal schema based query answering system

OpenAIRE

Smiljanic, M.; van Keulen, Maurice; Jonker, Willem

2004-01-01

In this report, we analyze the problem of personal schema matching. We define the ingredients of the XML schema matching problem using constraint logic programming. This allows us to thourougly investigate specific matching problems. We do not have the ambition to provide for a formalism that covers all kinds of schema matching problems. The target is specifically personal schema matching using XML. The report is organized as follows. Chapter 2 provides a detailed description of our research ...

XSemantic: An Extension of LCA Based XML Semantic Search

Science.gov (United States)

Supasitthimethee, Umaporn; Shimizu, Toshiyuki; Yoshikawa, Masatoshi; Porkaew, Kriengkrai

One of the most convenient ways to query XML data is a keyword search because it does not require any knowledge of XML structure or learning a new user interface. However, the keyword search is ambiguous. The users may use different terms to search for the same information. Furthermore, it is difficult for a system to decide which node is likely to be chosen as a return node and how much information should be included in the result. To address these challenges, we propose an XML semantic search based on keywords called XSemantic. On the one hand, we give three definitions to complete in terms of semantics. Firstly, the semantic term expansion, our system is robust from the ambiguous keywords by using the domain ontology. Secondly, to return semantic meaningful answers, we automatically infer the return information from the user queries and take advantage of the shortest path to return meaningful connections between keywords. Thirdly, we present the semantic ranking that reflects the degree of similarity as well as the semantic relationship so that the search results with the higher relevance are presented to the users first. On the other hand, in the LCA and the proximity search approaches, we investigated the problem of information included in the search results. Therefore, we introduce the notion of the Lowest Common Element Ancestor (LCEA) and define our simple rule without any requirement on the schema information such as the DTD or XML Schema. The first experiment indicated that XSemantic not only properly infers the return information but also generates compact meaningful results. Additionally, the benefits of our proposed semantics are demonstrated by the second experiment.

Implementasi XML Encryption (XML Enc) Menggunakan Java

OpenAIRE

Tenia Wahyuningrum

2012-01-01

Seiring dengan semakin luasnya penggunaan XML pada berbagai layanan di internet, yang penyebaran informasinya sebagian besar menggunakan infrastruktur jaringan umum, maka mulai muncul permasalahan mengenai kebutuhan akan keamanan data bagi informasi yang terkandung didalam sebuah dokumen XML. Salah satu caranya adalah dengan menggunakan teknologi XML Enc. Pada makalah ini akan dibahas mengenai cara menggunakan XML Enc menggunakan bahasa pemrograman java, khususnya menyandikan dokumen XML (enk...

Structuring Legacy Pathology Reports by openEHR Archetypes to Enable Semantic Querying.

Science.gov (United States)

Kropf, Stefan; Krücken, Peter; Mueller, Wolf; Denecke, Kerstin

2017-05-18

Clinical information is often stored as free text, e.g. in discharge summaries or pathology reports. These documents are semi-structured using section headers, numbered lists, items and classification strings. However, it is still challenging to retrieve relevant documents since keyword searches applied on complete unstructured documents result in many false positive retrieval results. We are concentrating on the processing of pathology reports as an example for unstructured clinical documents. The objective is to transform reports semi-automatically into an information structure that enables an improved access and retrieval of relevant data. The data is expected to be stored in a standardized, structured way to make it accessible for queries that are applied to specific sections of a document (section-sensitive queries) and for information reuse. Our processing pipeline comprises information modelling, section boundary detection and section-sensitive queries. For enabling a focused search in unstructured data, documents are automatically structured and transformed into a patient information model specified through openEHR archetypes. The resulting XML-based pathology electronic health records (PEHRs) are queried by XQuery and visualized by XSLT in HTML. Pathology reports (PRs) can be reliably structured into sections by a keyword-based approach. The information modelling using openEHR allows saving time in the modelling process since many archetypes can be reused. The resulting standardized, structured PEHRs allow accessing relevant data by retrieving data matching user queries. Mapping unstructured reports into a standardized information model is a practical solution for a better access to data. Archetype-based XML enables section-sensitive retrieval and visualisation by well-established XML techniques. Focussing the retrieval to particular sections has the potential of saving retrieval time and improving the accuracy of the retrieval.

Monet: a next-generation database kernel for query-intensive applications

NARCIS (Netherlands)

P.A. Boncz (Peter)

2002-01-01

htmlabstractMonet is a database kernel targeted at query-intensive, heavy analysis applications (the opposite of transaction processing), which include OLAP and data mining, but also go beyond the business domain in GIS processing, multi-media retrieval and XML. The clean sheet approach of Monet

A browser-based tool for conversion between Fortran NAMELIST and XML/HTML

Science.gov (United States)

Naito, O.

A browser-based tool for conversion between Fortran NAMELIST and XML/HTML is presented. It runs on an HTML5 compliant browser and generates reusable XML files to aid interoperability. It also provides a graphical interface for editing and annotating variables in NAMELIST, hence serves as a primitive code documentation environment. Although the tool is not comprehensive, it could be viewed as a test bed for integrating legacy codes into modern systems.

A browser-based tool for conversion between Fortran NAMELIST and XML/HTML

Directory of Open Access Journals (Sweden)

O. Naito

2017-01-01

Full Text Available A browser-based tool for conversion between Fortran NAMELIST and XML/HTML is presented. It runs on an HTML5 compliant browser and generates reusable XML files to aid interoperability. It also provides a graphical interface for editing and annotating variables in NAMELIST, hence serves as a primitive code documentation environment. Although the tool is not comprehensive, it could be viewed as a test bed for integrating legacy codes into modern systems.

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

Science.gov (United States)

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...

Interactive and Animated Scalable Vector Graphics and R Data Displays

Directory of Open Access Journals (Sweden)

Deborah Nolan

2012-01-01

Full Text Available We describe an approach to creating interactive and animated graphical displays using R's graphics engine and Scalable Vector Graphics, an XML vocabulary for describing two-dimensional graphical displays. We use the svg( graphics device in R and then post-process the resulting XML documents. The post-processing identities the elements in the SVG that correspond to the different components of the graphical display, e.g., points, axes, labels, lines. One can then annotate these elements to add interactivity and animation effects. One can also use JavaScript to provide dynamic interactive effects to the plot, enabling rich user interactions and compelling visualizations. The resulting SVG documents can be embedded withinHTML documents and can involve JavaScript code that integrates the SVG and HTML objects. The functionality is provided via the SVGAnnotation package and makes static plots generated via R graphics functions available as stand-alone, interactive and animated plots for the Web and other venues.

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

Science.gov (United States)

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

2002-12-01

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

NeXML: rich, extensible, and verifiable representation of comparative data and metadata.

Science.gov (United States)

Vos, Rutger A; Balhoff, James P; Caravas, Jason A; Holder, Mark T; Lapp, Hilmar; Maddison, Wayne P; Midford, Peter E; Priyam, Anurag; Sukumaran, Jeet; Xia, Xuhua; Stoltzfus, Arlin

2012-07-01

In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.

Invisible XML

NARCIS (Netherlands)

S. Pemberton (Steven)

2013-01-01

htmlabstractWhat if you could see everything as XML? XML has many strengths for data exchange, strengths both inherent in the nature of XML markup and strengths that derive from the ubiquity of tools that can process XML. For authoring, however, other forms are preferred: no one writes CSS or

Defining the XML schema matching problem for a personal schema based query answering system

NARCIS (Netherlands)

Smiljanic, M.; van Keulen, Maurice; Jonker, Willem

In this report, we analyze the problem of personal schema matching. We define the ingredients of the XML schema matching problem using constraint logic programming. This allows us to thourougly investigate specific matching problems. We do not have the ambition to provide for a formalism that covers

RelaXML

DEFF Research Database (Denmark)

Knudsen, Steffen Ulsø; Pedersen, Torben Bach; Thomsen, Christian

In modern enterprises, almost all data is stored in relational databases. Additionally, most enterprises increasingly collaborate with other enterprises in long-running read-write workflows, primarily through XML-based data exchange technologies such as web services. However, bidirectional XML data...... exchange is cumbersome and must often be hand-coded, at considerable expense. This paper remedies the situation by proposing RELAXML, an automatic and effective approach to bidirectional XML-based exchange of relational data. RELAXML supports re-use through multiple inheritance, and handles both export...... of relational data to XML documents and (re-)import of XML documents with a large degree of flexibility in terms of the SQL statements and XML document structures supported. Import and export are formally defined so as to avoid semantic problems, and algorithms to implement both are given. A performance study...

RelaXML

DEFF Research Database (Denmark)

Knudsen, Steffen Ulsø; Pedersen, Torben Bach; Thomsen, Christian

exchange is cumbersome and must often be hand-coded, at considerable expense. This paper remedies the situation by proposing RELAXML, an automatic and effective approach to bidirectional XML-based exchange of relational data. RELAXML supports re-use through multiple inheritance, and handles both export...... of relational data to XML documents and (re-)import of XML documents with a large degree of flexibility in terms of the SQL statements and XML document structures supported. Import and export are formally defined so as to avoid semantic problems, and algorithms to implement both are given. A performance study......In modern enterprises, almost all data is stored in relational databases. Additionally, most enterprises increasingly collaborate with other enterprises in long-running read-write workflows, primarily through XML-based data exchange technologies such as web services. However, bidirectional XML data...

XML Files

Science.gov (United States)

... this page: https://medlineplus.gov/xml.html MedlinePlus XML Files To use the sharing features on this page, please enable JavaScript. MedlinePlus produces XML data sets that you are welcome to download ...

Node Query Preservation for Deterministic Linear Top-Down Tree Transducers

Directory of Open Access Journals (Sweden)

Kazuki Miyahara

2013-11-01

Full Text Available This paper discusses the decidability of node query preservation problems for XML document transformations. We assume a transformation given by a deterministic linear top-down data tree transducer (abbreviated as DLT^V and an n-ary query based on runs of a tree automaton. We say that a DLT^V Tr strongly preserves a query Q if there is a query Q' such that for every document t, the answer set of Q' for Tr(t is equal to the answer set of Q for t. Also we say that Tr weakly preserves Q if there is a query Q' such that for every t_d in the range of Tr, the answer set of Q' for t_d is equal to the union of the answer set of Q for t such that t_d = Tr(t. We show that the weak preservation problem is coNP-complete and the strong preservation problem is in 2-EXPTIME.

Responsive web design with jQuery

CERN Document Server

Carlos, Gilberto

2013-01-01

Responsive Web Design with jQuery follows a standard tutorial-based approach, covering various aspects of responsive web design by building a comprehensive website.""Responsive Web Design with jQuery"" is aimed at web designers who are interested in building device-agnostic websites. You should have a grasp of standard HTML, CSS, and JavaScript development, and have a familiarity with graphic design. Some exposure to jQuery and HTML5 will be beneficial but isn't essential.

phyloXML: XML for evolutionary biology and comparative genomics.

Science.gov (United States)

Han, Mira V; Zmasek, Christian M

2009-10-27

Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types. We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data. PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at http://www.phyloxml.org.

An SML Driven Graphical User Interface and Application Management Toolkit

International Nuclear Information System (INIS)

White, Greg R

2002-01-01

In the past, the features of a user interface were limited by those available in the existing graphical widgets it used. Now, improvements in processor speed have fostered the emergence of interpreted languages, in which the appropriate method to render a given data object can be loaded at runtime. XML can be used to precisely describe the association of data types with their graphical handling (beans), and Java provides an especially rich environment for programming the graphics. We present a graphical user interface builder based on Java Beans and XML, in which the graphical screens are described textually (in files or a database) in terms of their screen components. Each component may be a simple text read back, or a complex plot. The programming model provides for dynamic data pertaining to a component to be forwarded synchronously or asynchronously, to the appropriate handler, which may be a built-in method, or a complex applet. This work was initially motivated by the need to move the legacy VMS display interface of the SLAC Control Program to another platform while preserving all of its existing functionality. However the model allows us a powerful and generic system for adding new kinds of graphics, such as Matlab, data sources, such as EPICS, middleware, such as AIDA[1], and transport, such as XML and SOAP. The system will also include a management console, which will be able to report on the present usage of the system, for instance who is running it where and connected to which channels

Archaeological Vector Graphics and SVG: A case study from Cricklade

Directory of Open Access Journals (Sweden)

Holly Wright

2006-07-01

Full Text Available Currently, there are a variety of ways to make vector-based information available on the Web, but most are browser- and platform-dependent, proprietary, and unevenly supported (Laaker 2002, 13. Of the various solutions currently being explored by the greater Web community, one of the most promising is called Scalable Vector Graphics (SVG, which is part of the eXtensible Markup Language (XML. SVG was defined by a working group of the World Wide Web Consortium (W3C and has subsequently become their official recommendation for representing vector graphics on the Web in XML (Eisenberg 2002, 6; Watt 2002, xviii. Because SVG is an XML application, it is freely available, not dependent on a particular browser or platform, and interoperable with other XML applications. While there is no guarantee that SVG will be widely adopted for rendering vector-based information on the Web, development and recommendation by the W3C generally carries a great deal of weight, especially as browser developers move towards less proprietary support of W3C standards. In addition, use of XML continues to grow, so XML-based solutions like SVG should be explored by those interested in presenting vector graphics on the Web (Harold and Means 2002, 3. This discussion explores SVG as a potential tool for archaeologists. It includes some of the ways vector graphics are used in archaeology, and outlines the development and features of SVG, which are then demonstrated in the form of a case study. Large-scale plan and section drawings originally created on Permatrace were digitised by Guy Hopkinson for use in the Internet Archaeology publication Excavations at Cricklade, Wiltshire, 1975, by Jeremy Haslam, designed as an exercise in 'retrospective publication', to illustrate how traditional forms of visual recording might be digitised for online publication. Hopkinson went on to publish his methodology jointly with Internet Archaeology editor, Judith Winters in Problems with

Plug-and-Play XML

Science.gov (United States)

Schweiger, Ralf; Hoelzer, Simon; Altmann, Udo; Rieger, Joerg; Dudeck, Joachim

2002-01-01

The application of XML (Extensible Markup Language) is still costly. The authors present an approach to ease the development of XML applications. They have developed a Web-based framework that combines existing XML resources into a comprehensive XML application. The XML framework is model-driven, i.e., the authors primarily design XML document models (XML schema, document type definition), and users can enter, search, and view related XML documents using a Web browser. The XML model itself is flexible and might be composed of existing model standards. The second part of the paper relates the approach of the authors to some problems frequently encountered in the clinical documentation process. PMID:11751802

On HTML and XML based web design and implementation techniques

International Nuclear Information System (INIS)

Bezboruah, B.; Kalita, M.

2006-05-01

Web implementation is truly a multidisciplinary field with influences from programming, choosing of scripting languages, graphic design, user interface design, and database design. The challenge of a Web designer/implementer is his ability to create an attractive and informative Web. To work with the universal framework and link diagrams from the design process as well as the Web specifications and domain information, it is essential to create Hypertext Markup Language (HTML) or other software and multimedia to accomplish the Web's objective. In this article we will discuss Web design standards and the techniques involved in Web implementation based on HTML and Extensible Markup Language (XML). We will also discuss the advantages and disadvantages of HTML over its successor XML in designing and implementing a Web. We have developed two Web pages, one utilizing the features of HTML and the other based on the features of XML to carry out the present investigation. (author)

Visual Querying in Chemical Databases using SMARTS Patterns

OpenAIRE

Šípek, Vojtěch

2014-01-01

The purpose of this thesis is to create framework for visual querying in chemical databases which will be implemented as a web application. By using graphical editor, which is a part of client side, the user creates queries which are translated into chemical query language SMARTS. This query is parsed on the application server which is connected to the chemical database. This framework also contains tooling for creating the database and index structure above it. 1

The Graphical Representation of the Digital Astronaut Physiology Backbone

Science.gov (United States)

Briers, Demarcus

2010-01-01

This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

Science.gov (United States)

Li, Feng; Li, Maoyu; Xiao, Zhiqiang; Zhang, Pengfei; Li, Jianling; Chen, Zhuchu

2006-01-11

Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database. The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML) editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database. Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.

XML under the Hood.

Science.gov (United States)

Scharf, David

2002-01-01

Discusses XML (extensible markup language), particularly as it relates to libraries. Topics include organizing information; cataloging; metadata; similarities to HTML; organizations dealing with XML; making XML useful; a history of XML; the semantic Web; related technologies; XML at the Library of Congress; and its role in improving the…

Semantically Interoperable XML Data.

Science.gov (United States)

Vergara-Niedermayr, Cristobal; Wang, Fusheng; Pan, Tony; Kurc, Tahsin; Saltz, Joel

2013-09-01

XML is ubiquitously used as an information exchange platform for web-based applications in healthcare, life sciences, and many other domains. Proliferating XML data are now managed through latest native XML database technologies. XML data sources conforming to common XML schemas could be shared and integrated with syntactic interoperability. Semantic interoperability can be achieved through semantic annotations of data models using common data elements linked to concepts from ontologies. In this paper, we present a framework and software system to support the development of semantic interoperable XML based data sources that can be shared through a Grid infrastructure. We also present our work on supporting semantic validated XML data through semantic annotations for XML Schema, semantic validation and semantic authoring of XML data. We demonstrate the use of the system for a biomedical database of medical image annotations and markups.

Semantically Interoperable XML Data

Science.gov (United States)

Vergara-Niedermayr, Cristobal; Wang, Fusheng; Pan, Tony; Kurc, Tahsin; Saltz, Joel

2013-01-01

XML is ubiquitously used as an information exchange platform for web-based applications in healthcare, life sciences, and many other domains. Proliferating XML data are now managed through latest native XML database technologies. XML data sources conforming to common XML schemas could be shared and integrated with syntactic interoperability. Semantic interoperability can be achieved through semantic annotations of data models using common data elements linked to concepts from ontologies. In this paper, we present a framework and software system to support the development of semantic interoperable XML based data sources that can be shared through a Grid infrastructure. We also present our work on supporting semantic validated XML data through semantic annotations for XML Schema, semantic validation and semantic authoring of XML data. We demonstrate the use of the system for a biomedical database of medical image annotations and markups. PMID:25298789

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database – Xindice

Directory of Open Access Journals (Sweden)

Li Jianling

2006-01-01

Full Text Available Abstract Background Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database. Results The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database. Conclusion Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.

Information persistence using XML database technology

Science.gov (United States)

Clark, Thomas A.; Lipa, Brian E. G.; Macera, Anthony R.; Staskevich, Gennady R.

2005-05-01

The Joint Battlespace Infosphere (JBI) Information Management (IM) services provide information exchange and persistence capabilities that support tailored, dynamic, and timely access to required information, enabling near real-time planning, control, and execution for DoD decision making. JBI IM services will be built on a substrate of network centric core enterprise services and when transitioned, will establish an interoperable information space that aggregates, integrates, fuses, and intelligently disseminates relevant information to support effective warfighter business processes. This virtual information space provides individual users with information tailored to their specific functional responsibilities and provides a highly tailored repository of, or access to, information that is designed to support a specific Community of Interest (COI), geographic area or mission. Critical to effective operation of JBI IM services is the implementation of repositories, where data, represented as information, is represented and persisted for quick and easy retrieval. This paper will address information representation, persistence and retrieval using existing database technologies to manage structured data in Extensible Markup Language (XML) format as well as unstructured data in an IM services-oriented environment. Three basic categories of database technologies will be compared and contrasted: Relational, XML-Enabled, and Native XML. These technologies have diverse properties such as maturity, performance, query language specifications, indexing, and retrieval methods. We will describe our application of these evolving technologies within the context of a JBI Reference Implementation (RI) by providing some hopefully insightful anecdotes and lessons learned along the way. This paper will also outline future directions, promising technologies and emerging COTS products that can offer more powerful information management representations, better persistence mechanisms and

On the effectiveness of XML schema validation for countering XML signature wrapping attacks

DEFF Research Database (Denmark)

Jensen, Meiko; Meyer, Christopher; Somorovsky, Juraj

2011-01-01

In the context of security of Web Services, the XML Signature Wrapping attack technique has lately received increasing attention. Following a broad range of real-world exploits, general interest in applicable countermeasures rises. However, few approaches for countering these attacks have been...... investigated closely enough to make any claims about their effectiveness. In this paper, we analyze the effectiveness of the specific countermeasure of XML Schema validation in terms of fending Signature Wrapping attacks. We investigate the problems of XML Schema validation for Web Services messages......, and discuss the approach of Schema Hardening, a technique for strengthening XML Schema declarations. We conclude that XML Schema validation with a hardened XML Schema is capable of fending XML Signature Wrapping attacks, but bears some pitfalls and disadvantages as well....

Federated querying architecture with clinical & translational health IT application.

Science.gov (United States)

Livne, Oren E; Schultz, N Dustin; Narus, Scott P

2011-10-01

We present a software architecture that federates data from multiple heterogeneous health informatics data sources owned by multiple organizations. The architecture builds upon state-of-the-art open-source Java and XML frameworks in innovative ways. It consists of (a) federated query engine, which manages federated queries and result set aggregation via a patient identification service; and (b) data source facades, which translate the physical data models into a common model on-the-fly and handle large result set streaming. System modules are connected via reusable Apache Camel integration routes and deployed to an OSGi enterprise service bus. We present an application of our architecture that allows users to construct queries via the i2b2 web front-end, and federates patient data from the University of Utah Enterprise Data Warehouse and the Utah Population database. Our system can be easily adopted, extended and integrated with existing SOA Healthcare and HL7 frameworks such as i2b2 and caGrid.

XML in Libraries.

Science.gov (United States)

Tennant, Roy, Ed.

This book presents examples of how libraries are using XML (eXtensible Markup Language) to solve problems, expand services, and improve systems. Part I contains papers on using XML in library catalog records: "Updating MARC Records with XMLMARC" (Kevin S. Clarke, Stanford University) and "Searching and Retrieving XML Records via the…

XML to XML through XML

NARCIS (Netherlands)

Lemmens, W.J.M.; Houben, G.J.P.M.

2001-01-01

XML documents are used to exchange data. Data exchange implies the transformation of the original data to a different structure. Often such transformations need to be adapted to some specific situation, like the rendering to non-standard platforms for display or the support of special user

XML-Based Generator of C++ Code for Integration With GUIs

Science.gov (United States)

Hua, Hook; Oyafuso, Fabiano; Klimeck, Gerhard

2003-01-01

An open source computer program has been developed to satisfy a need for simplified organization of structured input data for scientific simulation programs. Typically, such input data are parsed in from a flat American Standard Code for Information Interchange (ASCII) text file into computational data structures. Also typically, when a graphical user interface (GUI) is used, there is a need to completely duplicate the input information while providing it to a user in a more structured form. Heretofore, the duplication of the input information has entailed duplication of software efforts and increases in susceptibility to software errors because of the concomitant need to maintain two independent input-handling mechanisms. The present program implements a method in which the input data for a simulation program are completely specified in an Extensible Markup Language (XML)-based text file. The key benefit for XML is storing input data in a structured manner. More importantly, XML allows not just storing of data but also describing what each of the data items are. That XML file contains information useful for rendering the data by other applications. It also then generates data structures in the C++ language that are to be used in the simulation program. In this method, all input data are specified in one place only, and it is easy to integrate the data structures into both the simulation program and the GUI. XML-to-C is useful in two ways: 1. As an executable, it generates the corresponding C++ classes and 2. As a library, it automatically fills the objects with the input data values.

XML Graphs in Program Analysis

DEFF Research Database (Denmark)

Møller, Anders; Schwartzbach, Michael Ignatieff

2007-01-01

XML graphs have shown to be a simple and effective formalism for representing sets of XML documents in program analysis. It has evolved through a six year period with variants tailored for a range of applications. We present a unified definition, outline the key properties including validation...... of XML graphs against different XML schema languages, and provide a software package that enables others to make use of these ideas. We also survey four very different applications: XML in Java, Java Servlets and JSP, transformations between XML and non-XML data, and XSLT....

AQBE — QBE Style Queries for Archetyped Data

Science.gov (United States)

Sachdeva, Shelly; Yaginuma, Daigo; Chu, Wanming; Bhalla, Subhash

Large-scale adoption of electronic healthcare applications requires semantic interoperability. The new proposals propose an advanced (multi-level) DBMS architecture for repository services for health records of patients. These also require query interfaces at multiple levels and at the level of semi-skilled users. In this regard, a high-level user interface for querying the new form of standardized Electronic Health Records system has been examined in this study. It proposes a step-by-step graphical query interface to allow semi-skilled users to write queries. Its aim is to decrease user effort and communication ambiguities, and increase user friendliness.

Dual Syntax for XML Languages

DEFF Research Database (Denmark)

Brabrand, Claus; Møller, Anders; Schwartzbach, Michael Ignatieff

2005-01-01

XML is successful as a machine processable data interchange format, but it is often too verbose for human use. For this reason, many XML languages permit an alternative more legible non-XML syntax. XSLT stylesheets are often used to convert from the XML syntax to the alternative syntax; however......, such transformations are not reversible since no general tool exists to automatically parse the alternative syntax back into XML. We present XSugar, which makes it possible to manage dual syntax for XML languages. An XSugar specification is built around a context-free grammar that unifies the two syntaxes...... of a language. Given such a specification, the XSugar tool can translate from alternative syntax to XML and vice versa. Moreover, the tool statically checks that the transformations are reversible and that all XML documents generated from the alternative syntax are valid according to a given XML schema....

An XML-based system for synthesis of data from disparate databases.

Science.gov (United States)

Kurc, Tahsin; Janies, Daniel A; Johnson, Andrew D; Langella, Stephen; Oster, Scott; Hastings, Shannon; Habib, Farhat; Camerlengo, Terry; Ervin, David; Catalyurek, Umit V; Saltz, Joel H

2006-01-01

Diverse data sets have become key building blocks of translational biomedical research. Data types captured and referenced by sophisticated research studies include high throughput genomic and proteomic data, laboratory data, data from imagery, and outcome data. In this paper, the authors present the application of an XML-based data management system to support integration of data from disparate data sources and large data sets. This system facilitates management of XML schemas and on-demand creation and management of XML databases that conform to these schemas. They illustrate the use of this system in an application for genotype-phenotype correlation analyses. This application implements a method of phenotype-genotype correlation based on phylogenetic optimization of large data sets of mouse SNPs and phenotypic data. The application workflow requires the management and integration of genomic information and phenotypic data from external data repositories and from the results of phenotype-genotype correlation analyses. Our implementation supports the process of carrying out a complex workflow that includes large-scale phylogenetic tree optimizations and application of Maddison's concentrated changes test to large phylogenetic tree data sets. The data management system also allows collaborators to share data in a uniform way and supports complex queries that target data sets.

XML Graphs in Program Analysis

DEFF Research Database (Denmark)

Møller, Anders; Schwartzbach, Michael I.

2011-01-01

of XML graphs against different XML schema languages, and provide a software package that enables others to make use of these ideas. We also survey the use of XML graphs for program analysis with four very different languages: XACT (XML in Java), Java Servlets (Web application programming), XSugar......XML graphs have shown to be a simple and effective formalism for representing sets of XML documents in program analysis. It has evolved through a six year period with variants tailored for a range of applications. We present a unified definition, outline the key properties including validation...

Expressiveness considerations of XML signatures

DEFF Research Database (Denmark)

Jensen, Meiko; Meyer, Christopher

2011-01-01

XML Signatures are used to protect XML-based Web Service communication against a broad range of attacks related to man-in-the-middle scenarios. However, due to the complexity of the Web Services specification landscape, the task of applying XML Signatures in a robust and reliable manner becomes...... more and more challenging. In this paper, we investigate this issue, describing how an attacker can still interfere with Web Services communication even in the presence of XML Signatures. Additionally, we discuss the interrelation of XML Signatures and XML Encryption, focussing on their security...

EFFECTIVELY SEARCHING SPECIMEN AND OBSERVATION DATA WITH TOQE, THE THESAURUS OPTIMIZED QUERY EXPANDER

Directory of Open Access Journals (Sweden)

Anton Güntsch

2009-09-01

Full Text Available Today’s specimen and observation data portals lack a flexible mechanism, able to link up thesaurus-enabled data sources such as taxonomic checklist databases and expand user queries to related terms, significantly enhancing result sets. The TOQE system (Thesaurus Optimized Query Expander is a REST-like XML web-service implemented in Python and designed for this purpose. Acting as an interface between portals and thesauri, TOQE allows the implementation of specialized portal systems with a set of thesauri supporting its specific focus. It is both easy to use for portal programmers and easy to configure for thesaurus database holders who want to expose their system as a service for query expansions. Currently, TOQE is used in four specimen and observation data portals. The documentation is available from http://search.biocase.org/toqe/.

Dual Syntax for XML Languages

DEFF Research Database (Denmark)

Brabrand, Claus; Møller, Anders; Schwartzbach, Michael Ignatieff

2005-01-01

XML is successful as a machine processable data interchange format, but it is often too verbose for human use. For this reason, many XML languages permit an alternative more legible non-XML syntax. XSLT stylesheets are often used to convert from the XML syntax to the alternative syntax; however......, such transformations are not reversible since no general tool exists to automatically parse the alternative syntax back into XML. We present XSugar, which makes it possible to manage dual syntax for XML languages. An XSugar specification is built around a context-free grammar that unifies the two syntaxes...

TME2/342: The Role of the EXtensible Markup Language (XML) for Future Healthcare Application Development

Science.gov (United States)

Noelle, G; Dudeck, J

1999-01-01

Two years, since the World Wide Web Consortium (W3C) has published the first specification of the eXtensible Markup Language (XML) there exist some concrete tools and applications to work with XML-based data. In particular, new generation Web browsers offer great opportunities to develop new kinds of medical, web-based applications. There are several data-exchange formats in medicine, which have been established in the last years: HL-7, DICOM, EDIFACT and, in the case of Germany, xDT. Whereas communication and information exchange becomes increasingly important, the development of appropriate and necessary interfaces causes problems, rising costs and effort. It has been also recognised that it is difficult to define a standardised interchange format, for one of the major future developments in medical telematics: the electronic patient record (EPR) and its availability on the Internet. Whereas XML, especially in an industrial environment, is celebrated as a generic standard and a solution for all problems concerning e-commerce, in a medical context there are only few applications developed. Nevertheless, the medical environment is an appropriate area for building XML applications: as the information and communication management becomes increasingly important in medical businesses, the role of the Internet changes quickly from an information to a communication medium. The first XML based applications in healthcare show us the advantage for a future engagement of the healthcare industry in XML: such applications are open, easy to extend and cost-effective. Additionally, XML is much more than a simple new data interchange format: many proposals for data query (XQL), data presentation (XSL) and other extensions have been proposed to the W3C and partly realised in medical applications.

Compression of Probabilistic XML documents

NARCIS (Netherlands)

Veldman, Irma

2009-01-01

Probabilistic XML (PXML) files resulting from data integration can become extremely large, which is undesired. For XML there are several techniques available to compress the document and since probabilistic XML is in fact (a special form of) XML, it might benefit from these methods even more. In

XML-Intensive software development

OpenAIRE

Ibañez Anfurrutia, Felipe

2016-01-01

168 p. 1. IntroducciónXML es un lenguaje de meta-etiquetas, es decir, puede ser utilizado fundamentalmentepara crear lenguajes de etiquetas . La presencia de XML es unfenómeno generalizado. Sin embargo, su juventud hace que los desarrolladores seenfrentan a muchos desafíos al utilizar XML en aplicaciones de vanguardia. Estatesis enfrenta XML a tres escenarios diferentes: intercambio de documentos,Líneas de Producto Software (LPS) y Lenguajes eSpecíficos de Dominio (LSD).El intercambio digi...

DICOM involving XML path-tag

Science.gov (United States)

Zeng, Qiang; Yao, Zhihong; Liu, Lei

2011-03-01

Digital Imaging and Communications in Medicine (DICOM) is a standard for handling, storing, printing, and transmitting information in medical imaging. XML (Extensible Markup Language) is a set of rules for encoding documents in machine-readable form which has become more and more popular. The combination of these two is very necessary and promising. Using XML tags instead of numeric labels in DICOM files will effectively increase the readability and enhance the clear hierarchical structure of DICOM files. However, due to the fact that the XML tags rely heavily on the orders of the tags, the strong data dependency has a lot of influence on the flexibility of inserting and exchanging data. In order to improve the extensibility and sharing of DICOM files, this paper introduces XML Path-Tag to DICOM. When a DICOM file is converted to XML format, adding simple Path-Tag into the DICOM file in place of complex tags will keep the flexibility of a DICOM file while inserting data elements and give full play to the advantages of the structure and readability of an XML file. Our method can solve the weak readability problem of DICOM files and the tedious work of inserting data into an XML file. In addition, we set up a conversion engine that can transform among traditional DICOM files, XML-DCM and XML-DCM files involving XML Path-Tag efficiently.

XML Based Course Websites.

Science.gov (United States)

Wollowski, Michael

XML, the extensible markup language, is a quickly evolving technology that presents a viable alternative to courseware products and promises to ease the burden of Web authors, who edit their course pages directly. XML uses tags to label kinds of contents, rather than format information. The use of XML enables faculty to focus on providing…

Evaluating SPARQL queries on massive RDF datasets

KAUST Repository

Al-Harbi, Razen; Abdelaziz, Ibrahim; Kalnis, Panos; Mamoulis, Nikos

2015-01-01

In this paper, we propose AdHash, a distributed RDF system which addresses the shortcomings of previous work. First, AdHash initially applies lightweight hash partitioning, which drastically minimizes the startup cost, while favoring the parallel processing of join patterns on subjects, without any data communication. Using a locality-aware planner, queries that cannot be processed in parallel are evaluated with minimal communication. Second, AdHash monitors the data access patterns and adapts dynamically to the query load by incrementally redistributing and replicating frequently accessed data. As a result, the communication cost for future queries is drastically reduced or even eliminated. Our experiments with synthetic and real data verify that AdHash (i) starts faster than all existing systems, (ii) processes thousands of queries before other systems become online, and (iii) gracefully adapts to the query load, being able to evaluate queries on billion-scale RDF data in sub-seconds. In this demonstration, audience can use a graphical interface of AdHash to verify its performance superiority compared to state-of-the-art distributed RDF systems.

XWeB: The XML Warehouse Benchmark

Science.gov (United States)

Mahboubi, Hadj; Darmont, Jérôme

With the emergence of XML as a standard for representing business data, new decision support applications are being developed. These XML data warehouses aim at supporting On-Line Analytical Processing (OLAP) operations that manipulate irregular XML data. To ensure feasibility of these new tools, important performance issues must be addressed. Performance is customarily assessed with the help of benchmarks. However, decision support benchmarks do not currently support XML features. In this paper, we introduce the XML Warehouse Benchmark (XWeB), which aims at filling this gap. XWeB derives from the relational decision support benchmark TPC-H. It is mainly composed of a test data warehouse that is based on a unified reference model for XML warehouses and that features XML-specific structures, and its associate XQuery decision support workload. XWeB's usage is illustrated by experiments on several XML database management systems.

XML-BSPM: an XML format for storing Body Surface Potential Map recordings.

Science.gov (United States)

Bond, Raymond R; Finlay, Dewar D; Nugent, Chris D; Moore, George

2010-05-14

The Body Surface Potential Map (BSPM) is an electrocardiographic method, for recording and displaying the electrical activity of the heart, from a spatial perspective. The BSPM has been deemed more accurate for assessing certain cardiac pathologies when compared to the 12-lead ECG. Nevertheless, the 12-lead ECG remains the most popular ECG acquisition method for non-invasively assessing the electrical activity of the heart. Although data from the 12-lead ECG can be stored and shared using open formats such as SCP-ECG, no open formats currently exist for storing and sharing the BSPM. As a result, an innovative format for storing BSPM datasets has been developed within this study. The XML vocabulary was chosen for implementation, as opposed to binary for the purpose of human readability. There are currently no standards to dictate the number of electrodes and electrode positions for recording a BSPM. In fact, there are at least 11 different BSPM electrode configurations in use today. Therefore, in order to support these BSPM variants, the XML-BSPM format was made versatile. Hence, the format supports the storage of custom torso diagrams using SVG graphics. This diagram can then be used in a 2D coordinate system for retaining electrode positions. This XML-BSPM format has been successfully used to store the Kornreich-117 BSPM dataset and the Lux-192 BSPM dataset. The resulting file sizes were in the region of 277 kilobytes for each BSPM recording and can be deemed suitable for example, for use with any telemonitoring application. Moreover, there is potential for file sizes to be further reduced using basic compression algorithms, i.e. the deflate algorithm. Finally, these BSPM files have been parsed and visualised within a convenient time period using a web based BSPM viewer. This format, if widely adopted could promote BSPM interoperability, knowledge sharing and data mining. This work could also be used to provide conceptual solutions and inspire existing formats

Updating Recursive XML Views of Relations

DEFF Research Database (Denmark)

Choi, Byron; Cong, Gao; Fan, Wenfei

2009-01-01

This paper investigates the view update problem for XML views published from relational data. We consider XML views defined in terms of mappings directed by possibly recursive DTDs compressed into DAGs and stored in relations. We provide new techniques to efficiently support XML view updates...... specified in terms of XPath expressions with recursion and complex filters. The interaction between XPath recursion and DAG compression of XML views makes the analysis of the XML view update problem rather intriguing. Furthermore, many issues are still open even for relational view updates, and need...... to be explored. In response to these, on the XML side, we revise the notion of side effects and update semantics based on the semantics of XML views, and present effecient algorithms to translate XML updates to relational view updates. On the relational side, we propose a mild condition on SPJ views, and show...

Storing XML Documents in Databases

NARCIS (Netherlands)

A.R. Schmidt; S. Manegold (Stefan); M.L. Kersten (Martin); L.C. Rivero; J.H. Doorn; V.E. Ferraggine

2005-01-01

textabstractThe authors introduce concepts for loading large amounts of XML documents into databases where the documents are stored and maintained. The goal is to make XML databases as unobtrusive in multi-tier systems as possible and at the same time provide as many services defined by the XML

Dual Syntax for XML Languages

DEFF Research Database (Denmark)

Brabrand, Claus; Møller, Anders; Schwartzbach, Michael Ignatieff

2008-01-01

of a language. Given such a specification, the XSugar tool can translate from alternative syntax to XML and vice versa. Moreover, the tool statically checks that the transformations are reversible and that all XML documents generated from the alternative syntax are valid according to a given XML schema....

Using XML to encode TMA DES metadata

Directory of Open Access Journals (Sweden)

Oliver Lyttleton

2011-01-01

Full Text Available Background: The Tissue Microarray Data Exchange Specification (TMA DES is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. Materials and Methods: We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. Results: We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. Conclusions: All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs.

Using XML to encode TMA DES metadata.

Science.gov (United States)

Lyttleton, Oliver; Wright, Alexander; Treanor, Darren; Lewis, Paul

2011-01-01

The Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs.

Using XML to encode TMA DES metadata

Science.gov (United States)

Lyttleton, Oliver; Wright, Alexander; Treanor, Darren; Lewis, Paul

2011-01-01

Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. Materials and Methods: We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. Results: We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. Conclusions: All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs. PMID:21969921

XML documents cluster research based on frequent subpatterns

Science.gov (United States)

Ding, Tienan; Li, Wei; Li, Xiongfei

2015-12-01

XML data is widely used in the information exchange field of Internet, and XML document data clustering is the hot research topic. In the XML document clustering process, measure differences between two XML documents is time costly, and impact the efficiency of XML document clustering. This paper proposed an XML documents clustering method based on frequent patterns of XML document dataset, first proposed a coding tree structure for encoding the XML document, and translate frequent pattern mining from XML documents into frequent pattern mining from string. Further, using the cosine similarity calculation method and cohesive hierarchical clustering method for XML document dataset by frequent patterns. Because of frequent patterns are subsets of the original XML document data, so the time consumption of XML document similarity measure is reduced. The experiment runs on synthetic dataset and the real datasets, the experimental result shows that our method is efficient.

XML and Better Web Searching.

Science.gov (United States)

Jackson, Joe; Gilstrap, Donald L.

1999-01-01

Addresses the implications of the new Web metalanguage XML for searching on the World Wide Web and considers the future of XML on the Web. Compared to HTML, XML is more concerned with structure of data than documents, and these data structures should prove conducive to precise, context rich searching. (Author/LRW)

Designing XML schemas for bioinformatics.

Science.gov (United States)

Bruhn, Russel Elton; Burton, Philip John

2003-06-01

Data interchange bioinformatics databases will, in the future, most likely take place using extensible markup language (XML). The document structure will be described by an XML Schema rather than a document type definition (DTD). To ensure flexibility, the XML Schema must incorporate aspects of Object-Oriented Modeling. This impinges on the choice of the data model, which, in turn, is based on the organization of bioinformatics data by biologists. Thus, there is a need for the general bioinformatics community to be aware of the design issues relating to XML Schema. This paper, which is aimed at a general bioinformatics audience, uses examples to describe the differences between a DTD and an XML Schema and indicates how Unified Modeling Language diagrams may be used to incorporate Object-Oriented Modeling in the design of schema.

XML for catalogers and metadata librarians

CERN Document Server

Cole, Timothy W

2013-01-01

How are today's librarians to manage and describe the everexpanding volumes of resources, in both digital and print formats? The use of XML in cataloging and metadata workflows can improve metadata quality, the consistency of cataloging workflows, and adherence to standards. This book is intended to enable current and future catalogers and metadata librarians to progress beyond a bare surfacelevel acquaintance with XML, thereby enabling them to integrate XML technologies more fully into their cataloging workflows. Building on the wealth of work on library descriptive practices, cataloging, and metadata, XML for Catalogers and Metadata Librarians explores the use of XML to serialize, process, share, and manage library catalog and metadata records. The authors' expert treatment of the topic is written to be accessible to those with little or no prior practical knowledge of or experience with how XML is used. Readers will gain an educated appreciation of the nuances of XML and grasp the benefit of more advanced ...

XML Transformations

Directory of Open Access Journals (Sweden)

Felician ALECU

2012-04-01

Full Text Available XSLT style sheets are designed to transform the XML documents into something else. The two most popular parsers of the moment are the Document Object Model (DOM and the Simple API for XML (SAX. DOM is an official recommendation of the W3C (available at http://www.w3.org/TR/REC-DOM-Level-1, while SAX is a de facto standard. A good parser should be fast, space efficient, rich in functionality and easy to use.

Beginning XML, 5th Edition

CERN Document Server

Fawcett, Joe; Quin, Liam R E

2012-01-01

A complete update covering the many advances to the XML language The XML language has become the standard for writing documents on the Internet and is constantly improving and evolving. This new edition covers all the many new XML-based technologies that have appeared since the previous edition four years ago, providing you with an up-to-date introductory guide and reference. Packed with real-world code examples, best practices, and in-depth coverage of the most important and relevant topics, this authoritative resource explores both the advantages and disadvantages of XML and addresses the mo

XML technology planning database : lessons learned

Science.gov (United States)

Some, Raphael R.; Neff, Jon M.

2005-01-01

A hierarchical Extensible Markup Language(XML) database called XCALIBR (XML Analysis LIBRary) has been developed by Millennium Program to assist in technology investment (ROI) analysis and technology Language Capability the New return on portfolio optimization. The database contains mission requirements and technology capabilities, which are related by use of an XML dictionary. The XML dictionary codifies a standardized taxonomy for space missions, systems, subsystems and technologies. In addition to being used for ROI analysis, the database is being examined for use in project planning, tracking and documentation. During the past year, the database has moved from development into alpha testing. This paper describes the lessons learned during construction and testing of the prototype database and the motivation for moving from an XML taxonomy to a standard XML-based ontology.

Desain Sistem Keamanan Distribusi Data Dengan Menerapkan XML Encryption Dan XML Signature Berbasis Teknologi Web Service

Directory of Open Access Journals (Sweden)

Slamet Widodo

2012-01-01

Full Text Available Development of information technologies is often misused by an organization or a person to take criminal acts, such as the ability to steal and modify information in the data distribution for evil criminal purpose. The Rural Bank of Boyolali is conducting online financial transactions rather intensively, thus it requiring a security system on the distribution of data and credit transactions for their customer among branches offices to head office. The purpose of this study was to build a security system in credit transactions in Rural Bank of Boyolali for their customers among branches offices to head office. One way in protecting data distribution was used XML encryption and XML signature. The application of encryption technique in XML and digital signature in XML by using web service by using the AES (Advanced Encryption Standard and RSA (Rivest-Shamir-Adleman algorithms. This study was resulted the SOAP (Simple Object Access Protocol message security system, with XML and WSDL (Web Services Description Language, over HTTP (Hypertext Transfer Protocol to protect the customers’ credit transactions from intruders. Analysis of examination indicated that the data size (bytes transferred as results of uncompressed XML encryption were larger than compressed XML Encryption, which leads to significant changes between the data transferred that was the processing time of the compressed data was faster than uncompressed XML encryption.

Towards the XML schema measurement based on mapping between XML and OO domain

Science.gov (United States)

Rakić, Gordana; Budimac, Zoran; Heričko, Marjan; Pušnik, Maja

2017-07-01

Measuring quality of IT solutions is a priority in software engineering. Although numerous metrics for measuring object-oriented code already exist, measuring quality of UML models or XML Schemas is still developing. One of the research questions in the overall research leaded by ideas described in this paper is whether we can apply already defined object-oriented design metrics on XML schemas based on predefined mappings. In this paper, basic ideas for mentioned mapping are presented. This mapping is prerequisite for setting the future approach to XML schema quality measuring with object-oriented metrics.

An effective XML based name mapping mechanism within StoRM

International Nuclear Information System (INIS)

Corso, E; Forti, A; Ghiselli, A; Magnoni, L; Zappi, R

2008-01-01

In a Grid environment the naming capability allows users to refer to specific data resources in a physical storage system using a high level logical identifier. This logical identifier is typically organized in a file system like structure, a hierarchical tree of names. Storage Resource Manager (SRM) services map the logical identifier to the physical location of data evaluating a set of parameters as the desired quality of services and the VOMS attributes specified in the requests. StoRM is a SRM service developed by INFN and ICTP-EGRID to manage file and space on standard POSIX and high performing parallel and cluster file systems. An upcoming requirement in the Grid data scenario is the orthogonality of the logical name and the physical location of data, in order to refer, with the same identifier, to different copies of data archived in various storage areas with different quality of service. The mapping mechanism proposed in StoRM is based on a XML document that represents the different storage components managed by the service, the storage areas defined by the site administrator, the quality of service they provide and the Virtual Organization that want to use the storage area. An appropriate directory tree is realized in each storage component reflecting the XML schema. In this scenario StoRM is able to identify the physical location of a requested data evaluating the logical identifier and the specified attributes following the XML schema, without querying any database service. This paper presents the namespace schema defined, the different entities represented and the technical details of the StoRM implementation

Prototype Development: Context-Driven Dynamic XML Ophthalmologic Data Capture Application

Science.gov (United States)

Schwei, Kelsey M; Kadolph, Christopher; Finamore, Joseph; Cancel, Efrain; McCarty, Catherine A; Okorie, Asha; Thomas, Kate L; Allen Pacheco, Jennifer; Pathak, Jyotishman; Ellis, Stephen B; Denny, Joshua C; Rasmussen, Luke V; Tromp, Gerard; Williams, Marc S; Vrabec, Tamara R; Brilliant, Murray H

2017-01-01

Background The capture and integration of structured ophthalmologic data into electronic health records (EHRs) has historically been a challenge. However, the importance of this activity for patient care and research is critical. Objective The purpose of this study was to develop a prototype of a context-driven dynamic extensible markup language (XML) ophthalmologic data capture application for research and clinical care that could be easily integrated into an EHR system. Methods Stakeholders in the medical, research, and informatics fields were interviewed and surveyed to determine data and system requirements for ophthalmologic data capture. On the basis of these requirements, an ophthalmology data capture application was developed to collect and store discrete data elements with important graphical information. Results The context-driven data entry application supports several features, including ink-over drawing capability for documenting eye abnormalities, context-based Web controls that guide data entry based on preestablished dependencies, and an adaptable database or XML schema that stores Web form specifications and allows for immediate changes in form layout or content. The application utilizes Web services to enable data integration with a variety of EHRs for retrieval and storage of patient data. Conclusions This paper describes the development process used to create a context-driven dynamic XML data capture application for optometry and ophthalmology. The list of ophthalmologic data elements identified as important for care and research can be used as a baseline list for future ophthalmologic data collection activities. PMID:28903894

XML Views: Part 1

NARCIS (Netherlands)

Rajugan, R.; Marik, V.; Retschitzegger, W.; Chang, E.; Dillon, T.; Stepankova, O.; Feng, L.

The exponential growth and the nature of Internet and web-based applications made eXtensible Markup Language (XML) as the de-facto standard for data exchange and data dissemination. Now it is gaining momentum in replacing conventional data models for data representation. XML with its self-describing

A standard format and a graphical user interface for spin system specification.

Science.gov (United States)

Biternas, A G; Charnock, G T P; Kuprov, Ilya

2014-03-01

We introduce a simple and general XML format for spin system description that is the result of extensive consultations within Magnetic Resonance community and unifies under one roof all major existing spin interaction specification conventions. The format is human-readable, easy to edit and easy to parse using standard XML libraries. We also describe a graphical user interface that was designed to facilitate construction and visualization of complicated spin systems. The interface is capable of generating input files for several popular spin dynamics simulation packages. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Automata, Logic, and XML

OpenAIRE

NEVEN, Frank

2002-01-01

We survey some recent developments in the broad area of automata and logic which are motivated by the advent of XML. In particular, we consider unranked tree automata, tree-walking automata, and automata over infinite alphabets. We focus on their connection with logic and on questions imposed by XML.

Speed up of XML parsers with PHP language implementation

Science.gov (United States)

Georgiev, Bozhidar; Georgieva, Adriana

2012-11-01

In this paper, authors introduce PHP5's XML implementation and show how to read, parse, and write a short and uncomplicated XML file using Simple XML in a PHP environment. The possibilities for mutual work of PHP5 language and XML standard are described. The details of parsing process with Simple XML are also cleared. A practical project PHP-XML-MySQL presents the advantages of XML implementation in PHP modules. This approach allows comparatively simple search of XML hierarchical data by means of PHP software tools. The proposed project includes database, which can be extended with new data and new XML parsing functions.

XML and Free Text.

Science.gov (United States)

Riggs, Ken Roger

2002-01-01

Discusses problems with marking free text, text that is either natural language or semigrammatical but unstructured, that prevent well-formed XML from marking text for readily available meaning. Proposes a solution to mark meaning in free text that is consistent with the intended simplicity of XML versus SGML. (Author/LRW)

Ajax, XSLT and SVG: Displaying ATLAS conditions data with new web technologies

Energy Technology Data Exchange (ETDEWEB)

Roe, S A, E-mail: shaun.roe@cern.c [CERN, CH-1211 Geneve 23 (Switzerland)

2010-04-01

The combination of three relatively recent technologies is described which allows an easy path from database retrieval to interactive web display. SQL queries on an Oracle database can be performed in a manner which directly return an XML description of the result, and Ajax techniques (Asynchronous JavaScript And XML) are used to dynamically inject the data into a web display accompanied by an XSLT transform template which determines how the data will be formatted. By tuning the transform to generate SVG (Scalable Vector Graphics) a direct graphical representation can be produced in the web page while retaining the database data as the XML source, allowing dynamic links to be generated in the web representation, but programmatic use of the data when used from a user application. With the release of the SVG 1.2 Tiny draft specification, the display can also be tailored for display on mobile devices. The technologies are described and a sample application demonstrated, showing conditions data from the ATLAS Semiconductor Tracker.

Ajax, XSLT and SVG: Displaying ATLAS conditions data with new web technologies

International Nuclear Information System (INIS)

Roe, S A

2010-01-01

The combination of three relatively recent technologies is described which allows an easy path from database retrieval to interactive web display. SQL queries on an Oracle database can be performed in a manner which directly return an XML description of the result, and Ajax techniques (Asynchronous JavaScript And XML) are used to dynamically inject the data into a web display accompanied by an XSLT transform template which determines how the data will be formatted. By tuning the transform to generate SVG (Scalable Vector Graphics) a direct graphical representation can be produced in the web page while retaining the database data as the XML source, allowing dynamic links to be generated in the web representation, but programmatic use of the data when used from a user application. With the release of the SVG 1.2 Tiny draft specification, the display can also be tailored for display on mobile devices. The technologies are described and a sample application demonstrated, showing conditions data from the ATLAS Semiconductor Tracker.

Ajax, XSLT and SVG: Displaying ATLAS conditions data with new web technologies

CERN Document Server

Roe, S A

2010-01-01

The combination of three relatively recent technologies is described which allows an easy path from database retrieval to interactive web display. SQL queries on an Oracle database can be performed in a manner which directly return an XML description of the result, and Ajax techniques (Asynchronous JavaScript And XML) are used to dynamically inject the data into a web display accompanied by an XSLT transform template which determines how the data will be formatted. By tuning the transform to generate SVG (Scalable Vector Graphics) a direct graphical representation can be produced in the web page while retaining the database data as the XML source, allowing dynamic links to be generated in the web representation, but programmatic use of the data when used from a user application. With the release of the SVG 1.2 Tiny draft specification, the display can also be tailored for display on mobile devices. The technologies are described and a sample application demonstrated, showing conditions data from the ATLAS Sem...

Evaluating SPARQL queries on massive RDF datasets

KAUST Repository

Al-Harbi, Razen

2015-08-01

Distributed RDF systems partition data across multiple computer nodes. Partitioning is typically based on heuristics that minimize inter-node communication and it is performed in an initial, data pre-processing phase. Therefore, the resulting partitions are static and do not adapt to changes in the query workload; as a result, existing systems are unable to consistently avoid communication for queries that are not favored by the initial data partitioning. Furthermore, for very large RDF knowledge bases, the partitioning phase becomes prohibitively expensive, leading to high startup costs. In this paper, we propose AdHash, a distributed RDF system which addresses the shortcomings of previous work. First, AdHash initially applies lightweight hash partitioning, which drastically minimizes the startup cost, while favoring the parallel processing of join patterns on subjects, without any data communication. Using a locality-aware planner, queries that cannot be processed in parallel are evaluated with minimal communication. Second, AdHash monitors the data access patterns and adapts dynamically to the query load by incrementally redistributing and replicating frequently accessed data. As a result, the communication cost for future queries is drastically reduced or even eliminated. Our experiments with synthetic and real data verify that AdHash (i) starts faster than all existing systems, (ii) processes thousands of queries before other systems become online, and (iii) gracefully adapts to the query load, being able to evaluate queries on billion-scale RDF data in sub-seconds. In this demonstration, audience can use a graphical interface of AdHash to verify its performance superiority compared to state-of-the-art distributed RDF systems.

Compressing Aviation Data in XML Format

Science.gov (United States)

Patel, Hemil; Lau, Derek; Kulkarni, Deepak

2003-01-01

Design, operations and maintenance activities in aviation involve analysis of variety of aviation data. This data is typically in disparate formats making it difficult to use with different software packages. Use of a self-describing and extensible standard called XML provides a solution to this interoperability problem. XML provides a standardized language for describing the contents of an information stream, performing the same kind of definitional role for Web content as a database schema performs for relational databases. XML data can be easily customized for display using Extensible Style Sheets (XSL). While self-describing nature of XML makes it easy to reuse, it also increases the size of data significantly. Therefore, transfemng a dataset in XML form can decrease throughput and increase data transfer time significantly. It also increases storage requirements significantly. A natural solution to the problem is to compress the data using suitable algorithm and transfer it in the compressed form. We found that XML-specific compressors such as Xmill and XMLPPM generally outperform traditional compressors. However, optimal use of Xmill requires of discovery of optimal options to use while running Xmill. This, in turn, depends on the nature of data used. Manual disc0ver.y of optimal setting can require an engineer to experiment for weeks. We have devised an XML compression advisory tool that can analyze sample data files and recommend what compression tool would work the best for this data and what are the optimal settings to be used with a XML compression tool.

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

Science.gov (United States)

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.

XML in Projects GNU Gama and 3DGI

DEFF Research Database (Denmark)

Kolar, Jan; Soucek, Petr; Cepek, Ales

2003-01-01

This paper presents our practical experiences with XML in geodetic and geographical applications. The main concepts and ideas of XML are introduced in an example of a simple web based information system, which exploits the XHTML language. The article further describes how XML is used in GNU Gama...... for structuring data for a geodetic network adjustment. In another application of XML, it is demonstrated how XML can be used for a unified description of data from leveling registration units. Finally, the use of XML for modelling 3D geographical features within the 3DGI project is presented and a relation...

XML Schema Representation of DICOM Structured Reporting.

Science.gov (United States)

Lee, K P; Hu, Jingkun

2003-01-01

The Digital Imaging and Communications in Medicine (DICOM) Structured Reporting (SR) standard improves the expressiveness, precision, and comparability of documentation about diagnostic images and waveforms. It supports the interchange of clinical reports in which critical features shown by images and waveforms can be denoted unambiguously by the observer, indexed, and retrieved selectively by subsequent reviewers. It is essential to provide access to clinical reports across the health care enterprise by using technologies that facilitate information exchange and processing by computers as well as provide support for robust and semantically rich standards, such as DICOM. This is supported by the current trend in the healthcare industry towards the use of Extensible Markup Language (XML) technologies for storage and exchange of medical information. The objective of the work reported here is to develop XML Schema for representing DICOM SR as XML documents. We briefly describe the document type definition (DTD) for XML and its limitations, followed by XML Schema (the intended replacement for DTD) and its features. A framework for generating XML Schema for representing DICOM SR in XML is presented next. None applicable. A schema instance based on an SR example in the DICOM specification was created and validated against the schema. The schema is being used extensively in producing reports on Philips Medical Systems ultrasound equipment. With the framework described it is feasible to generate XML Schema using the existing DICOM SR specification. It can also be applied to generate XML Schemas for other DICOM information objects.

The Cadmio XML healthcare record.

Science.gov (United States)

Barbera, Francesco; Ferri, Fernando; Ricci, Fabrizio L; Sottile, Pier Angelo

2002-01-01

The management of clinical data is a complex task. Patient related information reported in patient folders is a set of heterogeneous and structured data accessed by different users having different goals (in local or geographical networks). XML language provides a mechanism for describing, manipulating, and visualising structured data in web-based applications. XML ensures that the structured data is managed in a uniform and transparent manner independently from the applications and their providers guaranteeing some interoperability. Extracting data from the healthcare record and structuring them according to XML makes the data available through browsers. The MIC/MIE model (Medical Information Category/Medical Information Elements), which allows the definition and management of healthcare records and used in CADMIO, a HISA based project, is described in this paper, using XML for allowing the data to be visualised through web browsers.

XML Flight/Ground Data Dictionary Management

Science.gov (United States)

Wright, Jesse; Wiklow, Colette

2007-01-01

A computer program generates Extensible Markup Language (XML) files that effect coupling between the command- and telemetry-handling software running aboard a spacecraft and the corresponding software running in ground support systems. The XML files are produced by use of information from the flight software and from flight-system engineering. The XML files are converted to legacy ground-system data formats for command and telemetry, transformed into Web-based and printed documentation, and used in developing new ground-system data-handling software. Previously, the information about telemetry and command was scattered in various paper documents that were not synchronized. The process of searching and reading the documents was time-consuming and introduced errors. In contrast, the XML files contain all of the information in one place. XML structures can evolve in such a manner as to enable the addition, to the XML files, of the metadata necessary to track the changes and the associated documentation. The use of this software has reduced the extent of manual operations in developing a ground data system, thereby saving considerable time and removing errors that previously arose in the translation and transcription of software information from the flight to the ground system.

XML Publishing with Adobe InDesign

CERN Document Server

Hoskins, Dorothy

2010-01-01

From Adobe InDesign CS2 to InDesign CS5, the ability to work with XML content has been built into every version of InDesign. Some of the useful applications are importing database content into InDesign to create catalog pages, exporting XML that will be useful for subsequent publishing processes, and building chunks of content that can be reused in multiple publications. In this Short Cut, we'll play with the contents of a college course catalog and see how we can use XML for course descriptions, tables, and other content. Underlying principles of XML structure, DTDs, and the InDesign namesp

SU-E-T-327: The Update of a XML Composing Tool for TrueBeam Developer Mode

International Nuclear Information System (INIS)

Yan, Y; Mao, W; Jiang, S

2014-01-01

Purpose: To introduce a major upgrade of a novel XML beam composing tool to scientists and engineers who strive to translate certain capabilities of TrueBeam Developer Mode to future clinical benefits of radiation therapy. Methods: TrueBeam Developer Mode provides the users with a test bed for unconventional plans utilizing certain unique features not accessible at the clinical mode. To access the full set of capabilities, a XML beam definition file accommodating all parameters including kV/MV imaging triggers in the plan can be locally loaded at this mode, however it is difficult and laborious to compose one in a text editor. In this study, a stand-along interactive XML beam composing application, TrueBeam TeachMod, was developed on Windows platforms to assist users in making their unique plans in a WYSWYG manner. A conventional plan can be imported in a DICOM RT object as the start of the beam editing process in which trajectories of all axes of a TrueBeam machine can be modified to the intended values at any control point. TeachMod also includes libraries of predefined imaging and treatment procedures to further expedite the process. Results: The TeachMod application is a major of the TeachMod module within DICOManTX. It fully supports TrueBeam 2.0. Trajectories of all axes including all MLC leaves can be graphically rendered and edited as needed. The time for XML beam composing has been reduced to a negligible amount regardless the complexity of the plan. A good understanding of XML language and TrueBeam schema is not required though preferred. Conclusion: Creating XML beams manually in a text editor will be a lengthy error-prone process for sophisticated plans. A XML beam composing tool is highly desirable for R and D activities. It will bridge the gap between scopes of TrueBeam capabilities and their clinical application potentials

XML Schema Representation of DICOM Structured Reporting

Science.gov (United States)

Lee, K. P.; Hu, Jingkun

2003-01-01

Objective: The Digital Imaging and Communications in Medicine (DICOM) Structured Reporting (SR) standard improves the expressiveness, precision, and comparability of documentation about diagnostic images and waveforms. It supports the interchange of clinical reports in which critical features shown by images and waveforms can be denoted unambiguously by the observer, indexed, and retrieved selectively by subsequent reviewers. It is essential to provide access to clinical reports across the health care enterprise by using technologies that facilitate information exchange and processing by computers as well as provide support for robust and semantically rich standards, such as DICOM. This is supported by the current trend in the healthcare industry towards the use of Extensible Markup Language (XML) technologies for storage and exchange of medical information. The objective of the work reported here is to develop XML Schema for representing DICOM SR as XML documents. Design: We briefly describe the document type definition (DTD) for XML and its limitations, followed by XML Schema (the intended replacement for DTD) and its features. A framework for generating XML Schema for representing DICOM SR in XML is presented next. Measurements: None applicable. Results: A schema instance based on an SR example in the DICOM specification was created and validated against the schema. The schema is being used extensively in producing reports on Philips Medical Systems ultrasound equipment. Conclusion: With the framework described it is feasible to generate XML Schema using the existing DICOM SR specification. It can also be applied to generate XML Schemas for other DICOM information objects. PMID:12595410

The duality of XML Markup and Programming notation

DEFF Research Database (Denmark)

Nørmark, Kurt

2003-01-01

In web projects it is often necessary to mix XML notation and program notation in a single document or program. In mono-lingual situations, the XML notation is either subsumed in the program or the program notation is subsumed in the XML document. As an introduction we analyze XML notation and pr...

XML, TEI, and Digital Libraries in the Humanities.

Science.gov (United States)

Nellhaus, Tobin

2001-01-01

Describes the history and major features of XML and TEI, discusses their potential utility for the creation of digital libraries, and focuses on XML's application in the humanities, particularly theater and drama studies. Highlights include HTML and hyperlinks; the impact of XML on text encoding and document access; and XML and academic…

An Introduction to the Extensible Markup Language (XML).

Science.gov (United States)

Bryan, Martin

1998-01-01

Describes Extensible Markup Language (XML), a subset of the Standard Generalized Markup Language (SGML) that is designed to make it easy to interchange structured documents over the Internet. Topics include Document Type Definition (DTD), components of XML, the use of XML, text and non-text elements, and uses for XML-coded files. (LRW)

Graphic Data Display from Manufacturing on Web Pages

Directory of Open Access Journals (Sweden)

Martin VALAS

2009-06-01

Full Text Available Industrial data can by displayed in graphical form which is usually used by three types of users. The first, nonstop users, most frequent operational engineer, who checking actual displayed values and then intervene in operation. The second are occasional users who are interested in historical data e.g. for servicing reason. The last users’ types are tradesmen and managers. State comparison few days or months ago helps as decision-making support. Graph component with web application, which provides data as XML document, was designed for second users group. Graph component displays historical data. Students can fully understand all the problems go along with web application creation in ASP.NET, which provides data in XML document, as well as graph component creation in integrated development environment Flash, thanks in detail described solution using ActionScript.

XPIWIT--an XML pipeline wrapper for the Insight Toolkit.

Science.gov (United States)

Bartschat, Andreas; Hübner, Eduard; Reischl, Markus; Mikut, Ralf; Stegmaier, Johannes

2016-01-15

The Insight Toolkit offers plenty of features for multidimensional image analysis. Current implementations, however, often suffer either from a lack of flexibility due to hard-coded C++ pipelines for a certain task or by slow execution times, e.g. caused by inefficient implementations or multiple read/write operations for separate filter execution. We present an XML-based wrapper application for the Insight Toolkit that combines the performance of a pure C++ implementation with an easy-to-use graphical setup of dynamic image analysis pipelines. Created XML pipelines can be interpreted and executed by XPIWIT in console mode either locally or on large clusters. We successfully applied the software tool for the automated analysis of terabyte-scale, time-resolved 3D image data of zebrafish embryos. XPIWIT is implemented in C++ using the Insight Toolkit and the Qt SDK. It has been successfully compiled and tested under Windows and Unix-based systems. Software and documentation are distributed under Apache 2.0 license and are publicly available for download at https://bitbucket.org/jstegmaier/xpiwit/downloads/. johannes.stegmaier@kit.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

XML for data representation and model specification in neuroscience.

Science.gov (United States)

Crook, Sharon M; Howell, Fred W

2007-01-01

EXtensible Markup Language (XML) technology provides an ideal representation for the complex structure of models and neuroscience data, as it is an open file format and provides a language-independent method for storing arbitrarily complex structured information. XML is composed of text and tags that explicitly describe the structure and semantics of the content of the document. In this chapter, we describe some of the common uses of XML in neuroscience, with case studies in representing neuroscience data and defining model descriptions based on examples from NeuroML. The specific methods that we discuss include (1) reading and writing XML from applications, (2) exporting XML from databases, (3) using XML standards to represent neuronal morphology data, (4) using XML to represent experimental metadata, and (5) creating new XML specifications for models.

Static Analysis of XML Transformations in Java

DEFF Research Database (Denmark)

Kirkegaard, Christian; Møller, Anders; Schwartzbach, Michael I.

2004-01-01

of XML documents to be defined, there are generally no automatic mechanisms for statically checking that a program transforms from one class to another as intended. We introduce Xact, a high-level approach for Java using XML templates as a first-class data type with operations for manipulating XML values...

"The Wonder Years" of XML.

Science.gov (United States)

Gazan, Rich

2000-01-01

Surveys the current state of Extensible Markup Language (XML), a metalanguage for creating structured documents that describe their own content, and its implications for information professionals. Predicts that XML will become the common language underlying Web, word processing, and database formats. Also discusses Extensible Stylesheet Language…

XML specifications DanRIS

DEFF Research Database (Denmark)

2009-01-01

XML specifications for DanRIS (Danish Registration- og InformationsSystem), where the the aim is: Improved exchange of data Improved data processing Ensuring future access to all gathered data from the year 1999 until now......XML specifications for DanRIS (Danish Registration- og InformationsSystem), where the the aim is: Improved exchange of data Improved data processing Ensuring future access to all gathered data from the year 1999 until now...

δ-dependency for privacy-preserving XML data publishing.

Science.gov (United States)

Landberg, Anders H; Nguyen, Kinh; Pardede, Eric; Rahayu, J Wenny

2014-08-01

An ever increasing amount of medical data such as electronic health records, is being collected, stored, shared and managed in large online health information systems and electronic medical record systems (EMR) (Williams et al., 2001; Virtanen, 2009; Huang and Liou, 2007) [1-3]. From such rich collections, data is often published in the form of census and statistical data sets for the purpose of knowledge sharing and enabling medical research. This brings with it an increasing need for protecting individual people privacy, and it becomes an issue of great importance especially when information about patients is exposed to the public. While the concept of data privacy has been comprehensively studied for relational data, models and algorithms addressing the distinct differences and complex structure of XML data are yet to be explored. Currently, the common compromise method is to convert private XML data into relational data for publication. This ad hoc approach results in significant loss of useful semantic information previously carried in the private XML data. Health data often has very complex structure, which is best expressed in XML. In fact, XML is the standard format for exchanging (e.g. HL7 version 3(1)) and publishing health information. Lack of means to deal directly with data in XML format is inevitably a serious drawback. In this paper we propose a novel privacy protection model for XML, and an algorithm for implementing this model. We provide general rules, both for transforming a private XML schema into a published XML schema, and for mapping private XML data to the new privacy-protected published XML data. In addition, we propose a new privacy property, δ-dependency, which can be applied to both relational and XML data, and that takes into consideration the hierarchical nature of sensitive data (as opposed to "quasi-identifiers"). Lastly, we provide an implementation of our model, algorithm and privacy property, and perform an experimental analysis

How Does XML Help Libraries?

Science.gov (United States)

Banerjee, Kyle

2002-01-01

Discusses XML, how it has transformed the way information is managed and delivered, and its impact on libraries. Topics include how XML differs from other markup languages; the document object model (DOM); style sheets; practical applications for archival materials, interlibrary loans, digital collections, and MARC data; and future possibilities.…

Performance analysis of Java APIS for XML processing

OpenAIRE

Oliveira, Bruno; Santos, Vasco; Belo, Orlando

2013-01-01

Over time, XML markup language has acquired a considerable importance in applications development, standards definition and in the representation of large volumes of data, such as databases. Today, processing XML documents in a short period of time is a critical activity in a large range of applications, which imposes choosing the most appropriate mechanism to parse XML documents quickly and efficiently. When using a programming language for XML processing, such as ...

Processing XML with Java – a performance benchmark

OpenAIRE

Oliveira, Bruno; Santos, Vasco; Belo, Orlando

2013-01-01

Over time, XML markup language has acquired a considerable importance in applications development, standards definition and in the representation of large volumes of data, such as databases. Today, processing XML documents in a short period of time is a critical activity in a large range of applications, which imposes choosing the most appropriate mechanism to parse XML documents quickly and efficiently. When using a programming language for XML processing, suc...

The appliance of graphics modeling in nuclear plant information system

International Nuclear Information System (INIS)

Bai Zhe; Li Guofang

2010-01-01

The nuclear plants contain a lot of sub-system, such as operation management, manufacture system, inventory system, human resource system and so forth. The standardized data graphics modeling technology can ensure the data interaction, compress the design cycle, avoid the replicated design, ensure the data integrity and consistent. The standardized data format which is on the basis of STEP standard and complied with XML is competent tool in different sub-system of nuclear plants. In order to meet this demand, a data graphics modeling standard is proposed. It is shown the relationship between systems, in system, between data by the standard. The graphic modeling effectively improves the performance between systems, designers, engineers, operations, supports department. It also provides the reliable and available data source for data mining and business intelligence. (authors)

Principles of reusability of XML-based enterprise documents

Directory of Open Access Journals (Sweden)

Roman Malo

2010-01-01

Full Text Available XML (Extensible Markup Language represents one of flexible platforms for processing enterprise documents. Its simple syntax and powerful software infrastructure for processing this type of documents is a guarantee for high interoperability of individual documents. XML is today one of technologies influencing all aspects of ICT area.In the paper questions and basic principles of reusing XML-based documents are described in the field of enterprise documents. If we use XML databases or XML data types for storing these types of documents then partial redundancy could be expected due to possible documents’ similarity. This similarity can be found especially in documents’ structure and also in documents’ content and its elimination is necessary part of data optimization.The main idea of the paper is focused to possibilities how to think about dividing complex XML docu­ments into independent fragments that can be used as standalone documents and how to process them.Conclusions could be applied within software tools working with XML-based structured data and documents as document management systems or content management systems.

An XML-hierarchical data structure for ENSDF

International Nuclear Information System (INIS)

Hurst, Aaron M.

2016-01-01

A data structure based on an eXtensible Markup Language (XML) hierarchy according to experimental nuclear structure data in the Evaluated Nuclear Structure Data File (ENSDF) is presented. A Python-coded translator has been developed to interpret the standard one-card records of the ENSDF datasets, together with their associated quantities defined according to field position, and generate corresponding representative XML output. The quantities belonging to this mixed-record format are described in the ENSDF manual. Of the 16 ENSDF records in total, XML output has been successfully generated for 15 records. An XML-translation for the Comment Record is yet to be implemented; this will be considered in a separate phase of the overall translation effort. Continuation records, not yet implemented, will also be treated in a future phase of this work. Several examples are presented in this document to illustrate the XML schema and methods for handling the various ENSDF data types. However, the proposed nomenclature for the XML elements and attributes need not necessarily be considered as a fixed set of constructs. Indeed, better conventions may be suggested and a consensus can be achieved amongst the various groups of people interested in this project. The main purpose here is to present an initial phase of the translation effort to demonstrate the feasibility of interpreting ENSDF datasets and creating a representative XML-structured hierarchy for data storage.

XML Schema Languages: Beyond DTD.

Science.gov (United States)

Ioannides, Demetrios

2000-01-01

Discussion of XML (extensible markup language) and the traditional DTD (document type definition) format focuses on efforts of the World Wide Web Consortium's XML schema working group to develop a schema language to replace DTD that will be capable of defining the set of constraints of any possible data resource. (Contains 14 references.) (LRW)

Interactive graphics for data analysis principles and examples

CERN Document Server

Theus, Martin

2008-01-01

Introduction PRINCIPLESInteractivity Queries Selection and Linked Highlighting Linking AnalysesInteracting with Graphics Examining a Single Variable Categorical DataContinuous DataTransforming Data Weighted Plots Interactions between Two VariablesTwo Categorical VariablesOne Categorical Variable and One Continuous VariableTwo Continuous VariablesMultidimensional Plots Mosaic PlotsParallel Coordinate Plots Trellis Displays Plot Ensembles and Statistical ModelsResponse ModelsANOVALoglinear ModelsGeographical DataMore Interactivity Sorting and Ordering Zooming Multiple ViewsInteractive Graphics ?

Investigation of multiple visualisation techniques and dynamic queries in conjunction with direct sonification to support the browsing of audio resources

OpenAIRE

Brazil, Eoin

2003-01-01

non-peer-reviewed In this thesis, a prototype system for the browsing of audio resources was developed and an initial evaluation of this system was performed. The main contributions of this thesis are dynamic queries and multiple visualisation techniques in conjunction with direct sonification. Dynamic queries are queries that provide immediate feedback while maintaining consistency between the queries themselves and the graphical/auditory display. The multiple visualisation techniques are...

XML and E-Journals: The State of Play.

Science.gov (United States)

Wusteman, Judith

2003-01-01

Discusses the introduction of the use of XML (Extensible Markup Language) in publishing electronic journals. Topics include standards, including DTDs (Document Type Definition), or document type definitions; aggregator requirements; SGML (Standard Generalized Markup Language); benefits of XML for e-journals; XML metadata; the possibility of…

XML Syntax for Clinical Laboratory Procedure Manuals

OpenAIRE

Saadawi, Gilan; Harrison, James H.

2003-01-01

We have developed a document type description (DTD) in Extensable Markup Language (XML)1 for clinical laboratory procedures. Our XML syntax can adequately structure a variety of procedure types across different laboratories and is compatible with current procedure standards. The combination of this format with an XML content management system and appropriate style sheets will allow efficient procedure maintenance, distributed access, customized display and effective searching across a large b...

Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures.

Science.gov (United States)

Sankar, Punnaivanam; Aghila, Gnanasekaran

2007-01-01

The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

How will XML impact industrial automation?

CERN Multimedia

Pinceti, P

2002-01-01

A working group of the World Wide Web Consortium (W3C) has overcome the limits of both HTML and SGML with the definition of the extensible markup language - XML. This article looks at how XML will affect industrial automation (2 pages).

System architecture with XML

CERN Document Server

Daum, Berthold

2002-01-01

XML is bringing together some fairly disparate groups into a new cultural clash: document developers trying to understand what a transaction is, database analysts getting upset because the relational model doesn''t fit anymore, and web designers having to deal with schemata and rule based transformations. The key to rising above the confusion is to understand the different semantic structures that lie beneath the standards of XML, and how to model the semantics to achieve the goals of the organization. A pure architecture of XML doesn''t exist yet, and it may never exist as the underlying technologies are so diverse. Still, the key to understanding how to build the new web infrastructure for electronic business lies in understanding the landscape of these new standards.If your background is in document processing, this book will show how you can use conceptual modeling to model business scenarios consisting of business objects, relationships, processes, and transactions in a document-centric way. Database des...

NEOview: Near Earth Object Data Discovery and Query

Science.gov (United States)

Tibbetts, M.; Elvis, M.; Galache, J. L.; Harbo, P.; McDowell, J. C.; Rudenko, M.; Van Stone, D.; Zografou, P.

2013-10-01

Missions to Near Earth Objects (NEOs) figure prominently in NASA's Flexible Path approach to human space exploration. NEOs offer insight into both the origins of the Solar System and of life, as well as a source of materials for future missions. With NEOview scientists can locate NEO datasets, explore metadata provided by the archives, and query or combine disparate NEO datasets in the search for NEO candidates for exploration. NEOview is a software system that illustrates how standards-based interfaces facilitate NEO data discovery and research. NEOview software follows a client-server architecture. The server is a configurable implementation of the International Virtual Observatory Alliance (IVOA) Table Access Protocol (TAP), a general interface for tabular data access, that can be deployed as a front end to existing NEO datasets. The TAP client, seleste, is a graphical interface that provides intuitive means of discovering NEO providers, exploring dataset metadata to identify fields of interest, and constructing queries to retrieve or combine data. It features a powerful, graphical query builder capable of easing the user's introduction to table searches. Through science use cases, NEOview demonstrates how potential targets for NEO rendezvous could be identified by combining data from complementary sources. Through deployment and operations, it has been shown that the software components are data independent and configurable to many different data servers. As such, NEOview's TAP server and seleste TAP client can be used to create a seamless environment for data discovery and exploration for tabular data in any astronomical archive.

Publishing with XML structure, enter, publish

CERN Document Server

Prost, Bernard

2015-01-01

XML is now at the heart of book publishing techniques: it provides the industry with a robust, flexible format which is relatively easy to manipulate. Above all, it preserves the future: the XML text becomes a genuine tactical asset enabling publishers to respond quickly to market demands. When new publishing media appear, it will be possible to very quickly make your editorial content available at a lower cost. On the downside, XML can become a bottomless pit for publishers attracted by its possibilities. There is a strong temptation to switch to audiovisual production and to add video and a

Prototype Development: Context-Driven Dynamic XML Ophthalmologic Data Capture Application.

Science.gov (United States)

Peissig, Peggy; Schwei, Kelsey M; Kadolph, Christopher; Finamore, Joseph; Cancel, Efrain; McCarty, Catherine A; Okorie, Asha; Thomas, Kate L; Allen Pacheco, Jennifer; Pathak, Jyotishman; Ellis, Stephen B; Denny, Joshua C; Rasmussen, Luke V; Tromp, Gerard; Williams, Marc S; Vrabec, Tamara R; Brilliant, Murray H

2017-09-13

The capture and integration of structured ophthalmologic data into electronic health records (EHRs) has historically been a challenge. However, the importance of this activity for patient care and research is critical. The purpose of this study was to develop a prototype of a context-driven dynamic extensible markup language (XML) ophthalmologic data capture application for research and clinical care that could be easily integrated into an EHR system. Stakeholders in the medical, research, and informatics fields were interviewed and surveyed to determine data and system requirements for ophthalmologic data capture. On the basis of these requirements, an ophthalmology data capture application was developed to collect and store discrete data elements with important graphical information. The context-driven data entry application supports several features, including ink-over drawing capability for documenting eye abnormalities, context-based Web controls that guide data entry based on preestablished dependencies, and an adaptable database or XML schema that stores Web form specifications and allows for immediate changes in form layout or content. The application utilizes Web services to enable data integration with a variety of EHRs for retrieval and storage of patient data. This paper describes the development process used to create a context-driven dynamic XML data capture application for optometry and ophthalmology. The list of ophthalmologic data elements identified as important for care and research can be used as a baseline list for future ophthalmologic data collection activities. ©Peggy Peissig, Kelsey M Schwei, Christopher Kadolph, Joseph Finamore, Efrain Cancel, Catherine A McCarty, Asha Okorie, Kate L Thomas, Jennifer Allen Pacheco, Jyotishman Pathak, Stephen B Ellis, Joshua C Denny, Luke V Rasmussen, Gerard Tromp, Marc S Williams, Tamara R Vrabec, Murray H Brilliant. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 13.09.2017.

XML-RPC技术及其应用分析%Analysis of XML-RPC Technology and Its Application

Institute of Scientific and Technical Information of China (English)

姚鹤岭

2005-01-01

为了说明XML-RPC技术在特定场合的应用价值,介绍了基于XML语言的XML-RPC分布式技术的概念与特点,在编写Meerkat客户端程序时,使用Python语言实现了类似ArcWeb服务的功能.研究表明:XML-RPC技术在一定条件下能够很好地满足不同应用间的通信与互操作的需求.

Upgrading a TCABR data analysis and acquisition system for remote participation using Java, XML, RCP and modern client/server communication/authentication

International Nuclear Information System (INIS)

Sa, W.P. de

2010-01-01

The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The architecture of the new system uses Java language as programming environment. Since application parameters and hardware in a joint experiment are complex with a large variability of components, requirements and specification solutions need to be flexible and modular, independent from operating system and computer architecture. To describe and organize the information on all the components and the connections among them, systems are developed using the eXtensible Markup Language (XML) technology. The communication between clients and servers uses remote procedure call (RPC) based on the XML (RPC-XML technology). The integration among Java language, XML and RPC-XML technologies allows to develop easily a standard data and communication access layer between users and laboratories using common software libraries and Web application. The libraries allow data retrieval using the same methods for all user laboratories in the joint collaboration, and the Web application allows a simple graphical user interface (GUI) access. The TCABR tokamak team in collaboration with the IPFN (Instituto de Plasmas e Fusao Nuclear, Instituto Superior Tecnico, Universidade Tecnica de Lisboa) is implementing this remote participation technologies. The first version was tested at the Joint Experiment on TCABR (TCABRJE), a Host Laboratory Experiment, organized in cooperation with the IAEA (International Atomic Energy Agency) in the framework of the IAEA Coordinated Research Project (CRP) on 'Joint Research Using Small Tokamaks'.

Upgrading a TCABR data analysis and acquisition system for remote participation using Java, XML, RCP and modern client/server communication/authentication

Energy Technology Data Exchange (ETDEWEB)

Sa, W.P. de, E-mail: pires@if.usp.b [Instituto de Fisica, Universidade de Sao Paulo, Rua do Matao, Travessa R, 187 CEP 05508-090 Cidade Universitaria, Sao Paulo (Brazil)

2010-07-15

The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The architecture of the new system uses Java language as programming environment. Since application parameters and hardware in a joint experiment are complex with a large variability of components, requirements and specification solutions need to be flexible and modular, independent from operating system and computer architecture. To describe and organize the information on all the components and the connections among them, systems are developed using the eXtensible Markup Language (XML) technology. The communication between clients and servers uses remote procedure call (RPC) based on the XML (RPC-XML technology). The integration among Java language, XML and RPC-XML technologies allows to develop easily a standard data and communication access layer between users and laboratories using common software libraries and Web application. The libraries allow data retrieval using the same methods for all user laboratories in the joint collaboration, and the Web application allows a simple graphical user interface (GUI) access. The TCABR tokamak team in collaboration with the IPFN (Instituto de Plasmas e Fusao Nuclear, Instituto Superior Tecnico, Universidade Tecnica de Lisboa) is implementing this remote participation technologies. The first version was tested at the Joint Experiment on TCABR (TCABRJE), a Host Laboratory Experiment, organized in cooperation with the IAEA (International Atomic Energy Agency) in the framework of the IAEA Coordinated Research Project (CRP) on 'Joint Research Using Small Tokamaks'.

Sample Scripts for Generating PaGE-OM XML [

Lifescience Database Archive (English)

Full Text Available Sample Scripts for Generating PaGE-OM XML This page is offering some sample scripts...on MySQL. Outline chart of procedure 6. Creating RDB tables for Generating PaGE-OM XML These scripts help yo...wnload: create_tables_sql2.zip 7. Generating PaGE-OM XML from phenotype data This sample Perl script helps y

XML a bezpečnost I

Czech Academy of Sciences Publication Activity Database

Brechlerová, Dagmar

2007-01-01

Roč. 9, č. 1 (2007), s. 13-25 ISSN 1801-2140 R&D Projects: GA AV ČR 1ET200300413 Institutional research plan: CEZ:AV0Z10300504 Keywords : XML security * XML digitální podpis * XKMS Subject RIV: IN - Informatics, Computer Science http://crypto-world.info/index2.php

The curse of namespaces in the domain of XML signature

DEFF Research Database (Denmark)

Jensen, Meiko; Liao, Lijun; Schwenk, Jörg

2009-01-01

The XML signature wrapping attack is one of the most discussed security issues of the Web Services security community during the last years. Until now, the issue has not been solved, and all countermeasure approaches proposed so far were shown to be insufficient. In this paper, we present yet...... another way to perform signature wrapping attacks by using the XML namespace injection technique. We show that the interplay of XML Signature, XPath, and the XML namespace concept has severe flaws that can be exploited for an attack, and that XML namespaces in general pose real troubles to digital...... signatures in the XML domain. Additionally, we present and discuss some new approaches in countering the proposed attack vector....

Representing User Navigation in XML Retrieval with Structural Summaries

DEFF Research Database (Denmark)

Ali, M. S.; Consens, Mariano P.; Larsen, Birger

This poster presents a novel way to represent user navigation in XML retrieval using collection statistics from XML summaries. Currently, developing user navigation models in XML retrieval is costly and the models are specific to collected user assessments. We address this problem by proposing...

KoralQuery -- A General Corpus Query Protocol

DEFF Research Database (Denmark)

Bingel, Joachim; Diewald, Nils

2015-01-01

. In this paper, we present KoralQuery, a JSON-LD based general corpus query protocol, aiming to be independent of particular QLs, tasks and corpus formats. In addition to describing the system of types and operations that KoralQuery is built on, we exemplify the representation of corpus queries in the serialized...

Efficiently adapting graphical models for selectivity estimation

DEFF Research Database (Denmark)

Tzoumas, Kostas; Deshpande, Amol; Jensen, Christian S.

2013-01-01

cardinality estimation without making the independence assumption. By carefully using concepts from the field of graphical models, we are able to factor the joint probability distribution over all the attributes in the database into small, usually two-dimensional distributions, without a significant loss...... in estimation accuracy. We show how to efficiently construct such a graphical model from the database using only two-way join queries, and we show how to perform selectivity estimation in a highly efficient manner. We integrate our algorithms into the PostgreSQL DBMS. Experimental results indicate...

Static Analysis for Event-Based XML Processing

DEFF Research Database (Denmark)

Møller, Anders

2008-01-01

Event-based processing of XML data - as exemplified by the popular SAX framework - is a powerful alternative to using W3C's DOM or similar tree-based APIs. The event-based approach is a streaming fashion with minimal memory consumption. This paper discusses challenges for creating program analyses...... for SAX applications. In particular, we consider the problem of statically guaranteeing the a given SAX program always produces only well-formed and valid XML output. We propose an analysis technique based on ecisting anglyses of Servlets, string operations, and XML graphs....

Building adaptable and reusable XML applications with model transformations

NARCIS (Netherlands)

Ivanov, Ivan; van den Berg, Klaas

2005-01-01

We present an approach in which the semantics of an XML language is defined by means of a transformation from an XML document model (an XML schema) to an application specific model. The application specific model implements the intended behavior of documents written in the language. A transformation

Schema Design and Normalization Algorithm for XML Databases Model

Directory of Open Access Journals (Sweden)

Samir Abou El-Seoud

2009-06-01

Full Text Available In this paper we study the problem of schema design and normalization in XML databases model. We show that, like relational databases, XML documents may contain redundant information, and this redundancy may cause update anomalies. Furthermore, such problems are caused by certain functional dependencies among paths in the document. Based on our research works, in which we presented the functional dependencies and normal forms of XML Schema, we present the decomposition algorithm for converting any XML Schema into normalized one, that satisfies X-BCNF.

The Big Bang - XML expanding the information universe

International Nuclear Information System (INIS)

Rutt, S.; Chamberlain, M.; Buckley, G.

2004-01-01

The XML language is discussed as a tool in the information management. Industries are adopting XML as a means of making disparate systems talk with each other or as a means of swapping information between different organisations and different operating systems by using a common set of mark-up. More important to this discussion is the ability to use XML within the field of Technical Documentation and Publication. The capabilities of XML in work with different types of documents are presented. In conclusion, a summary is given of the benefits of using an XML solution: Precisely match your requirements at no more initial cost; Single Source Dynamic Content Delivery and Management; 100% of authors time is spent creating content; Content is no longer locked into its format; Reduced hardware and data storage requirements; Content survives the publishing lifecycle; Auto-versioning/release management control; Workflows can be mapped and electronic audit trails made

Profex: a graphical user interface for the Rietveld refinement program BGMN

OpenAIRE

Doebelin, Nicola; Kleeberg, Reinhard

2015-01-01

Profex is a graphical user interface for the Rietveld refinement program BGMN. Its interface focuses on preserving BGMN’s powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal str...

ADASS Web Database XML Project

Science.gov (United States)

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

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

TIJAH: Embracing IR Methods in XML Databases

NARCIS (Netherlands)

List, Johan; Mihajlovic, V.; Ramirez, Georgina; de Vries, A.P.; Hiemstra, Djoerd; Blok, H.E.

2005-01-01

This paper discusses our participation in INEX (the Initiative for the Evaluation of XML Retrieval) using the TIJAH XML-IR system. TIJAH's system design follows a `standard' layered database architecture, carefully separating the conceptual, logical and physical levels. At the conceptual level, we

Clinical map document based on XML (cMDX): document architecture with mapping feature for reporting and analysing prostate cancer in radical prostatectomy specimens.

Science.gov (United States)

Eminaga, Okyaz; Hinkelammert, Reemt; Semjonow, Axel; Neumann, Joerg; Abbas, Mahmoud; Koepke, Thomas; Bettendorf, Olaf; Eltze, Elke; Dugas, Martin

2010-11-15

The pathology report of radical prostatectomy specimens plays an important role in clinical decisions and the prognostic evaluation in Prostate Cancer (PCa). The anatomical schema is a helpful tool to document PCa extension for clinical and research purposes. To achieve electronic documentation and analysis, an appropriate documentation model for anatomical schemas is needed. For this purpose we developed cMDX. The document architecture of cMDX was designed according to Open Packaging Conventions by separating the whole data into template data and patient data. Analogue custom XML elements were considered to harmonize the graphical representation (e.g. tumour extension) with the textual data (e.g. histological patterns). The graphical documentation was based on the four-layer visualization model that forms the interaction between different custom XML elements. Sensible personal data were encrypted with a 256-bit cryptographic algorithm to avoid misuse. In order to assess the clinical value, we retrospectively analysed the tumour extension in 255 patients after radical prostatectomy. The pathology report with cMDX can represent pathological findings of the prostate in schematic styles. Such reports can be integrated into the hospital information system. "cMDX" documents can be converted into different data formats like text, graphics and PDF. Supplementary tools like cMDX Editor and an analyser tool were implemented. The graphical analysis of 255 prostatectomy specimens showed that PCa were mostly localized in the peripheral zone (Mean: 73% ± 25). 54% of PCa showed a multifocal growth pattern. cMDX can be used for routine histopathological reporting of radical prostatectomy specimens and provide data for scientific analysis.

A comparison of database systems for XML-type data

NARCIS (Netherlands)

Risse, J.E.; Leunissen, J.A.M.

2010-01-01

Background: 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

An XML-based framework for personalized health management.

Science.gov (United States)

Lee, Hiye-Ja; Park, Seung-Hun; Jeong, Byeong-Soo

2006-01-01

This paper proposes a framework for personalized health management. In this framework, XML technology is used for representing and managing the health information and knowledge. Major components of the framework are Health Management Prescription (HMP) Expert System and Health Information Repository. The HMP Expert System generates a HMP efficiently by using XML-based templates. Health Information Repository provides integrated health information and knowledge for personalized health management by using XML and relational database together.

Exploring PSI-MI XML Collections Using DescribeX

Directory of Open Access Journals (Sweden)

Samavi Reza

2007-12-01

Full Text Available PSI-MI has been endorsed by the protein informatics community as a standard XML data exchange format for protein-protein interaction datasets. While many public databases support the standard, there is a degree of heterogeneity in the way the proposed XML schema is interpreted and instantiated by different data providers. Analysis of schema instantiation in large collections of XML data is a challenging task that is unsupported by existing tools.

PDBML: the representation of archival macromolecular structure data in XML.

Science.gov (United States)

Westbrook, John; Ito, Nobutoshi; Nakamura, Haruki; Henrick, Kim; Berman, Helen M

2005-04-01

The Protein Data Bank (PDB) has recently released versions of the PDB Exchange dictionary and the PDB archival data files in XML format collectively named PDBML. The automated generation of these XML files is driven by the data dictionary infrastructure in use at the PDB. The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files.

An Introduction to XML and Web Technologies

DEFF Research Database (Denmark)

Møller, Anders; Schwartzbach, Michael Ignatieff

, building on top of the early foundations. This book offers a comprehensive introduction to the area. There are two main threads of development, corresponding to the two parts of this book. XML technologies generalize the notion of data on the Web from hypertext documents to arbitrary data, including those...... that have traditionally been the realm of databases. In this book we cover the basic XML technology and the supporting technologies of XPath, DTD, XML Schema, DSD2, RELAX NG, XSLT, XQuery, DOM, JDOM, JAXB, SAX, STX, SDuce, and XACT. Web technologies build on top of the HTTP protocol to provide richer...

Graphical Model Theory for Wireless Sensor Networks

International Nuclear Information System (INIS)

Davis, William B.

2002-01-01

Information processing in sensor networks, with many small processors, demands a theory of computation that allows the minimization of processing effort, and the distribution of this effort throughout the network. Graphical model theory provides a probabilistic theory of computation that explicitly addresses complexity and decentralization for optimizing network computation. The junction tree algorithm, for decentralized inference on graphical probability models, can be instantiated in a variety of applications useful for wireless sensor networks, including: sensor validation and fusion; data compression and channel coding; expert systems, with decentralized data structures, and efficient local queries; pattern classification, and machine learning. Graphical models for these applications are sketched, and a model of dynamic sensor validation and fusion is presented in more depth, to illustrate the junction tree algorithm

XML-based DICOM data format.

Science.gov (United States)

Yu, Cong; Yao, Zhihong

2010-04-01

To enhance the readability, improve the structure, and facilitate the sharing of digital imaging and communications in medicine (DICOM) files, this research proposed one kind of XML-based DICOM data format. Because XML Schema offers great flexibility for expressing constraints on the content model of elements, we used it to describe the new format, thus making it consistent with the one originally defined by DICOM. Meanwhile, such schemas can be used in the creation and validation of the XML-encoded DICOM files, acting as a standard for data transmission and sharing on the Web. Upon defining the new data format, we started with representing a single data element and further improved the whole data structure with the method of modularization. In contrast to the original format, the new one possesses better structure without loss of related information. In addition, we demonstrated the application of XSLT and XQuery. All of the advantages mentioned above resulted from this new data format.

ANALISIS KOMUNIKASI DATA DENGAN XML DAN JSON PADA WEBSERVICE

Directory of Open Access Journals (Sweden)

Sudirman M.Kom

2016-08-01

Full Text Available Abstrak— Ukuran data pada proses komunikasi data menggunakan web service dalam jaringan akan sangat memengaruhi kecepatan proses transfer. XML dan JSON merupakan format data yang digunakan pada saat komunikasi data pada web service. JSON akan menghasilkan ukuran data yang lebih kecil jika dibandingkan dengan format XML. Keywords— komunikasi data, web service, XML, JSON.

Flight Dynamic Model Exchange using XML

Science.gov (United States)

Jackson, E. Bruce; Hildreth, Bruce L.

2002-01-01

The AIAA Modeling and Simulation Technical Committee has worked for several years to develop a standard by which the information needed to develop physics-based models of aircraft can be specified. The purpose of this standard is to provide a well-defined set of information, definitions, data tables and axis systems so that cooperating organizations can transfer a model from one simulation facility to another with maximum efficiency. This paper proposes using an application of the eXtensible Markup Language (XML) to implement the AIAA simulation standard. The motivation and justification for using a standard such as XML is discussed. Necessary data elements to be supported are outlined. An example of an aerodynamic model as an XML file is given. This example includes definition of independent and dependent variables for function tables, definition of key variables used to define the model, and axis systems used. The final steps necessary for implementation of the standard are presented. Software to take an XML-defined model and import/export it to/from a given simulation facility is discussed, but not demonstrated. That would be the next step in final implementation of standards for physics-based aircraft dynamic models.

Query translation for XPath-based security views

NARCIS (Netherlands)

Vercammen, R.; Hidders, A.J.H.; Paredaens, J.; Grust, T.; Hopfner, H.; Illarramendi, A.

2006-01-01

Since XML is used as a storage format in an increasing number of applications, security has become an important issue in XML databases. One aspect of security is restricting access to data by certain users. This can, for example, be achieved by means of access rules or XML security views, which

Profex: a graphical user interface for the Rietveld refinement program BGMN.

Science.gov (United States)

Doebelin, Nicola; Kleeberg, Reinhard

2015-10-01

Profex is a graphical user interface for the Rietveld refinement program BGMN . Its interface focuses on preserving BGMN 's powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems.

XML-kieliperhe tietokannan hallintajärjestelmien näkökulmasta

OpenAIRE

Imeläinen, Jani

2006-01-01

Tutkielmassa tarkastellaan XML-kieliperheen määrityksiä tietokannan hallintajärjestelmien näkökulmasta. Tutkielmassa verrataan XML-määrityksiä tietokannan hallintajärjestelmien peruskäsitteistöön ja esitellään näin rajaten olennaisimmat XML-määritykset. Päätavoitteena on selvittää XML-kieliperheen määritysten merkitys ja rooli XML-dokumenttien käsittelyssä tietokannan hallintajärjestelmissä. Tutkielman keskeinen tulos on viitekehys, jossa havainnollistetaan tietokannan halli...

Embedded XML DOM Parser: An Approach for XML Data Processing on Networked Embedded Systems with Real-Time Requirements

Directory of Open Access Journals (Sweden)

Cavia Soto MAngeles

2008-01-01

Full Text Available Abstract Trends in control and automation show an increase in data processing and communication in embedded automation controllers. The eXtensible Markup Language (XML is emerging as a dominant data syntax, fostering interoperability, yet little is still known about how to provide predictable real-time performance in XML processing, as required in the domain of industrial automation. This paper presents an XML processor that is designed with such real-time performance in mind. The publication attempts to disclose insight gained in applying techniques such as object pooling and reuse, and other methods targeted at avoiding dynamic memory allocation and its consequent memory fragmentation. Benchmarking tests are reported in order to illustrate the benefits of the approach.

XML — an opportunity for data standards in the geosciences

Science.gov (United States)

Houlding, Simon W.

2001-08-01

Extensible markup language (XML) is a recently introduced meta-language standard on the Web. It provides the rules for development of metadata (markup) standards for information transfer in specific fields. XML allows development of markup languages that describe what information is rather than how it should be presented. This allows computer applications to process the information in intelligent ways. In contrast hypertext markup language (HTML), which fuelled the initial growth of the Web, is a metadata standard concerned exclusively with presentation of information. Besides its potential for revolutionizing Web activities, XML provides an opportunity for development of meaningful data standards in specific application fields. The rapid endorsement of XML by science, industry and e-commerce has already spawned new metadata standards in such fields as mathematics, chemistry, astronomy, multi-media and Web micro-payments. Development of XML-based data standards in the geosciences would significantly reduce the effort currently wasted on manipulating and reformatting data between different computer platforms and applications and would ensure compatibility with the new generation of Web browsers. This paper explores the evolution, benefits and status of XML and related standards in the more general context of Web activities and uses this as a platform for discussion of its potential for development of data standards in the geosciences. Some of the advantages of XML are illustrated by a simple, browser-compatible demonstration of XML functionality applied to a borehole log dataset. The XML dataset and the associated stylesheet and schema declarations are available for FTP download.

Get It Together: Integrating Data with XML.

Science.gov (United States)

Miller, Ron

2003-01-01

Discusses the use of XML for data integration to move data across different platforms, including across the Internet, from a variety of sources. Topics include flexibility; standards; organizing databases; unstructured data and the use of meta tags to encode it with XML information; cost effectiveness; and eliminating client software licenses.…

Design of the XML Security System for Electronic Commerce Application

Institute of Scientific and Technical Information of China (English)

无

2003-01-01

The invocation of World Wide Web (www) first triggered mass adoption of the Internet for public access to digital information exchanges across the globe. To get a big market on the Web, a special security infrastructure would need to be put into place transforming the wild-and-woolly Internet into a network with end-to-end protections. XML (extensible Markup Language) is widely accepted as powerful data representation standard for electronic documents, so a security mechanism for XML documents must be provided in the first place to secure electronic commerce over Internet. In this paper the authors design and implement a secure framework that provides XML signature function, XML Element-wise Encryption function, smart card based crypto API library and Public Key Infrastructure (PKI) security functions to achieve confidentiality, integrity, message authentication, and/or signer authentication services for XML documents and existing non-XML documents that are exchanged by Internet for E-commerce application.

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

Science.gov (United States)

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-01

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. PMID:27733503

Modeling the Arden Syntax for medical decisions in XML.

Science.gov (United States)

Kim, Sukil; Haug, Peter J; Rocha, Roberto A; Choi, Inyoung

2008-10-01

A new model expressing Arden Syntax with the eXtensible Markup Language (XML) was developed to increase its portability. Every example was manually parsed and reviewed until the schema and the style sheet were considered to be optimized. When the first schema was finished, several MLMs in Arden Syntax Markup Language (ArdenML) were validated against the schema. They were then transformed to HTML formats with the style sheet, during which they were compared to the original text version of their own MLM. When faults were found in the transformed MLM, the schema and/or style sheet was fixed. This cycle continued until all the examples were encoded into XML documents. The original MLMs were encoded in XML according to the proposed XML schema and reverse-parsed MLMs in ArdenML were checked using a public domain Arden Syntax checker. Two hundred seventy seven examples of MLMs were successfully transformed into XML documents using the model, and the reverse-parse yielded the original text version of MLMs. Two hundred sixty five of the 277 MLMs showed the same error patterns before and after transformation, and all 11 errors related to statement structure were resolved in XML version. The model uses two syntax checking mechanisms, first an XML validation process, and second, a syntax check using an XSL style sheet. Now that we have a schema for ArdenML, we can also begin the development of style sheets for transformation ArdenML into other languages.

Juwele in XML

OpenAIRE

Habekost, Engelbert

2005-01-01

In der Forschungsabteilung der Humboldt-Universität wird die Schriftenreihe »Öffentliche Vorlesungen« seit 2002 mit der Software FrameMaker produziert. Verbunden damit war die Umstellung des Produktionsprozesses auf eine XML-basierte Dokumenterstellung sowie die Inhouse-Betreuung der kompletten Druckvorstufe.

Java facilities in processing XML files - JAXB and generating PDF reports

Directory of Open Access Journals (Sweden)

Danut-Octavian SIMION

2008-01-01

Full Text Available The paper presents the Java programming language facilities in working with XML files using JAXB (The Java Architecture for XML Binding technology and generating PDF reports from XML files using Java objects. The XML file can be an existing one and could contain the data about an entity (Clients for example or it might be the result of a SELECT-SQL statement. JAXB generates JAVA classes through xs rules and a Marshalling, Unmarshalling compiler. The PDF file is build from a XML file and uses XSL-FO formatting file and a Java ResultSet object.

XML Translator for Interface Descriptions

Science.gov (United States)

Boroson, Elizabeth R.

2009-01-01

A computer program defines an XML schema for specifying the interface to a generic FPGA from the perspective of software that will interact with the device. This XML interface description is then translated into header files for C, Verilog, and VHDL. User interface definition input is checked via both the provided XML schema and the translator module to ensure consistency and accuracy. Currently, programming used on both sides of an interface is inconsistent. This makes it hard to find and fix errors. By using a common schema, both sides are forced to use the same structure by using the same framework and toolset. This makes for easy identification of problems, which leads to the ability to formulate a solution. The toolset contains constants that allow a programmer to use each register, and to access each field in the register. Once programming is complete, the translator is run as part of the make process, which ensures that whenever an interface is changed, all of the code that uses the header files describing it is recompiled.

XML: How It Will Be Applied to Digital Library Systems.

Science.gov (United States)

Kim, Hyun-Hee; Choi, Chang-Seok

2000-01-01

Shows how XML is applied to digital library systems. Compares major features of XML with those of HTML and describes an experimental XML-based metadata retrieval system, which is based on the Dublin Core and is designed as a subsystem of the Korean Virtual Library and Information System (VINIS). (Author/LRW)

Clinical map document based on XML (cMDX: document architecture with mapping feature for reporting and analysing prostate cancer in radical prostatectomy specimens

Directory of Open Access Journals (Sweden)

Bettendorf Olaf

2010-11-01

Full Text Available Abstract Background The pathology report of radical prostatectomy specimens plays an important role in clinical decisions and the prognostic evaluation in Prostate Cancer (PCa. The anatomical schema is a helpful tool to document PCa extension for clinical and research purposes. To achieve electronic documentation and analysis, an appropriate documentation model for anatomical schemas is needed. For this purpose we developed cMDX. Methods The document architecture of cMDX was designed according to Open Packaging Conventions by separating the whole data into template data and patient data. Analogue custom XML elements were considered to harmonize the graphical representation (e.g. tumour extension with the textual data (e.g. histological patterns. The graphical documentation was based on the four-layer visualization model that forms the interaction between different custom XML elements. Sensible personal data were encrypted with a 256-bit cryptographic algorithm to avoid misuse. In order to assess the clinical value, we retrospectively analysed the tumour extension in 255 patients after radical prostatectomy. Results The pathology report with cMDX can represent pathological findings of the prostate in schematic styles. Such reports can be integrated into the hospital information system. "cMDX" documents can be converted into different data formats like text, graphics and PDF. Supplementary tools like cMDX Editor and an analyser tool were implemented. The graphical analysis of 255 prostatectomy specimens showed that PCa were mostly localized in the peripheral zone (Mean: 73% ± 25. 54% of PCa showed a multifocal growth pattern. Conclusions cMDX can be used for routine histopathological reporting of radical prostatectomy specimens and provide data for scientific analysis.

Design of XML-based plant data model

International Nuclear Information System (INIS)

Nair, Preetha M.; Padmini, S.; Gaur, Swati; Diwakar, M.P.

2013-01-01

XML has emerged as an open standard for exchanging structured data on various platforms to handle rich, nested, complex data structures. XML with its flexible tree-like data structure allows a more natural representation as compared to traditional databases. In this paper we present data model for plant data acquisition systems captured using XML technologies. Plant data acquisition systems in a typical Nuclear Power Plant consists of embedded nodes at the first tier and operator consoles at the second tier for operator operation, interaction and display of Plant parameters. This paper discusses a generic data model that was designed to capture process, network architecture, communication/interface protocol and diagnostics aspects required for a Nuclear Power Plant. (author)

An Extended Role Based Access Control Method for XML Documents

Institute of Scientific and Technical Information of China (English)

MENG Xiao-feng; LUO Dao-feng; OU Jian-bo

2004-01-01

As XML has been increasingly important as the Data-change format of Internet and Intranet, access-control-on-XML-properties rises as a new issue.Role-based access control (RBAC) is an access control method that has been widely used in Internet, Operation System and Relation Data Base these 10 years.Though RBAC is already relatively mature in the above fields, new problems occur when it is used in XML properties.This paper proposes an integrated model to resolve these problems, after the fully analysis on the features of XML and RBAC.

IMPROVED COMPRESSION OF XML FILES FOR FAST IMAGE TRANSMISSION

Directory of Open Access Journals (Sweden)

S. Manimurugan

2011-02-01

Full Text Available The eXtensible Markup Language (XML is a format that is widely used as a tool for data exchange and storage. It is being increasingly used in secure transmission of image data over wireless network and World Wide Web. Verbose in nature, XML files can be tens of megabytes long. Thus, to reduce their size and to allow faster transmission, compression becomes vital. Several general purpose compression tools have been proposed without satisfactory results. This paper proposes a novel technique using modified BWT for compressing XML files in a lossless fashion. The experimental results show that the performance of the proposed technique outperforms both general purpose and XML-specific compressors.

Specifying OLAP Cubes On XML Data

DEFF Research Database (Denmark)

Jensen, Mikael Rune; Møller, Thomas Holmgren; Pedersen, Torben Bach

in modern enterprises. In the data warehousing approach, selected information is extracted in advance and stored in a repository. This approach is used because of its high performance. However, in many situations a logical (rather than physical) integration of data is preferable. Previous web-based data......On-Line Analytical Processing (OLAP) enables analysts to gain insight into data through fast and interactive access to a variety of possible views on information, organized in a dimensional model. The demand for data integration is rapidly becoming larger as more and more information sources appear....... Extensible Markup Language (XML) is fast becoming the new standard for data representation and exchange on the World Wide Web. The rapid emergence of XML data on the web, e.g., business-to-business (B2B) ecommerce, is making it necessary for OLAP and other data analysis tools to handleXML data as well...

Application of XML in real-time data warehouse

Science.gov (United States)

Zhao, Yanhong; Wang, Beizhan; Liu, Lizhao; Ye, Su

2009-07-01

At present, XML is one of the most widely-used technologies of data-describing and data-exchanging, and the needs for real-time data make real-time data warehouse a popular area in the research of data warehouse. What effects can we have if we apply XML technology to the research of real-time data warehouse? XML technology solves many technologic problems which are impossible to be addressed in traditional real-time data warehouse, and realize the integration of OLAP (On-line Analytical Processing) and OLTP (Online transaction processing) environment. Then real-time data warehouse can truly be called "real time".

Realization Of Algebraic Processor For XML Documents Processing

International Nuclear Information System (INIS)

Georgiev, Bozhidar; Georgieva, Adriana

2010-01-01

In this paper, are presented some possibilities concerning the implementation of an algebraic method for XML hierarchical data processing which makes faster the XML search mechanism. Here is offered a different point of view for creation of advanced algebraic processor (with all necessary software tools and programming modules respectively). Therefore, this nontraditional approach for fast XML navigation with the presented algebraic processor may help to build an easier user-friendly interface provided XML transformations, which can avoid the difficulties in the complicated language constructions of XSL, XSLT and XPath. This approach allows comparatively simple search of XML hierarchical data by means of the following types of functions: specification functions and so named build-in functions. The choice of programming language Java may appear strange at first, but it isn't when you consider that the applications can run on different kinds of computers. The specific search mechanism based on the linear algebra theory is faster in comparison with MSXML parsers (on the basis of the developed examples with about 30%). Actually, there exists the possibility for creating new software tools based on the linear algebra theory, which cover the whole navigation and search techniques characterizing XSLT/XPath. The proposed method is able to replace more complicated operations in other SOA components.

A Runtime System for XML Transformations in Java

DEFF Research Database (Denmark)

Christensen, Aske Simon; Kirkegaard, Christian; Møller, Anders

2004-01-01

We show that it is possible to extend a general-purpose programming language with a convenient high-level data-type for manipulating XML documents while permitting (1) precise static analysis for guaranteeing validity of the constructed XML documents relative to the given DTD schemas, and (2...

A Layered View Model for XML Repositories and XML Data Warehouses

NARCIS (Netherlands)

Rajugan, R.; Chang, E.; Dillon, T.; Feng, L.

The Object-Oriented (OO) conceptual models have the power in describing and modeling real-world data semantics and their inter-relationships in a form that is precise and comprehensible to users. Conversely, XML is fast emerging as the dominant standard for storing, describing and interchanging data

Generando datos XML a partir de bases de datos relacionales

OpenAIRE

Migani, Silvina; Correa, Carlos; Vera, Cristina; Romera, Liliana

2012-01-01

El lenguaje XML, los lenguajes que permiten manipular datos XML, y su impacto en el mundo de las bases de datos, es el área donde este proyecto se desarrolla. Surge como una iniciativa de docentes del área bases de datos, con la finalidad de profundizar en el estudio de XML y experimentar motores de bases de datos que lo soportan.

Modeling business objects with XML schema

CERN Document Server

Daum, Berthold

2003-01-01

XML Schema is the new language standard from the W3C and the new foundation for defining data in Web-based systems. There is a wealth of information available about Schemas but very little understanding of how to use this highly formal specification for creating documents. Grasping the power of Schemas means going back to the basics of documents themselves, and the semantic rules, or grammars, that define them. Written for schema designers, system architects, programmers, and document authors, Modeling Business Objects with XML Schema guides you through understanding Schemas from the basic concepts, type systems, type derivation, inheritance, namespace handling, through advanced concepts in schema design.*Reviews basic XML syntax and the Schema recommendation in detail.*Builds a knowledge base model step by step (about jazz music) that is used throughout the book.*Discusses Schema design in large environments, best practice design patterns, and Schema''s relation to object-oriented concepts.

XML Based Scientific Data Management Facility

Science.gov (United States)

Mehrotra, P.; Zubair, M.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

The World Wide Web consortium has developed an Extensible Markup Language (XML) to support the building of better information management infrastructures. The scientific computing community realizing the benefits of XML has designed markup languages for scientific data. In this paper, we propose a XML based scientific data management ,facility, XDMF. The project is motivated by the fact that even though a lot of scientific data is being generated, it is not being shared because of lack of standards and infrastructure support for discovering and transforming the data. The proposed data management facility can be used to discover the scientific data itself, the transformation functions, and also for applying the required transformations. We have built a prototype system of the proposed data management facility that can work on different platforms. We have implemented the system using Java, and Apache XSLT engine Xalan. To support remote data and transformation functions, we had to extend the XSLT specification and the Xalan package.

Interpreting XML documents via an RDF schema ontology

NARCIS (Netherlands)

Klein, Michel

2002-01-01

Many business documents are represented in XML. However XML only describes the structure of data, not its meaning. The meaning of data is required for advanced automated processing, as is envisaged in the "Semantic Web". Ontologies are often used to describe the meaning of data items. Many ontology

ECG and XML: an instance of a possible XML schema for the ECG telemonitoring.

Science.gov (United States)

Di Giacomo, Paola; Ricci, Fabrizio L

2005-03-01

Management of many types of chronic diseases relies heavily on patients' self-monitoring of their disease conditions. In recent years, Internet-based home telemonitoring systems allowing transmission of patient data to a central database and offering immediate access to the data by the care providers have become available. The adoption of Extensible Mark-up Language (XML) as a W3C standard has generated considerable interest in the potential value of this language in health informatics. However, the telemonitoring systems often work with only one or a few types of medical devices. This is because different medical devices produce different types of data, and the existing telemonitoring systems are generally built around a proprietary data schema. In this paper, we describe a generic data schema for a telemonitoring system that is applicable to different types of medical devices and different diseases, and then we present an architecture for the exchange of clinical information as data, signals of telemonitoring and clinical reports in the XML standard, up-to-date information in each electronic patient record and integration in real time with the information collected during the telemonitoring activities in the XML schema, between all the structures involved in the healthcare process of the patient.

Query deforestation

OpenAIRE

Grust, Torsten; Scholl, Marc H.

1998-01-01

The construction of a declarative query engine for a DBMS includes the challenge of compiling algebraic queries into efficient execution plans that can be run on top of the persistent storage. This work pursues the goal of employing foldr-build deforestation for the derivation of efficient streaming programs - programs that do not allocate intermediate data structures to perform their task - from algebraic (combinator) query plans. The query engine is based on the insertion representation of ...

The XSD-Builder Specification Language—Toward a Semantic View of XML Schema Definition

Science.gov (United States)

Fong, Joseph; Cheung, San Kuen

In the present database market, XML database model is a main structure for the forthcoming database system in the Internet environment. As a conceptual schema of XML database, XML Model has its limitation on presenting its data semantics. System analyst has no toolset for modeling and analyzing XML system. We apply XML Tree Model (shown in Figure 2) as a conceptual schema of XML database to model and analyze the structure of an XML database. It is important not only for visualizing, specifying, and documenting structural models, but also for constructing executable systems. The tree model represents inter-relationship among elements inside different logical schema such as XML Schema Definition (XSD), DTD, Schematron, XDR, SOX, and DSD (shown in Figure 1, an explanation of the terms in the figure are shown in Table 1). The XSD-Builder consists of XML Tree Model, source language, translator, and XSD. The source language is called XSD-Source which is mainly for providing an environment with concept of user friendliness while writing an XSD. The source language will consequently be translated by XSD-Translator. Output of XSD-Translator is an XSD which is our target and is called as an object language.

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

Science.gov (United States)

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-04

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Achieving Adaptivity For OLAP-XML Federations

DEFF Research Database (Denmark)

Pedersen, D.; Pedersen, Torben Bach

2003-01-01

Motivated by the need for more flexible OLAP systems, this paper presents the results of work on logical integration of external data in OLAP databases, carried out in cooperation between the Danish OLAP client vendor \\targit and Aalborg University. Flexibility is ensured by supporting XML......'s ability to adapt to changes in its surroundings. This paper describes the potential problems that may interrupt the operation of the integration system, in particular those caused by the often autonomous and unreliable nature of external XML data sources, and methods for handling these problems...

Work orders management based on XML file in printing

Directory of Open Access Journals (Sweden)

Ran Peipei

2018-01-01

Full Text Available The Extensible Markup Language (XML technology is increasingly used in various field, if it’s used to express the information of work orders will improve efficiency for management and production. According to the features, we introduce the technology of management for work orders and get a XML file through the Document Object Model (DOM technology in the paper. When we need the information to conduct production, parsing the XML file and save the information in database, this is beneficial to the preserve and modify for information.

XML as a standard I/O data format in scientific software development

International Nuclear Information System (INIS)

Song Tianming; Yang Jiamin; Yi Rongqing

2010-01-01

XML is an open standard data format with strict syntax rules, which is widely used in large-scale software development. It is adopted as I/O file format in the development of SpectroSim, a simulation and data-processing system for soft x-ray spectrometer used in ICF experiments. XML data that describe spectrometer configurations, schema codes that define syntax rules for XML and report generation technique for visualization of XML data are introduced. The characteristics of XML such as the capability to express structured information, self-descriptive feature, automation of visualization are explained with examples, and its feasibility as a standard scientific I/O data file format is discussed. (authors)

An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results

Directory of Open Access Journals (Sweden)

Arthur John

2004-01-01

Full Text Available Abstract Background Many proteomics initiatives require a seamless bioinformatics integration of a range of analytical steps between sample collection and systems modeling immediately assessable to the participants involved in the process. Proteomics profiling by 2D gel electrophoresis to the putative identification of differentially expressed proteins by comparison of mass spectrometry results with reference databases, includes many components of sample processing, not just analysis and interpretation, are regularly revisited and updated. In order for such updates and dissemination of data, a suitable data structure is needed. However, there are no such data structures currently available for the storing of data for multiple gels generated through a single proteomic experiments in a single XML file. This paper proposes a data structure based on XML standards to fill the void that exists between data generated by proteomics experiments and storing of data. Results In order to address the resulting procedural fluidity we have adopted and implemented a data model centered on the concept of annotated gel (AG as the format for delivery and management of 2D Gel electrophoresis results. An eXtensible Markup Language (XML schema is proposed to manage, analyze and disseminate annotated 2D Gel electrophoresis results. The structure of AG objects is formally represented using XML, resulting in the definition of the AGML syntax presented here. Conclusion The proposed schema accommodates data on the electrophoresis results as well as the mass-spectrometry analysis of selected gel spots. A web-based software library is being developed to handle data storage, analysis and graphic representation. Computational tools described will be made available at http://bioinformatics.musc.edu/agml. Our development of AGML provides a simple data structure for storing 2D gel electrophoresis data.

An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.

Science.gov (United States)

Stanislaus, Romesh; Jiang, Liu Hong; Swartz, Martha; Arthur, John; Almeida, Jonas S

2004-01-29

Many proteomics initiatives require a seamless bioinformatics integration of a range of analytical steps between sample collection and systems modeling immediately assessable to the participants involved in the process. Proteomics profiling by 2D gel electrophoresis to the putative identification of differentially expressed proteins by comparison of mass spectrometry results with reference databases, includes many components of sample processing, not just analysis and interpretation, are regularly revisited and updated. In order for such updates and dissemination of data, a suitable data structure is needed. However, there are no such data structures currently available for the storing of data for multiple gels generated through a single proteomic experiments in a single XML file. This paper proposes a data structure based on XML standards to fill the void that exists between data generated by proteomics experiments and storing of data. In order to address the resulting procedural fluidity we have adopted and implemented a data model centered on the concept of annotated gel (AG) as the format for delivery and management of 2D Gel electrophoresis results. An eXtensible Markup Language (XML) schema is proposed to manage, analyze and disseminate annotated 2D Gel electrophoresis results. The structure of AG objects is formally represented using XML, resulting in the definition of the AGML syntax presented here. The proposed schema accommodates data on the electrophoresis results as well as the mass-spectrometry analysis of selected gel spots. A web-based software library is being developed to handle data storage, analysis and graphic representation. Computational tools described will be made available at http://bioinformatics.musc.edu/agml. Our development of AGML provides a simple data structure for storing 2D gel electrophoresis data.

XML Schema Guide for Primary CDR Submissions

Science.gov (United States)

This document presents the extensible markup language (XML) schema guide for the Office of Pollution Prevention and Toxics’ (OPPT) e-CDRweb tool. E-CDRweb is the electronic, web-based tool provided by Environmental Protection Agency (EPA) for the submission of Chemical Data Reporting (CDR) information. This document provides the user with tips and guidance on correctly using the version 1.7 XML schema. Please note that the order of the elements must match the schema.

Adaptive Hypermedia Educational System Based on XML Technologies.

Science.gov (United States)

Baek, Yeongtae; Wang, Changjong; Lee, Sehoon

This paper proposes an adaptive hypermedia educational system using XML technologies, such as XML, XSL, XSLT, and XLink. Adaptive systems are capable of altering the presentation of the content of the hypermedia on the basis of a dynamic understanding of the individual user. The user profile can be collected in a user model, while the knowledge…

Using XML to Separate Content from the Presentation Software in eLearning Applications

Science.gov (United States)

Merrill, Paul F.

2005-01-01

This paper has shown how XML (extensible Markup Language) can be used to mark up content. Since XML documents, with meaningful tags, can be interpreted easily by humans as well as computers, they are ideal for the interchange of information. Because XML tags can be defined by an individual or organization, XML documents have proven useful in a…

Query transformations and their role in Web searching by the members of the general public

Directory of Open Access Journals (Sweden)

Martin Whittle

2006-01-01

Full Text Available Introduction. This paper reports preliminary research in a primarily experimental study of how the general public search for information on the Web. The focus is on the query transformation patterns that characterise searching. Method. In this work, we have used transaction logs from the Excite search engine to develop methods for analysing query transformations that should aid the analysis of our ongoing experimental work. Our methods involve the use of similarity techniques to link queries with the most similar previous query in a train. The resulting query transformations are represented as a list of codes representing a whole search. Analysis. It is shown how query transformation sequences can be represented as graphical networks and some basic statistical results are shown. A correlation analysis is performed to examine the co-occurrence of Boolean and quotation mark changes with the syntactic changes. Results. A frequency analysis of the occurrence of query transformation codes is presented. The connectivity of graphs obtained from the query transformation is investigated and found to follow an exponential scaling law. The correlation analysis reveals a number of patterns that provide some interesting insights into Web searching by the general public. Conclusion. We have developed analytical methods based on query similarity that can be applied to our current experimental work with volunteer subjects. The results of these will form part of a database with the aim of developing an improved understanding of how the public search the Web.

Development of XML Schema for Broadband Digital Seismograms and Data Center Portal

Science.gov (United States)

Takeuchi, N.; Tsuboi, S.; Ishihara, Y.; Nagao, H.; Yamagishi, Y.; Watanabe, T.; Yanaka, H.; Yamaji, H.

2008-12-01

There are a number of data centers around the globe, where the digital broadband seismograms are opened to researchers. Those centers use their own user interfaces and there are no standard to access and retrieve seismograms from different data centers using unified interface. One of the emergent technologies to realize unified user interface for different data centers is the concept of WebService and WebService portal. Here we have developed a prototype of data center portal for digital broadband seismograms. This WebService portal uses WSDL (Web Services Description Language) to accommodate differences among the different data centers. By using the WSDL, alteration and addition of data center user interfaces can be easily managed. This portal, called NINJA Portal, assumes three WebServices: (1) database Query service, (2) Seismic event data request service, and (3) Seismic continuous data request service. Current system supports both station search of database Query service and seismic continuous data request service. Data centers supported by this NINJA portal will be OHP data center in ERI and Pacific21 data center in IFREE/JAMSTEC in the beginning. We have developed metadata standard for seismological data based on QuakeML for parametric data, which has been developed by ETH Zurich, and XML-SEED for waveform data, which was developed by IFREE/JAMSTEC. The prototype of NINJA portal is now released through IFREE web page (http://www.jamstec.go.jp/pacific21/).

XML Storage for Magnetotelluric Transfer Functions: Towards a Comprehensive Online Reference Database

Science.gov (United States)

Kelbert, A.; Blum, C.

2015-12-01

Magnetotelluric Transfer Functions (MT TFs) represent most of the information about Earth electrical conductivity found in the raw electromagnetic data, providing inputs for further inversion and interpretation. To be useful for scientific interpretation, they must also contain carefully recorded metadata. Making these data available in a discoverable and citable fashion would provide the most benefit to the scientific community, but such a development requires that the metadata is not only present in the file but is also searchable. The most commonly used MT TF format to date, the historical Society of Exploration Geophysicists Electromagnetic Data Interchange Standard 1987 (EDI), no longer supports some of the needs of modern magnetotellurics, most notably accurate error bars recording. Moreover, the inherent heterogeneity of EDI's and other historic MT TF formats has mostly kept the community away from healthy data sharing practices. Recently, the MT team at Oregon State University in collaboration with IRIS Data Management Center developed a new, XML-based format for MT transfer functions, and an online system for long-term storage, discovery and sharing of MT TF data worldwide (IRIS SPUD; www.iris.edu/spud/emtf). The system provides a query page where all of the MT transfer functions collected within the USArray MT experiment and other field campaigns can be searched for and downloaded; an automatic on-the-fly conversion to the historic EDI format is also included. To facilitate conversion to the new, more comprehensive and sustainable, XML format for MT TFs, and to streamline inclusion of historic data into the online database, we developed a set of open source format conversion tools, which can be used for rotation of MT TFs as well as a general XML EDI converter (https://seiscode.iris.washington.edu/projects/emtf-fcu). Here, we report on the newly established collaboration between the USGS Geomagnetism Program and the Oregon State University to gather and

An XML-Based Protocol for Distributed Event Services

Science.gov (United States)

Smith, Warren; Gunter, Dan; Quesnel, Darcy; Biegel, Bryan (Technical Monitor)

2001-01-01

This viewgraph presentation provides information on the application of an XML (extensible mark-up language)-based protocol to the developing field of distributed processing by way of a computational grid which resembles an electric power grid. XML tags would be used to transmit events between the participants of a transaction, namely, the consumer and the producer of the grid scheme.

Semantic reasoning with XML-based biomedical information models.

Science.gov (United States)

O'Connor, Martin J; Das, Amar

2010-01-01

The Extensible Markup Language (XML) is increasingly being used for biomedical data exchange. The parallel growth in the use of ontologies in biomedicine presents opportunities for combining the two technologies to leverage the semantic reasoning services provided by ontology-based tools. There are currently no standardized approaches for taking XML-encoded biomedical information models and representing and reasoning with them using ontologies. To address this shortcoming, we have developed a workflow and a suite of tools for transforming XML-based information models into domain ontologies encoded using OWL. In this study, we applied semantics reasoning methods to these ontologies to automatically generate domain-level inferences. We successfully used these methods to develop semantic reasoning methods for information models in the HIV and radiological image domains.

Overview of the INEX 2008 XML Mining Track

Science.gov (United States)

Denoyer, Ludovic; Gallinari, Patrick

We describe here the XML Mining Track at INEX 2008. This track was launched for exploring two main ideas: first identifying key problems for mining semi-structured documents and new challenges of this emerging field and second studying and assessing the potential of machine learning techniques for dealing with generic Machine Learning (ML) tasks in the structured domain i.e. classification and clustering of semi structured documents. This year, the track focuses on the supervised classification and the unsupervised clustering of XML documents using link information. We consider a corpus of about 100,000 Wikipedia pages with the associated hyperlinks. The participants have developed models using the content information, the internal structure information of the XML documents and also the link information between documents.

Streaming-based verification of XML signatures in SOAP messages

DEFF Research Database (Denmark)

Somorovsky, Juraj; Jensen, Meiko; Schwenk, Jörg

2010-01-01

approach for XML processing, the Web Services servers easily become a target of Denial-of-Service attacks. We present a solution for these problems: an external streaming-based WS-Security Gateway. Our implementation is capable of processing XML Signatures in SOAP messages using a streaming-based approach...

The Format Converting/Transfer Agent and Repository System based on ebXML

Directory of Open Access Journals (Sweden)

KyeongRim Ahn

2004-12-01

Full Text Available As introducing XML in EC-environment, various document formats have been used due to XML characteristic. Also, other document format except XML have been used to exchange EC-related information. That is, as increasing trading partner, as increasing exchanged document format and business processing being complex. So, management difficulty and duplication problem happened as trading partners increasing. And, they want to change plural business workflow to general and uniform form as defining and arranging BP(Business Process. Therefore, in this paper, we define XML as future document standard agreement and discuss about service system architecture and Repository. Repository stores and manages document standard, information related to Business Processing, Messaging Profile, and so on. Repository structure is designed to cover various XML standards. Also, we design system to support ebXML communication protocol, MSH, as well as traditional communication protocol, such as X.25, X.400, etc. and implement to exchange information via FTP.

Model tool to describe chemical structures in XML format utilizing structural fragments and chemical ontology.

Science.gov (United States)

Sankar, Punnaivanam; Alain, Krief; Aghila, Gnanasekaran

2010-05-24

We have developed a model structure-editing tool, ChemEd, programmed in JAVA, which allows drawing chemical structures on a graphical user interface (GUI) by selecting appropriate structural fragments defined in a fragment library. The terms representing the structural fragments are organized in fragment ontology to provide a conceptual support. ChemEd describes the chemical structure in an XML document (ChemFul) with rich semantics explicitly encoding the details of the chemical bonding, the hybridization status, and the electron environment around each atom. The document can be further processed through suitable algorithms and with the support of external chemical ontologies to generate understandable reports about the functional groups present in the structure and their specific environment.

XML-based analysis interface for particle physics data analysis

International Nuclear Information System (INIS)

Hu Jifeng; Lu Xiaorui; Zhang Yangheng

2011-01-01

The letter emphasizes on an XML-based interface and its framework for particle physics data analysis. The interface uses a concise XML syntax to describe, in data analysis, the basic tasks: event-selection, kinematic fitting, particle identification, etc. and a basic processing logic: the next step goes on if and only if this step succeeds. The framework can perform an analysis without compiling by loading the XML-interface file, setting p in run-time and running dynamically. An analysis coding in XML instead of C++, easy-to-understood arid use, effectively reduces the work load, and enables users to carry out their analyses quickly. The framework has been developed on the BESⅢ offline software system (BOSS) with the object-oriented C++ programming. These functions, required by the regular tasks and the basic processing logic, are implemented with both standard modules or inherited from the modules in BOSS. The interface and its framework have been tested to perform physics analysis. (authors)

Decision-cache based XACML authorisation and anonymisation for XML documents

OpenAIRE

Ulltveit-Moe, Nils; Oleshchuk, Vladimir A

2012-01-01

Author's version of an article in the journal: Computer Standards and Interfaces. Also available from the publisher at: http://dx.doi.org/10.1016/j.csi.2011.10.007 This paper describes a decision cache for the eXtensible Access Control Markup Language (XACML) that supports fine-grained authorisation and anonymisation of XML based messages and documents down to XML attribute and element level. The decision cache is implemented as an XACML obligation service, where a specification of the XML...

XML Schema Guide for Secondary CDR Submissions

Science.gov (United States)

This document presents the extensible markup language (XML) schema guide for the Office of Pollution Prevention and Toxics’ (OPPT) e-CDRweb tool. E-CDRweb is the electronic, web-based tool provided by Environmental Protection Agency (EPA) for the submission of Chemical Data Reporting (CDR) information. This document provides the user with tips and guidance on correctly using the version 1.1 XML schema for the Joint Submission Form. Please note that the order of the elements must match the schema.

Integrity Checking and Maintenance with Active Rules in XML Databases

DEFF Research Database (Denmark)

Christiansen, Henning; Rekouts, Maria

2007-01-01

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

Web-based infectious disease reporting using XML forms.

Science.gov (United States)

Liu, Danhong; Wang, Xia; Pan, Feng; Xu, Yongyong; Yang, Peng; Rao, Keqin

2008-09-01

Exploring solutions for infectious disease information sharing among hospital and public health information systems is imperative to the improvement of disease surveillance and emergent response. This paper aimed at developing a method to directly transmit real-time data of notifiable infectious diseases from hospital information systems to public health information systems on the Internet by using a standard eXtensible Markup Language (XML) format. The mechanism and work flow by which notifiable infectious disease data are created, reported and used at health agencies in China was evaluated. The capacity of all participating providers to use electronic data interchange to submit transactions of data required for the notifiable infectious disease reporting was assessed. The minimum data set at national level that is required for reporting for national notifiable infectious disease surveillance was determined. The standards and techniques available worldwide for electronic health data interchange, such as XML, HL7 messaging, CDA and ATSM CCR, etc. were reviewed and compared, and an XML implementation format needed for this purpose was defined for hospitals that are able to access the Internet to provide a complete infectious disease reporting. There are 18,703 county or city hospitals in China. All of them have access to basic information infrastructures including computers, e-mail and the Internet. Nearly 10,000 hospitals possess hospital information systems used for electronically recording, retrieving and manipulating patients' information. These systems collect 23 data items required in the minimum data set for national notifiable infectious disease reporting. In order to transmit these data items to the disease surveillance system and local health information systems instantly and without duplication of data input, an XML schema and a set of standard data elements were developed to define the content, structure and semantics of the data set. These standards

Generating XML schemas for DICOM structured reporting templates.

Science.gov (United States)

Zhao, Luyin; Lee, Kwok Pun; Hu, Jingkun

2005-01-01

In this paper, the authors describe a methodology to transform programmatically structured reporting (SR) templates defined by the Digital Imaging and Communications for Medicine (DICOM) standard into an XML schema representation. Such schemas can be used in the creation and validation of XML-encoded SR documents that use templates. Templates are a means to put additional constraints on an SR document to promote common formats for specific reporting applications or domains. As the use of templates becomes more widespread in the production of SR documents, it is important to ensure validity of such documents. The work described in this paper is an extension of the authors' previous work on XML schema representation for DICOM SR. Therefore, this paper inherits and partially modifies the structure defined in the earlier work.

XML as a format of expression of Object-Oriented Petri Nets

Directory of Open Access Journals (Sweden)

Petr Jedlička

2004-01-01

Full Text Available A number of object-oriented (OO variants have so far been devised for Petri Nets (PN. However, none of these variants has ever been described using an open, independent format – such as XML. This article suggests several possibilities and advantages of such a description. The outlined XML language definition for the description of object-oriented Petri Nets (OOPN is based on XMI (description of UML object-oriented models, SOX (simple description of general OO systems and PNML (an XML-based language used for the description of structured and modular PN. For OOPN, the XML form of description represents a standard format for storing as well as for transfer between various OOPN-processing (analysis, simulation, ... tools.

Approximate dictionary queries

DEFF Research Database (Denmark)

Brodal, Gerth Stølting; Gasieniec, Leszek

1996-01-01

Given a set of n binary strings of length m each. We consider the problem of answering d-queries. Given a binary query string of length m, a d-query is to report if there exists a string in the set within Hamming distance d of . We present a data structure of size O(nm) supporting 1-queries in ti...

A Query Cache Tool for Optimizing Repeatable and Parallel OLAP Queries

Science.gov (United States)

Santos, Ricardo Jorge; Bernardino, Jorge

On-line analytical processing against data warehouse databases is a common form of getting decision making information for almost every business field. Decision support information oftenly concerns periodic values based on regular attributes, such as sales amounts, percentages, most transactioned items, etc. This means that many similar OLAP instructions are periodically repeated, and simultaneously, between the several decision makers. Our Query Cache Tool takes advantage of previously executed queries, storing their results and the current state of the data which was accessed. Future queries only need to execute against the new data, inserted since the queries were last executed, and join these results with the previous ones. This makes query execution much faster, because we only need to process the most recent data. Our tool also minimizes the execution time and resource consumption for similar queries simultaneously executed by different users, putting the most recent ones on hold until the first finish and returns the results for all of them. The stored query results are held until they are considered outdated, then automatically erased. We present an experimental evaluation of our tool using a data warehouse based on a real-world business dataset and use a set of typical decision support queries to discuss the results, showing a very high gain in query execution time.

Lessons in scientific data interoperability: XML and the eMinerals project.

Science.gov (United States)

White, T O H; Bruin, R P; Chiang, G-T; Dove, M T; Tyer, R P; Walker, A M

2009-03-13

A collaborative environmental eScience project produces a broad range of data, notable as much for its diversity, in source and format, as its quantity. We find that extensible markup language (XML) and associated technologies are invaluable in managing this deluge of data. We describe Fo X, a toolkit for allowing Fortran codes to read and write XML, thus allowing existing scientific tools to be easily re-used in an XML-centric workflow.

Query responses

Directory of Open Access Journals (Sweden)

Paweł Łupkowski

2017-05-01

Full Text Available In this article we consider the phenomenon of answering a query with a query. Although such answers are common, no large scale, corpus-based characterization exists, with the exception of clarification requests. After briefly reviewing different theoretical approaches on this subject, we present a corpus study of query responses in the British National Corpus and develop a taxonomy for query responses. We point at a variety of response categories that have not been formalized in previous dialogue work, particularly those relevant to adversarial interaction. We show that different response categories have significantly different rates of subsequent answer provision. We provide a formal analysis of the response categories in the framework of KoS.

Recommending Multidimensional Queries

Science.gov (United States)

Giacometti, Arnaud; Marcel, Patrick; Negre, Elsa

Interactive analysis of datacube, in which a user navigates a cube by launching a sequence of queries is often tedious since the user may have no idea of what the forthcoming query should be in his current analysis. To better support this process we propose in this paper to apply a Collaborative Work approach that leverages former explorations of the cube to recommend OLAP queries. The system that we have developed adapts Approximate String Matching, a technique popular in Information Retrieval, to match the current analysis with the former explorations and help suggesting a query to the user. Our approach has been implemented with the open source Mondrian OLAP server to recommend MDX queries and we have carried out some preliminary experiments that show its efficiency for generating effective query recommendations.

An XML-based communication protocol for accelerator distributed controls

International Nuclear Information System (INIS)

Catani, L.

2008-01-01

This paper presents the development of XMLvRPC, an RPC-like communication protocol based, for this particular application, on the TCP/IP and XML (eXtensible Markup Language) tools built-in in LabVIEW. XML is used to format commands and data passed between client and server while socket interface for communication uses either TCP or UDP transmission protocols. This implementation extends the features of these general purpose libraries and incorporates solutions that might provide, with limited modifications, full compatibility with well established and more general communication protocol, i.e. XML-RPC, while preserving portability to different platforms supported by LabVIEW. The XMLvRPC suite of software has been equipped with specific tools for its deployment in distributed control systems as, for instance, a quasi-automatic configuration and registration of the distributed components and a simple plug-and-play approach to the installation of new services. Key feature is the management of large binary arrays that allow coding of large binary data set, e.g. raw images, more efficiently with respect to the standard XML coding

An XML-based communication protocol for accelerator distributed controls

Energy Technology Data Exchange (ETDEWEB)

Catani, L. [INFN-Roma Tor Vergata, Rome (Italy)], E-mail: luciano.catani@roma2.infn.it

2008-03-01

This paper presents the development of XMLvRPC, an RPC-like communication protocol based, for this particular application, on the TCP/IP and XML (eXtensible Markup Language) tools built-in in LabVIEW. XML is used to format commands and data passed between client and server while socket interface for communication uses either TCP or UDP transmission protocols. This implementation extends the features of these general purpose libraries and incorporates solutions that might provide, with limited modifications, full compatibility with well established and more general communication protocol, i.e. XML-RPC, while preserving portability to different platforms supported by LabVIEW. The XMLvRPC suite of software has been equipped with specific tools for its deployment in distributed control systems as, for instance, a quasi-automatic configuration and registration of the distributed components and a simple plug-and-play approach to the installation of new services. Key feature is the management of large binary arrays that allow coding of large binary data set, e.g. raw images, more efficiently with respect to the standard XML coding.

Upgrading a TCABR Data Analysis and Acquisition System for Remote Participation Using Java, XML, RCP and Modern Client/Server Communication/Authentication

Energy Technology Data Exchange (ETDEWEB)

De Sa, W. [University of Sao Paulo - Institute of Physics - Plasma Physics Laboratory, Sao Paulo (Brazil)

2009-07-01

Each plasma physics laboratory has a proprietary scheme to control and data acquisition system. Usually, it is different from one laboratory to another. It means that each laboratory has its own way of control the experiment and retrieving data from the database. Fusion research relies to a great extent on international collaboration and it is difficult to follow the work remotely with private system. The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The architecture of the new system uses Java language as programming environment. Since application parameters and hardware in a joint experiment are very complex and with a large variability of components, requirement and specification solutions need to be flexible and modular, independent from operating system and computers architecture. To describe and to organize the information on all the components and the connections among them, systems are developed using the extensible Markup Language (XML) technology. The communication between clients and servers use Remote Procedure Call (RPC) based on the XML (RPC-XML technology). The integration among Java language, XML and RPC-XML technologies allows developing easily a standard data and communication access layer between users and laboratories using common software libraries and Web application. The libraries allow data retrieval using the same methods for all user laboratories in the joint collaboration and the Web application allows a simple Graphical User Interface (GUI) access. TCABR tokamak team collaborating with the CFN (Nuclear Fusion Center, Technical University of Lisbon) are implementing this Remote Participation technologies that are going to be tested at the Joint Experiment on TCABR (TCABR-JE), a Host Laboratory Experiment, organized in cooperation with the IAEA (International Atomic Energy Agency) in the framework of the IAEA Coordinated Research Project (CRP) on

Health Topic XML File Description

Science.gov (United States)

... this page: https://medlineplus.gov/xmldescription.html Health Topic XML File Description: MedlinePlus To use the sharing ... information categories assigned. Example of a Full Health Topic Record A record for a MedlinePlus health topic ...

XBRL: Beyond Basic XML

Science.gov (United States)

VanLengen, Craig Alan

2010-01-01

The Securities and Exchange Commission (SEC) has recently announced a proposal that will require all public companies to report their financial data in Extensible Business Reporting Language (XBRL). XBRL is an extension of Extensible Markup Language (XML). Moving to a standard reporting format makes it easier for organizations to report the…

The role of economics in the QUERI program: QUERI Series.

Science.gov (United States)

Smith, Mark W; Barnett, Paul G

2008-04-22

The United States (U.S.) Department of Veterans Affairs (VA) Quality Enhancement Research Initiative (QUERI) has implemented economic analyses in single-site and multi-site clinical trials. To date, no one has reviewed whether the QUERI Centers are taking an optimal approach to doing so. Consistent with the continuous learning culture of the QUERI Program, this paper provides such a reflection. We present a case study of QUERI as an example of how economic considerations can and should be integrated into implementation research within both single and multi-site studies. We review theoretical and applied cost research in implementation studies outside and within VA. We also present a critique of the use of economic research within the QUERI program. Economic evaluation is a key element of implementation research. QUERI has contributed many developments in the field of implementation but has only recently begun multi-site implementation trials across multiple regions within the national VA healthcare system. These trials are unusual in their emphasis on developing detailed costs of implementation, as well as in the use of business case analyses (budget impact analyses). Economics appears to play an important role in QUERI implementation studies, only after implementation has reached the stage of multi-site trials. Economic analysis could better inform the choice of which clinical best practices to implement and the choice of implementation interventions to employ. QUERI economics also would benefit from research on costing methods and development of widely accepted international standards for implementation economics.

Using XML and Java for Astronomical Instrumentation Control

Science.gov (United States)

Ames, Troy; Koons, Lisa; Sall, Ken; Warsaw, Craig

2000-01-01

Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests, increasing software maintenance costs. Instrument description is too tightly coupled with details of implementation. NASA Goddard Space Flight Center is developing a general and highly extensible framework that applies to any kind of instrument that can be controlled by a computer. The software architecture combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML), a human readable and machine understandable way to describe structured data. A key aspect of the object-oriented architecture is software that is driven by an instrument description, written using the Instrument Markup Language (IML). ]ML is used to describe graphical user interfaces to control and monitor the instrument, command sets and command formats, data streams, and communication mechanisms. Although the current effort is targeted for the High-resolution Airborne Wideband Camera, a first-light instrument of the Stratospheric Observatory for Infrared Astronomy, the framework is designed to be generic and extensible so that it can be applied to any instrument.

Semi-automatic Citation Correction with Lemon8-XML

Directory of Open Access Journals (Sweden)

MJ Suhonos

2009-03-01

Full Text Available The Lemon8-XML software application, developed by the Public Knowledge Project (PKP, provides an open-source, computer-assisted interface for reliable citation structuring and validation. Lemon8-XML combines citation parsing algorithms with freely-available online indexes such as PubMed, WorldCat, and OAIster. Fully-automated markup of entire bibliographies may be a genuine possibility using this approach. Automated markup of citations would increase bibliographic accuracy while reducing copyediting demands.

The SGML Standardization Framework and the Introduction of XML

Science.gov (United States)

Grütter, Rolf

2000-01-01

Extensible Markup Language (XML) is on its way to becoming a global standard for the representation, exchange, and presentation of information on the World Wide Web (WWW). More than that, XML is creating a standardization framework, in terms of an open network of meta-standards and mediators that allows for the definition of further conventions and agreements in specific business domains. Such an approach is particularly needed in the healthcare domain; XML promises to especially suit the particularities of patient records and their lifelong storage, retrieval, and exchange. At a time when change rather than steadiness is becoming the faithful feature of our society, standardization frameworks which support a diversified growth of specifications that are appropriate to the actual needs of the users are becoming more and more important; and efforts should be made to encourage this new attempt at standardization to grow in a fruitful direction. Thus, the introduction of XML reflects a standardization process which is neither exclusively based on an acknowledged standardization authority, nor a pure market standard. Instead, a consortium of companies, academic institutions, and public bodies has agreed on a common recommendation based on an existing standardization framework. The consortium's process of agreeing to a standardization framework will doubtlessly be successful in the case of XML, and it is suggested that it should be considered as a generic model for standardization processes in the future. PMID:11720931

Using XML and XSLT for flexible elicitation of mental-health risk knowledge.

Science.gov (United States)

Buckingham, C D; Ahmed, A; Adams, A E

2007-03-01

Current tools for assessing risks associated with mental-health problems require assessors to make high-level judgements based on clinical experience. This paper describes how new technologies can enhance qualitative research methods to identify lower-level cues underlying these judgements, which can be collected by people without a specialist mental-health background. Content analysis of interviews with 46 multidisciplinary mental-health experts exposed the cues and their interrelationships, which were represented by a mind map using software that stores maps as XML. All 46 mind maps were integrated into a single XML knowledge structure and analysed by a Lisp program to generate quantitative information about the numbers of experts associated with each part of it. The knowledge was refined by the experts, using software developed in Flash to record their collective views within the XML itself. These views specified how the XML should be transformed by XSLT, a technology for rendering XML, which resulted in a validated hierarchical knowledge structure associating patient cues with risks. Changing knowledge elicitation requirements were accommodated by flexible transformations of XML data using XSLT, which also facilitated generation of multiple data-gathering tools suiting different assessment circumstances and levels of mental-health knowledge.

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

Science.gov (United States)

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.

Data Hiding and Security for XML Database: A TRBAC- Based Approach

Institute of Scientific and Technical Information of China (English)

ZHANG Wan-song; SUN Wei; LIU Da-xin

2005-01-01

In order to cope with varying protection granularity levels of XML (eXtensible Markup Language) documents, we propose a TXAC (Two-level XML Access Control) framework, in which an extended TRBAC (Temporal Role-Based Access Control) approach is proposed to deal with the dynamic XML data. With different system components,TXAC algorithm evaluates access requests efficiently by appropriate access control policy in dynamic web environment.The method is a flexible and powerful security system offering a multi-level access control solution.

A generic framework for extracting XML data from legacy databases

NARCIS (Netherlands)

Thiran, Ph.; Estiévenart, F.; Hainaut, J.L.; Houben, G.J.P.M.

2005-01-01

This paper describes a generic framework of which semantics-based XML data can be derived from legacy databases. It consists in first recovering the conceptual schema of the database through reverse engineering techniques, and then in converting this schema, or part of it, into XML-compliant data

Engineering XML Solutions Using Views

NARCIS (Netherlands)

Rajugan, R.; Chang, E.; Dillon, T.S.; Feng, L.

In industrial informatics, engineering data intensive Enterprise Information Systems (EIS) is a challenging task without abstraction and partitioning. Further, the introduction of semi-structured data (namely XML) and its rapid adaptation by the commercial and industrial systems increased the

The role of economics in the QUERI program: QUERI Series

Directory of Open Access Journals (Sweden)

Smith Mark W

2008-04-01

Full Text Available Abstract Background The United States (U.S. Department of Veterans Affairs (VA Quality Enhancement Research Initiative (QUERI has implemented economic analyses in single-site and multi-site clinical trials. To date, no one has reviewed whether the QUERI Centers are taking an optimal approach to doing so. Consistent with the continuous learning culture of the QUERI Program, this paper provides such a reflection. Methods We present a case study of QUERI as an example of how economic considerations can and should be integrated into implementation research within both single and multi-site studies. We review theoretical and applied cost research in implementation studies outside and within VA. We also present a critique of the use of economic research within the QUERI program. Results Economic evaluation is a key element of implementation research. QUERI has contributed many developments in the field of implementation but has only recently begun multi-site implementation trials across multiple regions within the national VA healthcare system. These trials are unusual in their emphasis on developing detailed costs of implementation, as well as in the use of business case analyses (budget impact analyses. Conclusion Economics appears to play an important role in QUERI implementation studies, only after implementation has reached the stage of multi-site trials. Economic analysis could better inform the choice of which clinical best practices to implement and the choice of implementation interventions to employ. QUERI economics also would benefit from research on costing methods and development of widely accepted international standards for implementation economics.

In-context query reformulation for failing SPARQL queries

Science.gov (United States)

Viswanathan, Amar; Michaelis, James R.; Cassidy, Taylor; de Mel, Geeth; Hendler, James

2017-05-01

Knowledge bases for decision support systems are growing increasingly complex, through continued advances in data ingest and management approaches. However, humans do not possess the cognitive capabilities to retain a bird's-eyeview of such knowledge bases, and may end up issuing unsatisfiable queries to such systems. This work focuses on the implementation of a query reformulation approach for graph-based knowledge bases, specifically designed to support the Resource Description Framework (RDF). The reformulation approach presented is instance-and schema-aware. Thus, in contrast to relaxation techniques found in the state-of-the-art, the presented approach produces in-context query reformulation.

Google BigQuery analytics

CERN Document Server

Tigani, Jordan

2014-01-01

How to effectively use BigQuery, avoid common mistakes, and execute sophisticated queries against large datasets Google BigQuery Analytics is the perfect guide for business and data analysts who want the latest tips on running complex queries and writing code to communicate with the BigQuery API. The book uses real-world examples to demonstrate current best practices and techniques, and also explains and demonstrates streaming ingestion, transformation via Hadoop in Google Compute engine, AppEngine datastore integration, and using GViz with Tableau to generate charts of query results. In addit

SpineCreator: a Graphical User Interface for the Creation of Layered Neural Models.

Science.gov (United States)

Cope, A J; Richmond, P; James, S S; Gurney, K; Allerton, D J

2017-01-01

There is a growing requirement in computational neuroscience for tools that permit collaborative model building, model sharing, combining existing models into a larger system (multi-scale model integration), and are able to simulate models using a variety of simulation engines and hardware platforms. Layered XML model specification formats solve many of these problems, however they are difficult to write and visualise without tools. Here we describe a new graphical software tool, SpineCreator, which facilitates the creation and visualisation of layered models of point spiking neurons or rate coded neurons without requiring the need for programming. We demonstrate the tool through the reproduction and visualisation of published models and show simulation results using code generation interfaced directly into SpineCreator. As a unique application for the graphical creation of neural networks, SpineCreator represents an important step forward for neuronal modelling.

A Study of XML in the Library Science Curriculum in Taiwan and South East Asia

Science.gov (United States)

Chang, Naicheng; Huang, Yuhui; Hopkinson, Alan

2011-01-01

This paper aims to investigate the current XML-related courses available in 96 LIS schools in South East Asia and Taiwan's 9 LIS schools. Also, this study investigates the linkage of library school graduates in Taiwan who took different levels of XML-related education (that is XML arranged as an individual course or XML arranged as a section unit…

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

Science.gov (United States)

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

Query optimization over crowdsourced data

KAUST Repository

Park, Hyunjung

2013-08-26

Deco is a comprehensive system for answering declarative queries posed over stored relational data together with data obtained on-demand from the crowd. In this paper we describe Deco\\'s cost-based query optimizer, building on Deco\\'s data model, query language, and query execution engine presented earlier. Deco\\'s objective in query optimization is to find the best query plan to answer a query, in terms of estimated monetary cost. Deco\\'s query semantics and plan execution strategies require several fundamental changes to traditional query optimization. Novel techniques incorporated into Deco\\'s query optimizer include a cost model distinguishing between "free" existing data versus paid new data, a cardinality estimation algorithm coping with changes to the database state during query execution, and a plan enumeration algorithm maximizing reuse of common subplans in a setting that makes reuse challenging. We experimentally evaluate Deco\\'s query optimizer, focusing on the accuracy of cost estimation and the efficiency of plan enumeration.

Methods and Technologies of XML Data Modeling for IP Mode Intelligent Measuring and Controlling System

International Nuclear Information System (INIS)

Liu, G X; Hong, X B; Liu, J G

2006-01-01

This paper presents the IP mode intelligent measuring and controlling system (IMIMCS). Based on object-oriented modeling technology of UML and XML Schema, the innovative methods and technologies of some key problems for XML data modeling in the IMIMCS were especially discussed, including refinement for systemic business by means of use-case diagram of UML, the confirmation of the content of XML data model and logic relationship of the objects of XML Schema with the aid of class diagram of UML, the mapping rules from the UML object model to XML Schema. Finally, the application of the IMIMCS based on XML for a modern greenhouse was presented. The results show that the modeling methods of the measuring and controlling data in the IMIMCS involving the multi-layer structure and many operating systems process strong reliability and flexibility, guarantee uniformity of complex XML documents and meet the requirement of data communication across platform

Enterprise Architecture Analysis with XML

NARCIS (Netherlands)

F.S. de Boer (Frank); M.M. Bonsangue (Marcello); J.F. Jacob (Joost); A. Stam; L.W.N. van der Torre (Leon)

2005-01-01

htmlabstractThis paper shows how XML can be used for static and dynamic analysis of architectures. Our analysis is based on the distinction between symbolic and semantic models of architectures. The core of a symbolic model consists of its signature that specifies symbolically its structural

Static Analysis for Dynamic XML

DEFF Research Database (Denmark)

Christensen, Aske Simon; Møller, Anders; Schwartzbach, Michael Ignatieff

2002-01-01

We describe the summary graph lattice for dataflow analysis of programs that dynamically construct XML documents. Summary graphs have successfully been used to provide static guarantees in the JWIG language for programming interactive Web services. In particular, the JWIG compiler is able to check...

Concurrent use of data base and graphics computer workstations to provide graphic access to large, complex data bases for robotics control of nuclear surveillance and maintenance

International Nuclear Information System (INIS)

Dalton, G.R.; Tulenko, J.S.; Zhou, X.

1990-01-01

The University of Florida is part of a multiuniversity research effort, sponsored by the US Department of Energy which is under way to develop and deploy an advanced semi-autonomous robotic system for use in nuclear power stations. This paper reports on the development of the computer tools necessary to gain convenient graphic access to the intelligence implicit in a large complex data base such as that in a nuclear reactor plant. This program is integrated as a man/machine interface within the larger context of the total computerized robotic planning and control system. The portion of the project described here addresses the connection between the three-dimensional displays on an interactive graphic workstation and a data-base computer running a large data-base server program. Programming the two computers to work together to accept graphic queries and return answers on the graphic workstation is a key part of the interactive capability developed

Representing nested semantic information in a linear string of text using XML.

OpenAIRE

Krauthammer, Michael; Johnson, Stephen B.; Hripcsak, George; Campbell, David A.; Friedman, Carol

2002-01-01

XML has been widely adopted as an important data interchange language. The structure of XML enables sharing of data elements with variable degrees of nesting as long as the elements are grouped in a strict tree-like fashion. This requirement potentially restricts the usefulness of XML for marking up written text, which often includes features that do not properly nest within other features. We encountered this problem while marking up medical text with structured semantic information from a N...

The Design Space of Type Checkers for XML Transformation Languages

DEFF Research Database (Denmark)

Møller, Anders; Schwartzbach, Michael Ignatieff

2005-01-01

We survey work on statically type checking XML transformations, covering a wide range of notations and ambitions. The concept of type may vary from idealizations of DTD to full-blown XML Schema or even more expressive formalisms. The notion of transformation may vary from clean and simple...... transductions to domain-specific languages or integration of XML in general-purpose programming languages. Type annotations can be either explicit or implicit, and type checking ranges from exact decidability to pragmatic approximations. We characterize and evaluate existing tools in this design space......, including a recent result of the authors providing practical type checking of full unannotated XSLT 1.0 stylesheets given general DTDs that describe the input and output languages....

Querying on Federated Sensor Networks

Directory of Open Access Journals (Sweden)

Zuhal Can

2016-09-01

Full Text Available A Federated Sensor Network (FSN is a network of geographically distributed Wireless Sensor Networks (WSNs called islands. For querying on an FSN, we introduce the Layered Federated Sensor Network (L-FSN Protocol. For layered management, L-FSN provides communication among islands by its inter-island querying protocol by which a query packet routing path is determined according to some path selection policies. L-FSN allows autonomous management of each island by island-specific intra-island querying protocols that can be selected according to island properties. We evaluate the applicability of L-FSN and compare the L-FSN protocol with various querying protocols running on the flat federation model. Flat federation is a method to federate islands by running a single querying protocol on an entire FSN without distinguishing communication among and within islands. For flat federation, we select a querying protocol from geometrical, hierarchical cluster-based, hash-based, and tree-based WSN querying protocol categories. We found that a layered federation of islands by L-FSN increases the querying performance with respect to energy-efficiency, query resolving distance, and query resolving latency. Moreover, L-FSN’s flexibility of choosing intra-island querying protocols regarding the island size brings advantages on energy-efficiency and query resolving latency.

New publicly available chemical query language, CSRML, to support chemotype representations for application to data mining and modeling.

Science.gov (United States)

Yang, Chihae; Tarkhov, Aleksey; Marusczyk, Jörg; Bienfait, Bruno; Gasteiger, Johann; Kleinoeder, Thomas; Magdziarz, Tomasz; Sacher, Oliver; Schwab, Christof H; Schwoebel, Johannes; Terfloth, Lothar; Arvidson, Kirk; Richard, Ann; Worth, Andrew; Rathman, James

2015-03-23

Chemotypes are a new approach for representing molecules, chemical substructures and patterns, reaction rules, and reactions. Chemotypes are capable of integrating types of information beyond what is possible using current representation methods (e.g., SMARTS patterns) or reaction transformations (e.g., SMIRKS, reaction SMILES). Chemotypes are expressed in the XML-based Chemical Subgraphs and Reactions Markup Language (CSRML), and can be encoded not only with connectivity and topology but also with properties of atoms, bonds, electronic systems, or molecules. CSRML 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 chemical patterns and properties especially relevant to various toxicity concerns. A software application, ChemoTyper has also been developed and made publicly available in order 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-based CSRML standard used to express chemotypes are publicly available to facilitate and encourage the exchange of structural knowledge.

Adding XML to the MIS Curriculum: Lessons from the Classroom

Science.gov (United States)

Wagner, William P.; Pant, Vik; Hilken, Ralph

2008-01-01

eXtensible Markup Language (XML) is a new technology that is currently being extolled by many industry experts and software vendors. Potentially it represents a platform independent language for sharing information over networks in a way that is much more seamless than with previous technologies. It is extensible in that XML serves as a "meta"…

The XBabelPhish MAGE-ML and XML translator.

Science.gov (United States)

Maier, Don; Wymore, Farrell; Sherlock, Gavin; Ball, Catherine A

2008-01-18

MAGE-ML has been promoted as a standard format for describing microarray experiments and the data they produce. Two characteristics of the MAGE-ML format compromise its use as a universal standard: First, MAGE-ML files are exceptionally large - too large to be easily read by most people, and often too large to be read by most software programs. Second, the MAGE-ML standard permits many ways of representing the same information. As a result, different producers of MAGE-ML create different documents describing the same experiment and its data. Recognizing all the variants is an unwieldy software engineering task, resulting in software packages that can read and process MAGE-ML from some, but not all producers. This Tower of MAGE-ML Babel bars the unencumbered exchange of microarray experiment descriptions couched in MAGE-ML. We have developed XBabelPhish - an XQuery-based technology for translating one MAGE-ML variant into another. XBabelPhish's use is not restricted to translating MAGE-ML documents. It can transform XML files independent of their DTD, XML schema, or semantic content. Moreover, it is designed to work on very large (> 200 Mb.) files, which are common in the world of MAGE-ML. XBabelPhish provides a way to inter-translate MAGE-ML variants for improved interchange of microarray experiment information. More generally, it can be used to transform most XML files, including very large ones that exceed the capacity of most XML tools.

Scripting XML with Generic Haskell

NARCIS (Netherlands)

Atanassow, F.; Clarke, D.; Jeuring, J.T.

2003-01-01

A generic program is written once and works on values of many data types. Generic Haskell is a recent extension of the functional programming language Haskell that supports generic programming. This paper discusses how Generic Haskell can be used to implement XML tools whose behaviour depends on

Scripting XML with Generic Haskell

NARCIS (Netherlands)

Atanassow, F.; Clarke, D.; Jeuring, J.T.

2007-01-01

A generic program is written once and works on values of many data types. Generic Haskell is a recent extension of the functional programming language Haskell that supports generic programming. This paper discusses how Generic Haskell can be used to implement XML tools whose behaviour depends on

Single event monitoring system based on Java 3D and XML data binding

International Nuclear Information System (INIS)

Wang Liang; Chinese Academy of Sciences, Beijing; Zhu Kejun; Zhao Jingwei

2007-01-01

Online single event monitoring is important to BESIII DAQ System. Java3D is extension of Java Language in 3D technology, XML data binding is more efficient to handle XML document than SAX and DOM. This paper mainly introduce the implementation of BESIII single event monitoring system with Java3D and XML data binding, and interface for track fitting software with JNI technology. (authors)

XML in an Adaptive Framework for Instrument Control

Science.gov (United States)

Ames, Troy J.

2004-01-01

NASA Goddard Space Flight Center is developing an extensible framework for instrument command and control, known as Instrument Remote Control (IRC), that combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML). A key aspect of the architecture is software that is driven by an instrument description, written using the Instrument Markup Language (IML). IML is an XML dialect used to describe interfaces to control and monitor the instrument, command sets and command formats, data streams, communication mechanisms, and data processing algorithms.

Using XML and Java Technologies for Astronomical Instrument Control

Science.gov (United States)

Ames, Troy; Case, Lynne; Powers, Edward I. (Technical Monitor)

2001-01-01

Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests, increasing software maintenance costs. Instrument description is too tightly coupled with details of implementation. NASA Goddard Space Flight Center, under the Instrument Remote Control (IRC) project, is developing a general and highly extensible framework that applies to any kind of instrument that can be controlled by a computer. The software architecture combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML), a human readable and machine understandable way to describe structured data. A key aspect of the object-oriented architecture is that the software is driven by an instrument description, written using the Instrument Markup Language (IML), a dialect of XML. IML is used to describe the command sets and command formats of the instrument, communication mechanisms, format of the data coming from the instrument, and characteristics of the graphical user interface to control and monitor the instrument. The IRC framework allows the users to define a data analysis pipeline which converts data coming out of the instrument. The data can be used in visualizations in order for the user to assess the data in real-time, if necessary. The data analysis pipeline algorithms can be supplied by the user in a variety of forms or programming languages. Although the current integration effort is targeted for the High-resolution Airborne Wideband Camera (HAWC) and the Submillimeter and Far Infrared Experiment (SAFIRE), first-light instruments of the Stratospheric Observatory for Infrared Astronomy (SOFIA), the framework is designed to be generic and extensible so that it can be applied to any instrument. Plans are underway to test the framework

Representing nested semantic information in a linear string of text using XML.

Science.gov (United States)

Krauthammer, Michael; Johnson, Stephen B; Hripcsak, George; Campbell, David A; Friedman, Carol

2002-01-01

XML has been widely adopted as an important data interchange language. The structure of XML enables sharing of data elements with variable degrees of nesting as long as the elements are grouped in a strict tree-like fashion. This requirement potentially restricts the usefulness of XML for marking up written text, which often includes features that do not properly nest within other features. We encountered this problem while marking up medical text with structured semantic information from a Natural Language Processor. Traditional approaches to this problem separate the structured information from the actual text mark up. This paper introduces an alternative solution, which tightly integrates the semantic structure with the text. The resulting XML markup preserves the linearity of the medical texts and can therefore be easily expanded with additional types of information.

Collective spatial keyword querying

DEFF Research Database (Denmark)

Cao, Xin; Cong, Gao; Jensen, Christian S.

2011-01-01

With the proliferation of geo-positioning and geo-tagging, spatial web objects that possess both a geographical location and a textual description are gaining in prevalence, and spatial keyword queries that exploit both location and textual description are gaining in prominence. However, the quer......With the proliferation of geo-positioning and geo-tagging, spatial web objects that possess both a geographical location and a textual description are gaining in prevalence, and spatial keyword queries that exploit both location and textual description are gaining in prominence. However......, the queries studied so far generally focus on finding individual objects that each satisfy a query rather than finding groups of objects where the objects in a group collectively satisfy a query. We define the problem of retrieving a group of spatial web objects such that the group's keywords cover the query......'s keywords and such that objects are nearest to the query location and have the lowest inter-object distances. Specifically, we study two variants of this problem, both of which are NP-complete. We devise exact solutions as well as approximate solutions with provable approximation bounds to the problems. We...

A Graphical Solution for Espaces Verts

CERN Document Server

Skelton, K

1999-01-01

'Espaces Verts' is responsible for the landscaping of the green areas, the cleaning of the roads, pavements, and car parks on the CERN site. This work is carried out by a contracting company. To control the work previously, there was a database of all the areas included in the contract and paper plans of the site. Given the size of the site the ideal solution was considered to be a visual system which integrates the maps and the database. To achieve this, the Surveying Department's graphical information system was used, linking it to the database for Espaces Verts, thus enabling the presentation of graphical thematic queries. This provides a useful management tool, which facilitates the task of ensuring that the contracting company carries out the work according to the agreed planning, and gives precise measurement of the site and thus of the contract. This paper will present how this has been achieved.

XML-based approaches for the integration of heterogeneous bio-molecular data.

Science.gov (United States)

Mesiti, Marco; Jiménez-Ruiz, Ernesto; Sanz, Ismael; Berlanga-Llavori, Rafael; Perlasca, Paolo; Valentini, Giorgio; Manset, David

2009-10-15

The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

AutoAssemblyD: a graphical user interface system for several genome assemblers.

Science.gov (United States)

Veras, Adonney Allan de Oliveira; de Sá, Pablo Henrique Caracciolo Gomes; Azevedo, Vasco; Silva, Artur; Ramos, Rommel Thiago Jucá

2013-01-01

Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.

XML Namespace與RDF的基本概念 | The Basic Concepts of XML Namespace and RDF

Directory of Open Access Journals (Sweden)

陳嵩榮 Sung-Jung Chen

1999-04-01

Full Text Available

頁次：88-100

XML Namespaces機制允許在XML文件中以一個URI 來限定元素名稱或屬性名稱，提供一種在Web上具有唯一性的命名方式，以解決不同的XML文件元素名稱與屬性名稱可能衝突的問題；RDF 主要是為Metadata在Web 上的各種應用提供一個基礎結構，使應用程式之間能夠在Web上交換Metadata，以促進網路資源的自動化處理。本文透過一連串的實例來介紹XML Namespace與RDF的資料模型及語法。

XML namespaces provide a simple method for qualifying element and attribute names used in XML documents by associating them with namespaces identified by URI references. RDF is a foundation for processing metadata. It provides interoperability between

Generic and updatable XML value indices covering equality and range lookups

NARCIS (Netherlands)

E. Sidirourgos (Eleftherios); P.A. Boncz (Peter)

2008-01-01

htmlabstractWe describe a collection of indices for XML text, element, and attribute node values that (i) consume little storage, (ii) have low maintenance overhead, (iii) permit fast equi-lookup on string values, and (iv) support range-lookup on any XML typed value (e.g., double, dateTime). The

Generic and Updatable XML Value Indices Covering Equality and Range Lookups

NARCIS (Netherlands)

E. Sidirourgos (Eleftherios); P.A. Boncz (Peter)

2009-01-01

textabstractWe describe a collection of indices for XML text, element, and attribute node values that (i) consume little storage, (ii) have low maintenance overhead, (iii) permit fast equilookup on string values, and (iv) support range-lookup on any XML typed value (e.g., double, dateTime). The

Querying Workflow Logs

Directory of Open Access Journals (Sweden)

Yan Tang

2018-01-01

Full Text Available A business process or workflow is an assembly of tasks that accomplishes a business goal. Business process management is the study of the design, configuration/implementation, enactment and monitoring, analysis, and re-design of workflows. The traditional methodology for the re-design and improvement of workflows relies on the well-known sequence of extract, transform, and load (ETL, data/process warehousing, and online analytical processing (OLAP tools. In this paper, we study the ad hoc queryiny of process enactments for (data-centric business processes, bypassing the traditional methodology for more flexibility in querying. We develop an algebraic query language based on “incident patterns” with four operators inspired from Business Process Model and Notation (BPMN representation, allowing the user to formulate ad hoc queries directly over workflow logs. A formal semantics of this query language, a preliminary query evaluation algorithm, and a group of elementary properties of the operators are provided.

Development Life Cycle and Tools for XML Content Models

Energy Technology Data Exchange (ETDEWEB)

Kulvatunyou, Boonserm [ORNL; Morris, Katherine [National Institute of Standards and Technology (NIST); Buhwan, Jeong [POSTECH University, South Korea; Goyal, Puja [National Institute of Standards and Technology (NIST)

2004-11-01

Many integration projects today rely on shared semantic models based on standards represented using Extensible Mark up Language (XML) technologies. Shared semantic models typically evolve and require maintenance. In addition, to promote interoperability and reduce integration costs, the shared semantics should be reused as much as possible. Semantic components must be consistent and valid in terms of agreed upon standards and guidelines. In this paper, we describe an activity model for creation, use, and maintenance of a shared semantic model that is coherent and supports efficient enterprise integration. We then use this activity model to frame our research and the development of tools to support those activities. We provide overviews of these tools primarily in the context of the W3C XML Schema. At the present, we focus our work on the W3C XML Schema as the representation of choice, due to its extensive adoption by industry.

Progress on an implementation of MIFlowCyt in XML

Science.gov (United States)

Leif, Robert C.; Leif, Stephanie H.

2015-03-01

Introduction: The International Society for Advancement of Cytometry (ISAC) Data Standards Task Force (DSTF) has created a standard for the Minimum Information about a Flow Cytometry Experiment (MIFlowCyt 1.0). The CytometryML schemas, are based in part upon the Flow Cytometry Standard and Digital Imaging and Communication (DICOM) standards. CytometryML has and will be extended and adapted to include MIFlowCyt, as well as to serve as a common standard for flow and image cytometry (digital microscopy). Methods: The MIFlowCyt data-types were created, as is the rest of CytometryML, in the XML Schema Definition Language (XSD1.1). Individual major elements of the MIFlowCyt schema were translated into XML and filled with reasonable data. A small section of the code was formatted with HTML formatting elements. Results: The differences in the amount of detail to be recorded for 1) users of standard techniques including data analysts and 2) others, such as method and device creators, laboratory and other managers, engineers, and regulatory specialists required that separate data-types be created to describe the instrument configuration and components. A very substantial part of the MIFlowCyt element that describes the Experimental Overview part of the MIFlowCyt and substantial parts of several other major elements have been developed. Conclusions: The future use of structured XML tags and web technology should facilitate searching of experimental information, its presentation, and inclusion in structured research, clinical, and regulatory documents, as well as demonstrate in publications adherence to the MIFlowCyt standard. The use of CytometryML together with XML technology should also result in the textual and numeric data being published using web technology without any change in composition. Preliminary testing indicates that CytometryML XML pages can be directly formatted with the combination of HTML and CSS.

PRIDEViewer: a novel user-friendly interface to visualize PRIDE XML files.

Science.gov (United States)

Medina-Aunon, J Alberto; Carazo, José M; Albar, Juan Pablo

2011-01-01

Current standardization initiatives have greatly contributed to share the information derived by proteomics experiments. One of these initiatives is the XML-based repository PRIDE (PRoteomics IDEntification database), although an XML-based document does not appear to present a user-friendly view at the first glance. PRIDEViewer is a novel Java-based application that presents the information available in a PRIDE XML file in a user-friendly manner, facilitating the interaction among end users as well as the understanding and evaluation of the compiled information. PRIDEViewer is freely available at: http://proteo.cnb.csic.es/prideviewer/. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

jQuery Pocket Reference

CERN Document Server

Flanagan, David

2010-01-01

"As someone who uses jQuery on a regular basis, it was surprising to discover how much of the library I'm not using. This book is indispensable for anyone who is serious about using jQuery for non-trivial applications."-- Raffaele Cecco, longtime developer of video games, including Cybernoid, Exolon, and Stormlord jQuery is the "write less, do more" JavaScript library. Its powerful features and ease of use have made it the most popular client-side JavaScript framework for the Web. This book is jQuery's trusty companion: the definitive "read less, learn more" guide to the library. jQuery P

jQuery UI cookbook

CERN Document Server

Boduch, Adam

2013-01-01

Filled with a practical collection of recipes, jQuery UI Cookbook is full of clear, step-by-step instructions that will help you harness the powerful UI framework in jQuery. Depending on your needs, you can dip in and out of the Cookbook and its recipes, or follow the book from start to finish.If you are a jQuery UI developer looking to improve your existing applications, extract ideas for your new application, or to better understand the overall widget architecture, then jQuery UI Cookbook is a must-have for you. The reader should at least have a rudimentary understanding of what jQuery UI is

Instant jQuery selectors

CERN Document Server

De Rosa, Aurelio

2013-01-01

Filled with practical, step-by-step instructions and clear explanations for the most important and useful tasks. Instant jQuery Selectors follows a simple how-to format with recipes aimed at making you well versed with the wide range of selectors that jQuery has to offer through a myriad of examples.Instant jQuery Selectors is for web developers who want to delve into jQuery from its very starting point: selectors. Even if you're already familiar with the framework and its selectors, you could find several tips and tricks that you aren't aware of, especially about performance and how jQuery ac

KNOWLEDGE AND XML BASED CAPP SYSTEM

Institute of Scientific and Technical Information of China (English)

ZHANG Shijie; SONG Laigang

2006-01-01

In order to enhance the intelligent level of system and improve the interactivity with other systems, a knowledge and XML based computer aided process planning (CAPP) system is implemented. It includes user management, bill of materials(BOM) management, knowledge based process planning, knowledge management and database maintaining sub-systems. This kind of nesting knowledge representation method the system provided can represent complicated arithmetic and logical relationship to deal with process planning tasks. With the representation and manipulation of XML based technological file, the system solves some important problems in web environment such as information interactive efficiency and refreshing of web page. The CAPP system is written in ASP VBScript, JavaScript, Visual C++ languages and Oracle database. At present, the CAPP system is running in Shenyang Machine Tools. The functions of it meet the requirements of enterprise production.

XML as a cross-platform representation for medical imaging with fuzzy algorithms.

Science.gov (United States)

Gal, Norbert; Stoicu-Tivadar, Vasile

2011-01-01

Machines that perform linguistic medical image interpretation are based on fuzzy algorithms. There are several frameworks that can edit and simulate fuzzy algorithms, but they are not compatible with most of the implemented applications. This paper suggests a representation for fuzzy algorithms in XML files, and using this XML as a cross-platform between the simulation framework and the software applications. The paper presents a parsing algorithm that can convert files created by simulation framework, and converts them dynamically into an XML file keeping the original logical structure of the files.

Secure combination of XML signature application with message aggregation in multicast settings

DEFF Research Database (Denmark)

Becker, Andreas; Jensen, Meiko

2013-01-01

The similarity-based aggregation of XML documents is a proven method for reducing network traffic. However, when used in conjunction with XML security standards, a lot of pitfalls, but also optimization potentials exist. In this paper, we investigate these issues, showing how to exploit similarity......-based aggregation for rapid distribution of digitally signed XML data. Using our own implementation in two different experimental settings, we provide both a thorough evaluation and a security proof for our approach. By this we prove both feasibility and security, and we illustrate how to achieve a network traffic...

Definition of an XML markup language for clinical laboratory procedures and comparison with generic XML markup.

Science.gov (United States)

Saadawi, Gilan M; Harrison, James H

2006-10-01

Clinical laboratory procedure manuals are typically maintained as word processor files and are inefficient to store and search, require substantial effort for review and updating, and integrate poorly with other laboratory information. Electronic document management systems could improve procedure management and utility. As a first step toward building such systems, we have developed a prototype electronic format for laboratory procedures using Extensible Markup Language (XML). Representative laboratory procedures were analyzed to identify document structure and data elements. This information was used to create a markup vocabulary, CLP-ML, expressed as an XML Document Type Definition (DTD). To determine whether this markup provided advantages over generic markup, we compared procedures structured with CLP-ML or with the vocabulary of the Health Level Seven, Inc. (HL7) Clinical Document Architecture (CDA) narrative block. CLP-ML includes 124 XML tags and supports a variety of procedure types across different laboratory sections. When compared with a general-purpose markup vocabulary (CDA narrative block), CLP-ML documents were easier to edit and read, less complex structurally, and simpler to traverse for searching and retrieval. In combination with appropriate software, CLP-ML is designed to support electronic authoring, reviewing, distributing, and searching of clinical laboratory procedures from a central repository, decreasing procedure maintenance effort and increasing the utility of procedure information. A standard electronic procedure format could also allow laboratories and vendors to share procedures and procedure layouts, minimizing duplicative word processor editing. Our results suggest that laboratory-specific markup such as CLP-ML will provide greater benefit for such systems than generic markup.

Database and Expert Systems Applications

DEFF Research Database (Denmark)

Viborg Andersen, Kim; Debenham, John; Wagner, Roland

schemata, query evaluation, semantic processing, information retrieval, temporal and spatial databases, querying XML, organisational aspects of databases, natural language processing, ontologies, Web data extraction, semantic Web, data stream management, data extraction, distributed database systems......This book constitutes the refereed proceedings of the 16th International Conference on Database and Expert Systems Applications, DEXA 2005, held in Copenhagen, Denmark, in August 2005.The 92 revised full papers presented together with 2 invited papers were carefully reviewed and selected from 390...... submissions. The papers are organized in topical sections on workflow automation, database queries, data classification and recommendation systems, information retrieval in multimedia databases, Web applications, implementational aspects of databases, multimedia databases, XML processing, security, XML...

A transaction model for XML databases

NARCIS (Netherlands)

Dekeyser, S.; Hidders, A.J.H.; Paredaens, J.

2004-01-01

Abstract The hierarchical and semistructured nature of XML data may cause complicated update behavior. Updates should not be limited to entire document trees, but should ideally involve subtrees and even individual elements. Providing a suitable scheduling algorithm for semistructured data can

Spatiotemporal conceptual platform for querying archaeological information systems

Science.gov (United States)

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

XML-based information system for planetary sciences

Science.gov (United States)

Carraro, F.; Fonte, S.; Turrini, D.

2009-04-01

EuroPlaNet (EPN in the following) has been developed by the planetological community under the "Sixth Framework Programme" (FP6 in the following), the European programme devoted to the improvement of the European research efforts through the creation of an internal market for science and technology. The goal of the EPN programme is the creation of a European network aimed to the diffusion of data produced by space missions dedicated to the study of the Solar System. A special place within the EPN programme is that of I.D.I.S. (Integrated and Distributed Information Service). The main goal of IDIS is to offer to the planetary science community a user-friendly access to the data and information produced by the various types of research activities, i.e. Earth-based observations, space observations, modeling, theory and laboratory experiments. During the FP6 programme IDIS development consisted in the creation of a series of thematic nodes, each of them specialized in a specific scientific domain, and a technical coordination node. The four thematic nodes are the Atmosphere node, the Plasma node, the Interiors & Surfaces node and the Small Bodies & Dust node. The main task of the nodes have been the building up of selected scientific cases related with the scientific domain of each node. The second work done by EPN nodes have been the creation of a catalogue of resources related to their main scientific theme. Both these efforts have been used as the basis for the development of the main IDIS goal, i.e. the integrated distributed service. An XML-based data model have been developed to describe resources using meta-data and to store the meta-data within an XML-based database called eXist. A search engine has been then developed in order to allow users to search resources within the database. Users can select the resource type and can insert one or more values or can choose a value among those present in a list, depending on selected resource. The system searches for all

Integrated Syntactic/Semantic XML Data Validation with a Reusable Software Component

Science.gov (United States)

Golikov, Steven

2013-01-01

Data integration is a critical component of enterprise system integration, and XML data validation is the foundation for sound data integration of XML-based information systems. Since B2B e-commerce relies on data validation as one of the critical components for enterprise integration, it is imperative for financial industries and e-commerce…

77 FR 46986 - Revisions to Electric Quarterly Report Filing Process; Availability of Draft XML Schema

Science.gov (United States)

2012-08-07

... Supplementary Information Section below for details. DATES: The draft XML Schema is now available at the links...] Revisions to Electric Quarterly Report Filing Process; Availability of Draft XML Schema AGENCY: Federal... Regulatory Commission is making available on its Web site ( http://www.ferc.gov ) a draft of the XML schema...

Fast and Reliable Mouse Picking Using Graphics Hardware

Directory of Open Access Journals (Sweden)

Hanli Zhao

2009-01-01

Full Text Available Mouse picking is the most commonly used intuitive operation to interact with 3D scenes in a variety of 3D graphics applications. High performance for such operation is necessary in order to provide users with fast responses. This paper proposes a fast and reliable mouse picking algorithm using graphics hardware for 3D triangular scenes. Our approach uses a multi-layer rendering algorithm to perform the picking operation in linear time complexity. The objectspace based ray-triangle intersection test is implemented in a highly parallelized geometry shader. After applying the hardware-supported occlusion queries, only a small number of objects (or sub-objects are rendered in subsequent layers, which accelerates the picking efficiency. Experimental results demonstrate the high performance of our novel approach. Due to its simplicity, our algorithm can be easily integrated into existing real-time rendering systems.

Association rule extraction from XML stream data for wireless sensor networks.

Science.gov (United States)

Paik, Juryon; Nam, Junghyun; Kim, Ung Mo; Won, Dongho

2014-07-18

With the advances of wireless sensor networks, they yield massive volumes of disparate, dynamic and geographically-distributed and heterogeneous data. The data mining community has attempted to extract knowledge from the huge amount of data that they generate. However, previous mining work in WSNs has focused on supporting simple relational data structures, like one table per network, while there is a need for more complex data structures. This deficiency motivates XML, which is the current de facto format for the data exchange and modeling of a wide variety of data sources over the web, to be used in WSNs in order to encourage the interchangeability of heterogeneous types of sensors and systems. However, mining XML data for WSNs has two challenging issues: one is the endless data flow; and the other is the complex tree structure. In this paper, we present several new definitions and techniques related to association rule mining over XML data streams in WSNs. To the best of our knowledge, this work provides the first approach to mining XML stream data that generates frequent tree items without any redundancy.

Learning semantic query suggestions

NARCIS (Netherlands)

Meij, E.; Bron, M.; Hollink, L.; Huurnink, B.; de Rijke, M.

2009-01-01

An important application of semantic web technology is recognizing human-defined concepts in text. Query transformation is a strategy often used in search engines to derive queries that are able to return more useful search results than the original query and most popular search engines provide

QuakeML - An XML Schema for Seismology

Science.gov (United States)

Wyss, A.; Schorlemmer, D.; Maraini, S.; Baer, M.; Wiemer, S.

2004-12-01

We propose an extensible format-definition for seismic data (QuakeML). Sharing data and seismic information efficiently is one of the most important issues for research and observational seismology in the future. The eXtensible Markup Language (XML) is playing an increasingly important role in the exchange of a variety of data. Due to its extensible definition capabilities, its wide acceptance and the existing large number of utilities and libraries for XML, a structured representation of various types of seismological data should in our opinion be developed by defining a 'QuakeML' standard. Here we present the QuakeML definitions for parameter databases and further efforts, e.g. a central QuakeML catalog database and a web portal for exchanging codes and stylesheets.

Indexing for summary queries

DEFF Research Database (Denmark)

Yi, Ke; Wang, Lu; Wei, Zhewei

2014-01-01

), of a particular attribute of these records. Aggregation queries are especially useful in business intelligence and data analysis applications where users are interested not in the actual records, but some statistics of them. They can also be executed much more efficiently than reporting queries, by embedding...... returned by reporting queries. In this article, we design indexing techniques that allow for extracting a statistical summary of all the records in the query. The summaries we support include frequent items, quantiles, and various sketches, all of which are of central importance in massive data analysis....... Our indexes require linear space and extract a summary with the optimal or near-optimal query cost. We illustrate the efficiency and usefulness of our designs through extensive experiments and a system demonstration....

FireCalc: An XML-based framework for distributed data analysis

International Nuclear Information System (INIS)

Duarte, A.S.; Santos, J.H.; Fernandes, H.; Neto, A.; Pereira, T.; Varandas, C.A.F.

2008-01-01

Requirements and specifications for Control Data Access and Communication (CODAC) systems in fusion reactors point towards flexible and modular solutions, independent from operating system and computer architecture. These concepts can also be applied to calculation and data analysis systems, where highly standardized solutions must also apply in order to anticipate long time-scales and high technology evolution changes. FireCalc is an analysis tool based on standard Extensible Markup Language (XML) technologies. Actions are described in an XML file, which contains necessary data specifications and the code or references to scripts. This is used by the user to send the analysis code and data to a server, which can be running either locally or remotely. Communications between the user and the server are performed through XML-RPC, an XML based remote procedure call, thus enabling the client and server to be coded in different computer languages. Access to the database, security procedures and calls to the code interpreter are handled through independent modules, which unbinds them from specific solutions. Currently there is an implementation of the FireCalc framework in Java, that uses the Shared Data Access System (SDAS) for accessing the ISTTOK database and the Scilab kernel for the numerical analysis

FireCalc: An XML-based framework for distributed data analysis

Energy Technology Data Exchange (ETDEWEB)

Duarte, A.S. [Associacao Euratom/IST, Centro de Fusao Nuclear, Av. Rovisco Pais P-1049-001 Lisboa (Portugal)], E-mail: andre.duarte@cfn.ist.utl.pt; Santos, J.H.; Fernandes, H.; Neto, A.; Pereira, T.; Varandas, C.A.F. [Associacao Euratom/IST, Centro de Fusao Nuclear, Av. Rovisco Pais P-1049-001 Lisboa (Portugal)

2008-04-15

Requirements and specifications for Control Data Access and Communication (CODAC) systems in fusion reactors point towards flexible and modular solutions, independent from operating system and computer architecture. These concepts can also be applied to calculation and data analysis systems, where highly standardized solutions must also apply in order to anticipate long time-scales and high technology evolution changes. FireCalc is an analysis tool based on standard Extensible Markup Language (XML) technologies. Actions are described in an XML file, which contains necessary data specifications and the code or references to scripts. This is used by the user to send the analysis code and data to a server, which can be running either locally or remotely. Communications between the user and the server are performed through XML-RPC, an XML based remote procedure call, thus enabling the client and server to be coded in different computer languages. Access to the database, security procedures and calls to the code interpreter are handled through independent modules, which unbinds them from specific solutions. Currently there is an implementation of the FireCalc framework in Java, that uses the Shared Data Access System (SDAS) for accessing the ISTTOK database and the Scilab kernel for the numerical analysis.

The CMS DBS query language

International Nuclear Information System (INIS)

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

2010-01-01

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.

ForConX: A forcefield conversion tool based on XML.

Science.gov (United States)

Lesch, Volker; Diddens, Diddo; Bernardes, Carlos E S; Golub, Benjamin; Dequidt, Alain; Zeindlhofer, Veronika; Sega, Marcello; Schröder, Christian

2017-04-05

The force field conversion from one MD program to another one is exhausting and error-prone. Although single conversion tools from one MD program to another exist not every combination and both directions of conversion are available for the favorite MD programs Amber, Charmm, Dl-Poly, Gromacs, and Lammps. We present here a general tool for the force field conversion on the basis of an XML document. The force field is converted to and from this XML structure facilitating the implementation of new MD programs for the conversion. Furthermore, the XML structure is human readable and can be manipulated before continuing the conversion. We report, as testcases, the conversions of topologies for acetonitrile, dimethylformamide, and 1-ethyl-3-methylimidazolium trifluoromethanesulfonate comprising also Urey-Bradley and Ryckaert-Bellemans potentials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The Simplest Evaluation Measures for XML Information Retrieval that Could Possibly Work

NARCIS (Netherlands)

Hiemstra, Djoerd; Mihajlovic, V.

2005-01-01

This paper reviews several evaluation measures developed for evaluating XML information retrieval (IR) systems. We argue that these measures, some of which are currently in use by the INitiative for the Evaluation of XML Retrieval (INEX), are complicated, hard to understand, and hard to explain to

Mastering jQuery mobile

CERN Document Server

Lambert, Chip

2015-01-01

You've started down the path of jQuery Mobile, now begin mastering some of jQuery Mobile's higher level topics. Go beyond jQuery Mobile's documentation and master one of the hottest mobile technologies out there. Previous JavaScript and PHP experience can help you get the most out of this book.

XVCL: XML-based Variant Configuration Language

DEFF Research Database (Denmark)

Jarzabek, Stan; Basset, Paul; Zhang, Hongyu

2003-01-01

XVCL (XML-based Variant Configuration Language) is a meta-programming technique and tool that provides effective reuse mechanisms. XVCL is an open source software developed at the National University of Singapore. Being a modern and versatile version of Bassett's frames, a technology that has...

CUFID-query: accurate network querying through random walk based network flow estimation.

Science.gov (United States)

Jeong, Hyundoo; Qian, Xiaoning; Yoon, Byung-Jun

2017-12-28

Functional modules in biological networks consist of numerous biomolecules and their complicated interactions. Recent studies have shown that biomolecules in a functional module tend to have similar interaction patterns and that such modules are often conserved across biological networks of different species. As a result, such conserved functional modules can be identified through comparative analysis of biological networks. In this work, we propose a novel network querying algorithm based on the CUFID (Comparative network analysis Using the steady-state network Flow to IDentify orthologous proteins) framework combined with an efficient seed-and-extension approach. The proposed algorithm, CUFID-query, can accurately detect conserved functional modules as small subnetworks in the target network that are expected to perform similar functions to the given query functional module. The CUFID framework was recently developed for probabilistic pairwise global comparison of biological networks, and it has been applied to pairwise global network alignment, where the framework was shown to yield accurate network alignment results. In the proposed CUFID-query algorithm, we adopt the CUFID framework and extend it for local network alignment, specifically to solve network querying problems. First, in the seed selection phase, the proposed method utilizes the CUFID framework to compare the query and the target networks and to predict the probabilistic node-to-node correspondence between the networks. Next, the algorithm selects and greedily extends the seed in the target network by iteratively adding nodes that have frequent interactions with other nodes in the seed network, in a way that the conductance of the extended network is maximally reduced. Finally, CUFID-query removes irrelevant nodes from the querying results based on the personalized PageRank vector for the induced network that includes the fully extended network and its neighboring nodes. Through extensive

jQuery cookbook

CERN Document Server

2010-01-01

jQuery simplifies building rich, interactive web frontends. Getting started with this JavaScript library is easy, but it can take years to fully realize its breadth and depth; this cookbook shortens the learning curve considerably. With these recipes, you'll learn patterns and practices from 19 leading developers who use jQuery for everything from integrating simple components into websites and applications to developing complex, high-performance user interfaces. Ideal for newcomers and JavaScript veterans alike, jQuery Cookbook starts with the basics and then moves to practical use cases w

User perspectives on query difficulty

DEFF Research Database (Denmark)

Lioma, Christina; Larsen, Birger; Schütze, Hinrich

2011-01-01

be difficult for the system to address? (2) Are users aware of specific features in their query (e.g., domain-specificity, vagueness) that may render their query difficult for an IR system to address? A study of 420 queries from a Web search engine query log that are pre-categorised as easy, medium, hard...

XML DTD and Schemas for HDF-EOS

Science.gov (United States)

Ullman, Richard; Yang, Jingli

2008-01-01

An Extensible Markup Language (XML) document type definition (DTD) standard for the structure and contents of HDF-EOS files and their contents, and an equivalent standard in the form of schemas, have been developed.

Heuristic query optimization for query multiple table and multiple clausa on mobile finance application

Science.gov (United States)

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.

XML databases and the semantic web

CERN Document Server

Thuraisingham, Bhavani

2002-01-01

Efficient access to data, sharing data, extracting information from data, and making use of the information have become urgent needs for today''s corporations. With so much data on the Web, managing it with conventional tools is becoming almost impossible. New tools and techniques are necessary to provide interoperability as well as warehousing between multiple data sources and systems, and to extract information from the databases. XML Databases and the Semantic Web focuses on critical and new Web technologies needed for organizations to carry out transactions on the Web, to understand how to use the Web effectively, and to exchange complex documents on the Web.This reference for database administrators, database designers, and Web designers working in tandem with database technologists covers three emerging technologies of significant impact for electronic business: Extensible Markup Language (XML), semi-structured databases, and the semantic Web. The first two parts of the book explore these emerging techn...

Internet-based data interchange with XML

Science.gov (United States)

Fuerst, Karl; Schmidt, Thomas

2000-12-01

In this paper, a complete concept for Internet Electronic Data Interchange (EDI) - a well-known buzzword in the area of logistics and supply chain management to enable the automation of the interactions between companies and their partners - using XML (eXtensible Markup Language) will be proposed. This approach is based on Internet and XML, because the implementation of traditional EDI (e.g. EDIFACT, ANSI X.12) is mostly too costly for small and medium sized enterprises, which want to integrate their suppliers and customers in a supply chain. The paper will also present the results of the implementation of a prototype for such a system, which has been developed for an industrial partner to improve the current situation of parts delivery. The main functions of this system are an early warning system to detect problems during the parts delivery process as early as possible, and a transport following system to pursue the transportation.

Mastering jQuery

CERN Document Server

Libby, Alex

2015-01-01

If you are a developer who is already familiar with using jQuery and wants to push your skill set further, then this book is for you. The book assumes an intermediate knowledge level of jQuery, JavaScript, HTML5, and CSS.

Association Rule Extraction from XML Stream Data for Wireless Sensor Networks

Science.gov (United States)

Paik, Juryon; Nam, Junghyun; Kim, Ung Mo; Won, Dongho

2014-01-01

With the advances of wireless sensor networks, they yield massive volumes of disparate, dynamic and geographically-distributed and heterogeneous data. The data mining community has attempted to extract knowledge from the huge amount of data that they generate. However, previous mining work in WSNs has focused on supporting simple relational data structures, like one table per network, while there is a need for more complex data structures. This deficiency motivates XML, which is the current de facto format for the data exchange and modeling of a wide variety of data sources over the web, to be used in WSNs in order to encourage the interchangeability of heterogeneous types of sensors and systems. However, mining XML data for WSNs has two challenging issues: one is the endless data flow; and the other is the complex tree structure. In this paper, we present several new definitions and techniques related to association rule mining over XML data streams in WSNs. To the best of our knowledge, this work provides the first approach to mining XML stream data that generates frequent tree items without any redundancy. PMID:25046017

Design and construction of a graphical interface for automatic generation of simulation code GEANT4

International Nuclear Information System (INIS)

Driss, Mozher; Bouzaine Ismail

2007-01-01

This work is set in the context of the engineering studies final project; it is accomplished in the center of nuclear sciences and technologies in Sidi Thabet. This project is about conceiving and developing a system based on graphical user interface which allows an automatic codes generation for simulation under the GEANT4 engine. This system aims to facilitate the use of GEANT4 by scientific not necessary expert in this engine and to be used in different areas: research, industry and education. The implementation of this project uses Root library and several programming languages such as XML and XSL. (Author). 5 refs

Smart Query Answering for Marine Sensor Data

Directory of Open Access Journals (Sweden)

Paulo de Souza

2011-03-01

Full Text Available We review existing query answering systems for sensor data. We then propose an extended query answering approach termed smart query, specifically for marine sensor data. The smart query answering system integrates pattern queries and continuous queries. The proposed smart query system considers both streaming data and historical data from marine sensor networks. The smart query also uses query relaxation technique and semantics from domain knowledge as a recommender system. The proposed smart query benefits in building data and information systems for marine sensor networks.

Smart query answering for marine sensor data.

Science.gov (United States)

Shahriar, Md Sumon; de Souza, Paulo; Timms, Greg

2011-01-01

We review existing query answering systems for sensor data. We then propose an extended query answering approach termed smart query, specifically for marine sensor data. The smart query answering system integrates pattern queries and continuous queries. The proposed smart query system considers both streaming data and historical data from marine sensor networks. The smart query also uses query relaxation technique and semantics from domain knowledge as a recommender system. The proposed smart query benefits in building data and information systems for marine sensor networks.

Rock.XML - Towards a library of rock physics models

Science.gov (United States)

Jensen, Erling Hugo; Hauge, Ragnar; Ulvmoen, Marit; Johansen, Tor Arne; Drottning, Åsmund

2016-08-01

Rock physics modelling provides tools for correlating physical properties of rocks and their constituents to the geophysical observations we measure on a larger scale. Many different theoretical and empirical models exist, to cover the range of different types of rocks. However, upon reviewing these, we see that they are all built around a few main concepts. Based on this observation, we propose a format for digitally storing the specifications for rock physics models which we have named Rock.XML. It does not only contain data about the various constituents, but also the theories and how they are used to combine these building blocks to make a representative model for a particular rock. The format is based on the Extensible Markup Language XML, making it flexible enough to handle complex models as well as scalable towards extending it with new theories and models. This technology has great advantages as far as documenting and exchanging models in an unambiguous way between people and between software. Rock.XML can become a platform for creating a library of rock physics models; making them more accessible to everyone.

XML como medio de normalización y desarrollo documental.

Directory of Open Access Journals (Sweden)

de la Rosa, Antonio

1999-12-01

Full Text Available The Web, as a working environment for information science professionals, demands the exploitation of new tools. These tools are intended to allow the information management in a structured and organised way. XML and its specifications offer a wide range of solutions for the problems of our domain: either for the development of documentary software or the day-to-day tasks. In this article, the XML standard is briefly presented and its possible impact in the profession is evaluated as well as the possibilities to use it as vehicle for the creation of information systems.

El Web, como entorno de trabajo para los profesionales de la documentación, requiere la utilización de nuevas herramientas que permitan gestionar la información de forma estructurada y organizada. XML y las especificaciones que se derivan de él ofrecen una amplia gama de soluciones a los diversos problemas que atañen a nuestra disciplina, tanto para el desarrollo de software documental como para las tareas cotidianas. En este artículo se presenta brevemente la norma XML y se evalúa su posible impacto en la profesión así como las posibilidades de utilizarlo como vehículo para la creación de sistemas de información.

jQuery For Dummies

CERN Document Server

Beighley, Lynn

2010-01-01

Learn how jQuery can make your Web page or blog stand out from the crowd!. jQuery is free, open source software that allows you to extend and customize Joomla!, Drupal, AJAX, and WordPress via plug-ins. Assuming no previous programming experience, Lynn Beighley takes you through the basics of jQuery from the very start. You'll discover how the jQuery library separates itself from other JavaScript libraries through its ease of use, compactness, and friendliness if you're a beginner programmer. Written in the easy-to-understand style of the For Dummies brand, this book demonstrates how you can a

Web development with jQuery

CERN Document Server

York, Richard

2015-01-01

Newly revised and updated resource on jQuery's many features and advantages Web Development with jQuery offers a major update to the popular Beginning JavaScript and CSS Development with jQuery from 2009. More than half of the content is new or updated, and reflects recent innovations with regard to mobile applications, jQuery mobile, and the spectrum of associated plugins. Readers can expect thorough revisions with expanded coverage of events, CSS, AJAX, animation, and drag and drop. New chapters bring developers up to date on popular features like jQuery UI, navigation, tables, interacti

Optimizing Temporal Queries

DEFF Research Database (Denmark)

Toman, David; Bowman, Ivan Thomas

2003-01-01

Recent research in the area of temporal databases has proposed a number of query languages that vary in their expressive power and the semantics they provide to users. These query languages represent a spectrum of solutions to the tension between clean semantics and efficient evaluation. Often, t...

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

Science.gov (United States)

Philippi, Stephan; Köhler, Jacob

2004-06-01

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

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

Directory of Open Access Journals (Sweden)

Sergio Miranda Freire

Full Text Available 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

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

Science.gov (United States)

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

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

Science.gov (United States)

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

Efficient XML Interchange (EXI) Compression and Performance Benefits: Development, Implementation and Evaluation

Science.gov (United States)

2010-03-01

181 a. Information Grammar Theory ( Chomsky ) ..........................181 b. Events...document. a. Information Grammar Theory ( Chomsky ) Both grammars and events are learned for each XML document by means of a supporting schema or by...processing the XML document. The learning process is similar to Chomsky grammars, a hierarchical-based formal grammar for defining a language

A new XML-aware compression technique for improving performance of healthcare information systems over hospital networks.

Science.gov (United States)

Al-Shammary, Dhiah; Khalil, Ibrahim

2010-01-01

Most organizations exchange, collect, store and process data over the Internet. Many hospital networks deploy Web services to send and receive patient information. SOAP (Simple Object Access Protocol) is the most usable communication protocol for Web services. XML is the standard encoding language of SOAP messages. However, the major drawback of XML messages is the high network traffic caused by large overheads. In this paper, two XML-aware compressors are suggested to compress patient messages stemming from any data transactions between Web clients and servers. The proposed compression techniques are based on the XML structure concepts and use both fixed-length and Huffman encoding methods for translating the XML message tree. Experiments show that they outperform all the conventional compression methods and can save tremendous amount of network bandwidth.

Encoding of Fundamental Chemical Entities of Organic Reactivity Interest using chemical ontology and XML.

Science.gov (United States)

Durairaj, Vijayasarathi; Punnaivanam, Sankar

2015-09-01

Fundamental chemical entities are identified in the context of organic reactivity and classified as appropriate concept classes namely ElectronEntity, AtomEntity, AtomGroupEntity, FunctionalGroupEntity and MolecularEntity. The entity classes and their subclasses are organized into a chemical ontology named "ChemEnt" for the purpose of assertion, restriction and modification of properties through entity relations. Individual instances of entity classes are defined and encoded as a library of chemical entities in XML. The instances of entity classes are distinguished with a unique notation and identification values in order to map them with the ontology definitions. A model GUI named Entity Table is created to view graphical representations of all the entity instances. The detection of chemical entities in chemical structures is achieved through suitable algorithms. The possibility of asserting properties to the entities at different levels and the mechanism of property flow within the hierarchical entity levels is outlined. Copyright © 2015 Elsevier Inc. All rights reserved.

The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.

Science.gov (United States)

Kikuchi, Norihiro; Kameyama, Akihiko; Nakaya, Shuuichi; Ito, Hiromi; Sato, Takashi; Shikanai, Toshihide; Takahashi, Yoriko; Narimatsu, Hisashi

2005-04-15

Bioinformatics resources for glycomics are very poor as compared with those for genomics and proteomics. The complexity of carbohydrate sequences makes it difficult to define a common language to represent them, and the development of bioinformatics tools for glycomics has not progressed. In this study, we developed a carbohydrate sequence markup language (CabosML), an XML description of carbohydrate structures. The language definition (XML Schema) and an experimental database of carbohydrate structures using an XML database management system are available at http://www.phoenix.hydra.mki.co.jp/CabosDemo.html kikuchi@hydra.mki.co.jp.

jQuery Mobile

CERN Document Server

Reid, Jon

2011-01-01

Native apps have distinct advantages, but the future belongs to mobile web apps that function on a broad range of smartphones and tablets. Get started with jQuery Mobile, the touch-optimized framework for creating apps that look and behave consistently across many devices. This concise book provides HTML5, CSS3, and JavaScript code examples, screen shots, and step-by-step guidance to help you build a complete working app with jQuery Mobile. If you're already familiar with the jQuery JavaScript library, you can use your existing skills to build cross-platform mobile web apps right now. This b

jMRUI plugin software (jMRUI2XML) to allow automated MRS processing and XML-based standardized output

Czech Academy of Sciences Publication Activity Database

Mocioiu, V.; Ortega-Martorell, S.; Olier, I.; Jabłoński, Michal; Starčuková, Jana; Lisboa, P.; Arús, C.; Julia-Sapé, M.

2015-01-01

Roč. 28, S1 (2015), S518 ISSN 0968-5243. [ESMRMB 2015. Annual Scientific Meeting /32./. 01.09.2015-03.09.2015, Edinburgh] Institutional support: RVO:68081731 Keywords : MR Spectroscopy * signal processing * jMRUI * software development * XML Subject RIV: BH - Optics, Masers, Lasers

Converting from XML to HDF-EOS

Science.gov (United States)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A computer program recreates an HDF-EOS file from an Extensible Markup Language (XML) representation of the contents of that file. This program is one of two programs written to enable testing of the schemas described in the immediately preceding article to determine whether the schemas capture all details of HDF-EOS files.

XTCE. XML Telemetry and Command Exchange Tutorial

Science.gov (United States)

Rice, Kevin; Kizzort, Brad; Simon, Jerry

2010-01-01

An XML Telemetry Command Exchange (XTCE) tutoral oriented towards packets or minor frames is shown. The contents include: 1) The Basics; 2) Describing Telemetry; 3) Describing the Telemetry Format; 4) Commanding; 5) Forgotten Elements; 6) Implementing XTCE; and 7) GovSat.

Transitioning from XML to RDF: Considerations for an effective move towards Linked Data and the Semantic Web

Directory of Open Access Journals (Sweden)

Juliet L. Hardesty

2016-04-01

Full Text Available Metadata, particularly within the academic library setting, is often expressed in eXtensible Markup Language (XML and managed with XML tools, technologies, and workflows. Managing a library’s metadata currently takes on a greater level of complexity as libraries are increasingly adopting the Resource Description Framework (RDF. Semantic Web initiatives are surfacing in the library context with experiments in publishing metadata as Linked Data sets and also with development efforts such as BIBFRAME and the Fedora 4 Digital Repository incorporating RDF. Use cases show that transitions into RDF are occurring in both XML standards and in libraries with metadata encoded in XML. It is vital to understand that transitioning from XML to RDF requires a shift in perspective from replicating structures in XML to defining meaningful relationships in RDF. Establishing coordination and communication among these efforts will help as more libraries move to use RDF, produce Linked Data, and approach the Semantic Web.

High-throughput sequence alignment using Graphics Processing Units

Directory of Open Access Journals (Sweden)

Trapnell Cole

2007-12-01

Full Text Available Abstract Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.

Incremental Query Rewriting with Resolution

Science.gov (United States)

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.

Range-clustering queries

NARCIS (Netherlands)

Abrahamsen, M.; de Berg, M.T.; Buchin, K.A.; Mehr, M.; Mehrabi, A.D.

2017-01-01

In a geometric k -clustering problem the goal is to partition a set of points in R d into k subsets such that a certain cost function of the clustering is minimized. We present data structures for orthogonal range-clustering queries on a point set S : given a query box Q and an integer k>2 , compute

XML Diagnostics Description Standard

International Nuclear Information System (INIS)

Neto, A.; Fernandes, H.; Varandas, C.; Lister, J.; Yonekawa, I.

2006-01-01

A standard for the self-description of fusion plasma diagnostics will be presented, based on the Extensible Markup Language (XML). The motivation is to maintain and organise the information on all the components of a laboratory experiment, from the hardware to the access security, to save time and money when problems arises. Since there is no existing standard to organise this kind of information, every Association stores and organises each experiment in different ways. This can lead to severe problems when the organisation schema is poorly documented or written in national languages. The exchange of scientists, researchers and engineers between laboratories is a common practice nowadays. Sometimes they have to install new diagnostics or to update existing ones and frequently they lose a great deal of time trying to understand the currently installed system. The most common problems are: no documentation available; the person who understands it has left; documentation written in the national language. Standardisation is the key to solving all the problems mentioned. From the commercial information on the diagnostic (component supplier; component price) to the hardware description (component specifications; drawings) to the operation of the equipment (finite state machines) through change control (who changed what and when) and internationalisation (information at least in the native language and in English), a common XML schema will be proposed. This paper will also discuss an extension of these ideas to the self-description of ITER plant systems, since the problems will be identical. (author)

SPARK: Adapting Keyword Query to Semantic Search

Science.gov (United States)

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.

An XML schema for automated data integration in a Multi-Source Information System dedicated to end-stage renal disease.

Science.gov (United States)

Dufour, Eric; Ben Saïd, Mohamed; Jais, Jean Philippe; Le Mignot, Loic; Richard, Jean-Baptiste; Landais, Paul

2009-01-01

Data exchange and interoperability between clinical information systems represent a crucial issue in the context of patient record data collection. An XML representation schema adapted to end-stage renal disease (ESRD) patients was developed and successfully tested against patient data in the dedicated Multi-Source Information System (MSIS) active file (more than 16,000 patient records). The ESRD-XML-Schema is organized into Schema subsets respecting the coherence of the clinical information and enriched with coherent data types. Tests are realized against XML-data files generated in conformity with the ESRD-XML Schema. Manual tests allowed the XML schema validation of the data format and content. Programmatic tests allowed the design of generic XML parsing routines, a portable object data model representation and the implementation of automatic data-exchange flows with the MSIS database system. The ESRD-XML-Schema represents a valid framework for data exchange and supports interoperability. Its modular design offers opportunity to simplify physicians' multiple tasks in order to privilege their clinical work.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

Science.gov (United States)

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

Directory of Open Access Journals (Sweden)

Hannes L Röst

Full Text Available In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size.Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11, making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data.Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS.

Using small XML elements to support relevance

NARCIS (Netherlands)

G. Ramirez Camps (Georgina); T.H.W. Westerveld (Thijs); A.P. de Vries (Arjen)

2006-01-01

htmlabstractSmall XML elements are often estimated relevant by the retrieval model but they are not desirable retrieval units. This paper presents a generic model that exploits the information obtained from small elements. We identify relationships between small and relevant elements and use this

Using a Combination of UML, C2RM, XML, and Metadata Registries to Support Long-Term Development/Engineering

Science.gov (United States)

2003-01-01

Authenticat’n (XCBF) Authorizat’n (XACML) (SAML) Privacy (P3P) Digital Rights Management (XrML) Content Mngmnt (DASL) (WebDAV) Content Syndicat’n...Registry/ Repository BPSS eCommerce XML/EDI Universal Business Language (UBL) Internet & Computing Human Resources (HR-XML) Semantic KEY XML SPECIFICATIONS

Querying and Mining Strings Made Easy

KAUST Repository

Sahli, Majed

2017-10-13

With the advent of large string datasets in several scientific and business applications, there is a growing need to perform ad-hoc analysis on strings. Currently, strings are stored, managed, and queried using procedural codes. This limits users to certain operations supported by existing procedural applications and requires manual query planning with limited tuning opportunities. This paper presents StarQL, a generic and declarative query language for strings. StarQL is based on a native string data model that allows StarQL to support a large variety of string operations and provide semantic-based query optimization. String analytic queries are too intricate to be solved on one machine. Therefore, we propose a scalable and efficient data structure that allows StarQL implementations to handle large sets of strings and utilize large computing infrastructures. Our evaluation shows that StarQL is able to express workloads of application-specific tools, such as BLAST and KAT in bioinformatics, and to mine Wikipedia text for interesting patterns using declarative queries. Furthermore, the StarQL query optimizer shows an order of magnitude reduction in query execution time.

The application of XML in the effluents data modeling of nuclear facilities

International Nuclear Information System (INIS)

Yue Feng; Lin Quanyi; Yue Huiguo; Zhang Yan; Zhang Peng; Cao Jun; Chen Bo

2013-01-01

The radioactive effluent data, which can provide information to distinguish whether facilities, waste disposal, and control system run normally, is an important basis of safety regulation and emergency management. It can also provide the information to start emergency alarm system as soon as possible. XML technology is an effective tool to realize the standard of effluent data exchange, in favor of data collection, statistics and analysis, strengthening the effectiveness of effluent regulation. This paper first introduces the concept of XML, the choices of effluent data modeling method, and then emphasizes the process of effluent model, finally the model and application are shown, While there is deficiency about the application of XML in the effluents data modeling of nuclear facilities, it is a beneficial attempt to the informatization management of effluents. (authors)

Secure Skyline Queries on Cloud Platform.

Science.gov (United States)

Liu, Jinfei; Yang, Juncheng; Xiong, Li; Pei, Jian

2017-04-01

Outsourcing data and computation to cloud server provides a cost-effective way to support large scale data storage and query processing. However, due to security and privacy concerns, sensitive data (e.g., medical records) need to be protected from the cloud server and other unauthorized users. One approach is to outsource encrypted data to the cloud server and have the cloud server perform query processing on the encrypted data only. It remains a challenging task to support various queries over encrypted data in a secure and efficient way such that the cloud server does not gain any knowledge about the data, query, and query result. In this paper, we study the problem of secure skyline queries over encrypted data. The skyline query is particularly important for multi-criteria decision making but also presents significant challenges due to its complex computations. We propose a fully secure skyline query protocol on data encrypted using semantically-secure encryption. As a key subroutine, we present a new secure dominance protocol, which can be also used as a building block for other queries. Finally, we provide both serial and parallelized implementations and empirically study the protocols in terms of efficiency and scalability under different parameter settings, verifying the feasibility of our proposed solutions.

XML and its impact on content and structure in electronic health care documents.

Science.gov (United States)

Sokolowski, R.; Dudeck, J.

1999-01-01

Worldwide information networks have the requirement that electronic documents must be easily accessible, portable, flexible and system-independent. With the development of XML (eXtensible Markup Language), the future of electronic documents, health care informatics and the Web itself are about to change. The intent of the recently formed ASTM E31.25 subcommittee, "XML DTDs for Health Care", is to develop standard electronic document representations of paper-based health care documents and forms. A goal of the subcommittee is to work together to enhance existing levels of interoperability among the various XML/SGML standardization efforts, products and systems in health care. The ASTM E31.25 subcommittee uses common practices and software standards to develop the implementation recommendations for XML documents in health care. The implementation recommendations are being developed to standardize the many different structures of documents. These recommendations are in the form of a set of standard DTDs, or document type definitions that match the electronic document requirements in the health care industry. This paper discusses recent efforts of the ASTM E31.25 subcommittee. PMID:10566338

Type Checking with XML Schema in XACT

DEFF Research Database (Denmark)

Kirkegaard, Christian; Møller, Anders

to support XML Schema as type formalism. The technique is able to model advanced features, such as type derivations and overloaded local element declarations, and also datatypes of attribute values and character data. Moreover, we introduce optional type annotations to improve modularity of the type checking...

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

Science.gov (United States)

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 PubMed queries in particular for researchers whose first language is not English.

Value of XML in the implementation of clinical practice guidelines--the issue of content retrieval and presentation.

Science.gov (United States)

Hoelzer, S; Schweiger, R K; Boettcher, H A; Tafazzoli, A G; Dudeck, J

2001-01-01

that preserves the original cohesiveness. The lack of structure limits the automatic identification and extraction of the information contained in these resources. For this reason, we have chosen a document-based approach using eXtensible Markup Language (XML) with its schema definition and related technologies. XML empowers the applications for in-context searching. In addition it allows the same content to be represented in different ways. Our XML reference clinical data model for guidelines has been realized with the XML schema definition. The schema is used for structuring new text-based guidelines and updating existing documents. It is also used to establish search strategies on the document base. We hypothesize that enabling the physicians to query the available CPGs easily, and to get access to selected and specific information at the point of care will foster increased use. Based on current evidence we are confident that it will have substantial impact on the care provided, and will improve health outcomes.

The role of XML in the CMS detector description

International Nuclear Information System (INIS)

Liendl, M.; Lingen, F.van; Todorov, T.; Arce, P.; Furtjes, A.; Innocente, V.; Roeck, A. de; Case, M.

2001-01-01

Offline Software such as Simulation, Reconstruction, Analysis, and Visualisation are all in need of a detector description. These applications have several common but also many specific requirements for the detector description in order to build up their internal representations. To achieve this in a consistent and coherent manner a common source of information, the detector description database, will be consulted by each of the applications. The role and suitability of XML in the design of the detector description database in the scope of the CMS detector at the LHC is discussed. Different aspects such as data modelling capabilities of XML, tool support, integration to C++ representations of data models are treated and recent results of prototype implementations are presented

Multi-Dimensional Path Queries

DEFF Research Database (Denmark)

Bækgaard, Lars

1998-01-01

to create nested path structures. We present an SQL-like query language that is based on path expressions and we show how to use it to express multi-dimensional path queries that are suited for advanced data analysis in decision support environments like data warehousing environments......We present the path-relationship model that supports multi-dimensional data modeling and querying. A path-relationship database is composed of sets of paths and sets of relationships. A path is a sequence of related elements (atoms, paths, and sets of paths). A relationship is a binary path...

Learning via Query Synthesis

KAUST Repository

Alabdulmohsin, Ibrahim

2017-01-01

Active learning is a subfield of machine learning that has been successfully used in many applications. One of the main branches of active learning is query synthe- sis, where the learning agent constructs artificial queries from scratch in order

Truth Space Method for Caching Database Queries

Directory of Open Access Journals (Sweden)

S. V. Mosin

2015-01-01

Full Text Available We propose a new method of client-side data caching for relational databases with a central server and distant clients. Data are loaded into the client cache based on queries executed on the server. Every query has the corresponding DB table – the result of the query execution. These queries have a special form called "universal relational query" based on three fundamental Relational Algebra operations: selection, projection and natural join. We have to mention that such a form is the closest one to the natural language and the majority of database search queries can be expressed in this way. Besides, this form allows us to analyze query correctness by checking lossless join property. A subsequent query may be executed in a client’s local cache if we can determine that the query result is entirely contained in the cache. For this we compare truth spaces of the logical restrictions in a new user’s query and the results of the queries execution in the cache. Such a comparison can be performed analytically , without need in additional Database queries. This method may be used to define lacking data in the cache and execute the query on the server only for these data. To do this the analytical approach is also used, what distinguishes our paper from the existing technologies. We propose four theorems for testing the required conditions. The first and the third theorems conditions allow us to define the existence of required data in cache. The second and the fourth theorems state conditions to execute queries with cache only. The problem of cache data actualizations is not discussed in this paper. However, it can be solved by cataloging queries on the server and their serving by triggers in background mode. The article is published in the author’s wording.

Treating JSON as a subset of XML

NARCIS (Netherlands)

S. Pemberton (Steven)

2012-01-01

textabstractXForms 1.0 was an XML technology originally designed as a replacement for HTML Forms. In addressing certain shortcomings of XForms 1.0, the next version, XForms 1.1 became far more than a forms language, but a declarative application language where application production time could be

Enterprise Architecture Analysis with XML

OpenAIRE

Boer, Frank; Bonsangue, Marcello; Jacob, Joost; Stam, A.; Torre, Leon

2005-01-01

htmlabstractThis paper shows how XML can be used for static and dynamic analysis of architectures. Our analysis is based on the distinction between symbolic and semantic models of architectures. The core of a symbolic model consists of its signature that specifies symbolically its structural elements and their relationships. A semantic model is defined as a formal interpretation of the symbolic model. This provides a formal approach to the design of architectural description languages and a g...

The CostGlue XML Schema

OpenAIRE

Furfari, Francesco; Potort?, Francesco; Savić, Dragan

2008-01-01

An XML schema for scientific metadata is described. It is used for the CostGlue archival program, developed in the framework of the European Union COST Action 285: "Modelling and simulation tools for research in emerging multi-service telecommunications". The schema is freely available under the GNU LGPL license at http://wnet.isti.cnr.it/software/costglue/schema/2007/CostGlue.xsd, or at its official repository, at http://lt.fe.uni-lj. si/costglue/schema/2007/costglue.xsd.

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

Science.gov (United States)

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

2018-03-19

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

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

Science.gov (United States)

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

2018-01-01

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

Optimizing Temporal Queries: Efficient Handling of Duplicates

DEFF Research Database (Denmark)

Toman, David; Bowman, Ivan Thomas

2001-01-01

, these query languages are implemented by translating temporal queries into standard relational queries. However, the compiled queries are often quite cumbersome and expensive to execute even using state-of-the- art relational products. This paper presents an optimization technique that produces more efficient...... translated SQL queries by taking into account the properties of the encoding used for temporal attributes. For concreteness, this translation technique is presented in the context of SQL/TP; however, these techniques are also applicable to other temporal query languages....

An XML Based Knowledge Management System for e-Collaboration and e-Learning

Directory of Open Access Journals (Sweden)

Varun Gopalakrishna

2004-02-01

Full Text Available This paper presents the development, key features, and the implementation principles of a sustainable and scaleable knowledge management system (KMS prototype for creating, capturing, organizing, and managing digital information in the form of Extensible Markup Language (XML documents and other popular file formats. It is aimed to provide a platform for global, instant, and secure access to and dissemination of information within a knowledge-intensive organization or a cluster of organizations through Internet or intranet. A three-tier system architecture was chosen for the KMS to provide performance and scalability while enabling future development that supports global, secure, real-time, and multi-media communication of information and knowledge among team members separated by great distance. An XML Content Server has been employed in this work to store, index, and retrieve large volumes of XML and binary content.

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

Science.gov (United States)

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

2016-08-02

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

Pro PHP and jQuery

CERN Document Server

Lengstorf, Jason

2010-01-01

This book is for intermediate programmers interested in building AJAX web applications using jQuery and PHP. Along with teaching some advanced PHP techniques, it will teach you how to take your dynamic applications to the next level by adding a JavaScript layer with jQuery. * Learn to utilize built-in PHP functions to build calendar tools.* Learn how jQuery can be used for AJAX, animation, client-side validation, and more.What you'll learn* Use PHP to build a calendar application that allows users to post, view, edit, and delete events.* Use jQuery to allow the calendar app to be viewed and ed

Query recommendation for children

NARCIS (Netherlands)

Duarte Torres, Sergio; Hiemstra, Djoerd; Weber, Ingmar; Serdyukov, Pavel

2012-01-01

One of the biggest problems that children experience while searching the web occurs during the query formulation process. Children have been found to struggle formulating queries based on keywords given their limited vocabulary and their difficulty to choose the right keywords. In this work we

An XML-based loose-schema approach to managing diagnostic data in heterogeneous formats

Energy Technology Data Exchange (ETDEWEB)

Naito, O., E-mail: naito.osamu@jaea.go.j [Japan Atomic Energy Agency, 801-1 Mukouyama, Naka, Ibaraki 311-0193 (Japan)

2010-07-15

An approach to managing diagnostic data in heterogenous formats by using XML-based (eXtensible Markup Language) tag files is discussed. The tag file functions like header information in ordinary data formats but it is separate from the main body of data, human readable, and self-descriptive. Thus all the necessary information for reading the contents of data can be obtained without prior information or reading the data body itself. In this paper, modeling of diagnostic data and its representation in XML are studied and a very primitive implementation of this approach in C++ is presented. The overhead of manipulating XML in a proof-of-principle code was found to be small. The merits, demerits, and possible extensions of this approach are also discussed.

An XML-based loose-schema approach to managing diagnostic data in heterogeneous formats

International Nuclear Information System (INIS)

Naito, O.

2010-01-01

An approach to managing diagnostic data in heterogenous formats by using XML-based (eXtensible Markup Language) tag files is discussed. The tag file functions like header information in ordinary data formats but it is separate from the main body of data, human readable, and self-descriptive. Thus all the necessary information for reading the contents of data can be obtained without prior information or reading the data body itself. In this paper, modeling of diagnostic data and its representation in XML are studied and a very primitive implementation of this approach in C++ is presented. The overhead of manipulating XML in a proof-of-principle code was found to be small. The merits, demerits, and possible extensions of this approach are also discussed.

Interpreting XML documents via an RDF schema

NARCIS (Netherlands)

Klein, Michel; Handschuh, Siegfried; Staab, Steffen

2003-01-01

One of the major problems in the realization of the vision of the ``Semantic Web''; is the transformation of existing web data into sources that can be processed and used by machines. This paper presents a procedure that can be used to turn XML documents into knowledge structures, by interpreting

Exploring the field of public construction clients by a graphical network analysis

OpenAIRE

Eisma, P.R.; Volker, L.

2014-01-01

Because public construction clients form the majority of construction clients and procure over 40% of the construction output in most countries, they are important actors in the construction industry. Yet, the field of research on clients is still underdeveloped. In order to identify the research gaps in this field, a graphical network analysis of existing literature is performed. The analysis is based on a query executed in the scientific database Scopus resulting in around 3,300 publication...

Advanced Query and Data Mining Capabilities for MaROS

Science.gov (United States)

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

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

Towards Verbalizing SPARQL Queries in Arabic

Directory of Open Access Journals (Sweden)

I. Al Agha

2016-04-01

Full Text Available With the wide spread of Open Linked Data and Semantic Web technologies, a larger amount of data has been published on the Web in the RDF and OWL formats. This data can be queried using SPARQL, the Semantic Web Query Language. SPARQL cannot be understood by ordinary users and is not directly accessible to humans, and thus they will not be able to check whether the retrieved answers truly correspond to the intended information need. Driven by this challenge, natural language generation from SPARQL data has recently attracted a considerable attention. However, most existing solutions to verbalize SPARQL in natural language focused on English and Latin-based languages. Little effort has been made on the Arabic language which has different characteristics and morphology. This work aims to particularly help Arab users to perceive SPARQL queries on the Semantic Web by translating SPARQL to Arabic. It proposes an approach that gets a SPARQL query as an input and generates a query expressed in Arabic as an output. The translation process combines both morpho-syntactic analysis and language dependencies to generate a legible and understandable Arabic query. The approach was preliminary assessed with a sample query set, and results indicated that 75% of the queries were correctly translated into Arabic.

A Framework for WWW Query Processing

Science.gov (United States)

Wu, Binghui Helen; Wharton, Stephen (Technical Monitor)

2000-01-01

Query processing is the most common operation in a DBMS. Sophisticated query processing has been mainly targeted at a single enterprise environment providing centralized control over data and metadata. Submitting queries by anonymous users on the web is different in such a way that load balancing or DBMS' accessing control becomes the key issue. This paper provides a solution by introducing a framework for WWW query processing. The success of this framework lies in the utilization of query optimization techniques and the ontological approach. This methodology has proved to be cost effective at the NASA Goddard Space Flight Center Distributed Active Archive Center (GDAAC).

XML schemas for common bioinformatic data types and their application in workflow systems.

Science.gov (United States)

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-11-06

Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.

XML schemas for common bioinformatic data types and their application in workflow systems

Science.gov (United States)

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-01-01

Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at . Conclusion The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios. PMID:17087823

Learning via Query Synthesis

KAUST Repository

Alabdulmohsin, Ibrahim Mansour

2017-05-07

Active learning is a subfield of machine learning that has been successfully used in many applications. One of the main branches of active learning is query synthe- sis, where the learning agent constructs artificial queries from scratch in order to reveal sensitive information about the underlying decision boundary. It has found applications in areas, such as adversarial reverse engineering, automated science, and computational chemistry. Nevertheless, the existing literature on membership query synthesis has, generally, focused on finite concept classes or toy problems, with a limited extension to real-world applications. In this thesis, I develop two spectral algorithms for learning halfspaces via query synthesis. The first algorithm is a maximum-determinant convex optimization method while the second algorithm is a Markovian method that relies on Khachiyan’s classical update formulas for solving linear programs. The general theme of these methods is to construct an ellipsoidal approximation of the version space and to synthesize queries, afterward, via spectral decomposition. Moreover, I also describe how these algorithms can be extended to other settings as well, such as pool-based active learning. Having demonstrated that halfspaces can be learned quite efficiently via query synthesis, the second part of this thesis proposes strategies for mitigating the risk of reverse engineering in adversarial environments. One approach that can be used to render query synthesis algorithms ineffective is to implement a randomized response. In this thesis, I propose a semidefinite program (SDP) for learning a distribution of classifiers, subject to the constraint that any individual classifier picked at random from this distributions provides reliable predictions with a high probability. This algorithm is, then, justified both theoretically and empirically. A second approach is to use a non-parametric classification method, such as similarity-based classification. In this

jQuery Tools UI Library

CERN Document Server

Libby, Alex

2012-01-01

A practical tutorial with powerful yet simple projects that are quick to implement. This book is aimed at developers who have prior jQuery knowledge, but may not have any prior experience with jQuery Tools. It is possible that they may have started with the basics of jQuery Tools, but want to learn more about how it can be used, as well as get ideas for future projects.

Joint Top-K Spatial Keyword Query Processing

DEFF Research Database (Denmark)

Wu, Dingming; Yiu, Man Lung; Cong, Gao

2012-01-01

Web users and content are increasingly being geopositioned, and increased focus is being given to serving local content in response to web queries. This development calls for spatial keyword queries that take into account both the locations and textual descriptions of content. We study the effici......Web users and content are increasingly being geopositioned, and increased focus is being given to serving local content in response to web queries. This development calls for spatial keyword queries that take into account both the locations and textual descriptions of content. We study...... the efficient, joint processing of multiple top-k spatial keyword queries. Such joint processing is attractive during high query loads and also occurs when multiple queries are used to obfuscate a user's true query. We propose a novel algorithm and index structure for the joint processing of top-k spatial...... keyword queries. Empirical studies show that the proposed solution is efficient on real data sets. We also offer analytical studies on synthetic data sets to demonstrate the efficiency of the proposed solution. Index Terms IEEE Terms Electronic mail , Google , Indexes , Joints , Mobile communication...

Implementing XML Schema Naming and Design Rules

Energy Technology Data Exchange (ETDEWEB)

Lubell, Joshua [National Institute of Standards and Technology (NIST); Kulvatunyou, Boonserm [ORNL; Morris, Katherine [National Institute of Standards and Technology (NIST); Harvey, Betty [Electronic Commerce Connection, Inc.

2006-08-01

We are building a methodology and tool kit for encoding XML schema Naming and Design Rules (NDRs) in a computer-interpretable fashion, enabling automated rule enforcement and improving schema quality. Through our experience implementing rules from various NDR specifications, we discuss some issues and offer practical guidance to organizations grappling with NDR development.

A Simple XML Producer-Consumer Protocol

Science.gov (United States)

Smith, Warren; Gunter, Dan; Quesnel, Darcy; Biegel, Bryan (Technical Monitor)

2001-01-01

There are many different projects from government, academia, and industry that provide services for delivering events in distributed environments. The problem with these event services is that they are not general enough to support all uses and they speak different protocols so that they cannot interoperate. We require such interoperability when we, for example, wish to analyze the performance of an application in a distributed environment. Such an analysis might require performance information from the application, computer systems, networks, and scientific instruments. In this work we propose and evaluate a standard XML-based protocol for the transmission of events in distributed systems. One recent trend in government and academic research is the development and deployment of computational grids. Computational grids are large-scale distributed systems that typically consist of high-performance compute, storage, and networking resources. Examples of such computational grids are the DOE Science Grid, the NASA Information Power Grid (IPG), and the NSF Partnerships for Advanced Computing Infrastructure (PACIs). The major effort to deploy these grids is in the area of developing the software services to allow users to execute applications on these large and diverse sets of resources. These services include security, execution of remote applications, managing remote data, access to information about resources and services, and so on. There are several toolkits for providing these services such as Globus, Legion, and Condor. As part of these efforts to develop computational grids, the Global Grid Forum is working to standardize the protocols and APIs used by various grid services. This standardization will allow interoperability between the client and server software of the toolkits that are providing the grid services. The goal of the Performance Working Group of the Grid Forum is to standardize protocols and representations related to the storage and distribution of

78 FR 28732 - Revisions to Electric Quarterly Report Filing Process; Availability of Draft XML Schema

Science.gov (United States)

2013-05-16

...] Revisions to Electric Quarterly Report Filing Process; Availability of Draft XML Schema AGENCY: Federal... the SUPPLEMENTARY INFORMATION Section below for details. DATES: The XML is now available at the links mentioned below. FOR FURTHER INFORMATION CONTACT: Christina Switzer, Office of the General Counsel, Federal...

The realization of the storage of XML and middleware-based data of electronic medical records

International Nuclear Information System (INIS)

Liu Shuzhen; Gu Peidi; Luo Yanlin

2007-01-01

In this paper, using the technology of XML and middleware to design and implement a unified electronic medical records storage archive management system and giving a common storage management model. Using XML to describe the structure of electronic medical records, transform the medical data from traditional 'business-centered' medical information into a unified 'patient-centered' XML document and using middleware technology to shield the types of the databases at different departments of the hospital and to complete the information integration of the medical data which scattered in different databases, conducive to information sharing between different hospitals. (authors)

Semantic validation of standard-based electronic health record documents with W3C XML schema.

Science.gov (United States)

Rinner, C; Janzek-Hawlat, S; Sibinovic, S; Duftschmid, G

2010-01-01

The goal of this article is to examine whether W3C XML Schema provides a practicable solution for the semantic validation of standard-based electronic health record (EHR) documents. With semantic validation we mean that the EHR documents are checked for conformance with the underlying archetypes and reference model. We describe an approach that allows XML Schemas to be derived from archetypes based on a specific naming convention. The archetype constraints are augmented with additional components of the reference model within the XML Schema representation. A copy of the EHR document that is transformed according to the before-mentioned naming convention is used for the actual validation against the XML Schema. We tested our approach by semantically validating EHR documents conformant to three different ISO/EN 13606 archetypes respective to three sections of the CDA implementation guide "Continuity of Care Document (CCD)" and an implementation guide for diabetes therapy data. We further developed a tool to automate the different steps of our semantic validation approach. For two particular kinds of archetype prescriptions, individual transformations are required for the corresponding EHR documents. Otherwise, a fully generic validation is possible. In general, we consider W3C XML Schema as a practicable solution for the semantic validation of standard-based EHR documents.

Research Issues in Mobile Querying

DEFF Research Database (Denmark)

Breunig, M.; Jensen, Christian Søndergaard; Klein, M.

2004-01-01

This document reports on key aspects of the discussions conducted within the working group. In particular, the document aims to offer a structured and somewhat digested summary of the group's discussions. The document first offers concepts that enable characterization of "mobile queries" as well...... as the types of systems that enable such queries. It explores the notion of context in mobile queries. The document ends with a few observations, mainly regarding challenges....

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

Science.gov (United States)

Detter, Ryan; Mooney, Michael; Fatig, Curtis

2003-01-01

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

On tractable query evaluation for SPARQL

OpenAIRE

Mengel, Stefan; Skritek, Sebastian

2017-01-01

Despite much work within the last decade on foundational properties of SPARQL - the standard query language for RDF data - rather little is known about the exact limits of tractability for this language. In particular, this is the case for SPARQL queries that contain the OPTIONAL-operator, even though it is one of the most intensively studied features of SPARQL. The aim of our work is to provide a more thorough picture of tractable classes of SPARQL queries. In general, SPARQL query evaluatio...

Man vs. Machine: Differences in SPARQL Queries

NARCIS (Netherlands)

Rietveld, L.; Hoekstra, R.

2014-01-01

Server-side SPARQL query logs have been a topic of study for some time now. The USEWOD collection of query logs is currently the primary source of information for researchers. A recurring problem is that these logs leave application queries and queries created by humans indistinguishable. In this

How Good Are Query Optimizers, Really?

NARCIS (Netherlands)

Leis, Viktor; Gubichev, Andrey; Mirchev, Atanas; Boncz, Peter; Kemper, Alfons; Neumann, Thomas

2016-01-01

Finding a good join order is crucial for query performance. In this paper, we introduce the Join Order Benchmark (JOB) and experimentally revisit the main components in the classic query optimizer architecture using a complex, real-world data set and realistic multi-join queries. We investigate the

The appropriateness of XML for diagnostic description

Energy Technology Data Exchange (ETDEWEB)

Neto, A. [Associacao Euratom/IST, Centro de Fusao Nuclear, Av. Rovisco Pais, P-1049-001 Lisboa (Portugal)], E-mail: andre.neto@cfn.ist.utl.pt; Lister, J.B. [CRPP-EPFL, Association EURATOM-Confederation Suisse, 1015 Lausanne (Switzerland); Fernandes, H. [Associacao Euratom/IST, Centro de Fusao Nuclear, Av. Rovisco Pais, P-1049-001 Lisboa (Portugal); Yonekawa, I. [JAEA, Japan Atomic Energy Agency Naka (Japan); Varandas, C.A.F. [Associacao Euratom/IST, Centro de Fusao Nuclear, Av. Rovisco Pais, P-1049-001 Lisboa (Portugal)

2007-10-15

A standard for the self-description of fusion plasma diagnostics will be required in the near future. The motivation is to maintain and organize the information on all the components of a laboratory experiment, from the hardware to the access security, to save time and money. Since there is no existing standard to organize this kind of information, every EU Association stores and organizes each experiment in different ways. This can lead to severe problems when the particular organization schema is poorly documented. Standardization is the key to solve these problems. From the commercial information on the diagnostic (component supplier; component price) to the hardware description (component specifications; drawings) to the operation of the equipment (finite state machines) through change control (who changed what and when) and internationalization (information at least in English and a local language). This problem will be met on the ITER project, for which a solution is essential. A strong candidate solution is the Extensible Markup Language (XML). In this paper, a review of the current status of XML related technologies will be presented.

The appropriateness of XML for diagnostic description

International Nuclear Information System (INIS)

Neto, A.; Lister, J.B.; Fernandes, H.; Yonekawa, I.; Varandas, C.A.F.

2007-01-01

A standard for the self-description of fusion plasma diagnostics will be required in the near future. The motivation is to maintain and organize the information on all the components of a laboratory experiment, from the hardware to the access security, to save time and money. Since there is no existing standard to organize this kind of information, every EU Association stores and organizes each experiment in different ways. This can lead to severe problems when the particular organization schema is poorly documented. Standardization is the key to solve these problems. From the commercial information on the diagnostic (component supplier; component price) to the hardware description (component specifications; drawings) to the operation of the equipment (finite state machines) through change control (who changed what and when) and internationalization (information at least in English and a local language). This problem will be met on the ITER project, for which a solution is essential. A strong candidate solution is the Extensible Markup Language (XML). In this paper, a review of the current status of XML related technologies will be presented

Cytometry metadata in XML

Science.gov (United States)

Leif, Robert C.; Leif, Stephanie H.

2016-04-01

Introduction: The International Society for Advancement of Cytometry (ISAC) has created a standard for the Minimum Information about a Flow Cytometry Experiment (MIFlowCyt 1.0). CytometryML will serve as a common metadata standard for flow and image cytometry (digital microscopy). Methods: The MIFlowCyt data-types were created, as is the rest of CytometryML, in the XML Schema Definition Language (XSD1.1). The datatypes are primarily based on the Flow Cytometry and the Digital Imaging and Communication (DICOM) standards. A small section of the code was formatted with standard HTML formatting elements (p, h1, h2, etc.). Results:1) The part of MIFlowCyt that describes the Experimental Overview including the specimen and substantial parts of several other major elements has been implemented as CytometryML XML schemas (www.cytometryml.org). 2) The feasibility of using MIFlowCyt to provide the combination of an overview, table of contents, and/or an index of a scientific paper or a report has been demonstrated. Previously, a sample electronic publication, EPUB, was created that could contain both MIFlowCyt metadata as well as the binary data. Conclusions: The use of CytometryML technology together with XHTML5 and CSS permits the metadata to be directly formatted and together with the binary data to be stored in an EPUB container. This will facilitate: formatting, data- mining, presentation, data verification, and inclusion in structured research, clinical, and regulatory documents, as well as demonstrate a publication's adherence to the MIFlowCyt standard, promote interoperability and should also result in the textual and numeric data being published using web technology without any change in composition.

XML for Detector Description at GLAST

Energy Technology Data Exchange (ETDEWEB)

Bogart, Joanne

2002-04-30

The problem of representing a detector in a form which is accessible to a variety of applications, allows retrieval of information in ways which are natural to those applications, and is maintainable has been vexing physicists for some time. Although invented to address an entirely different problem domain, the document markup meta-language XML is well-suited to detector description. This paper describes its use for a GLAST detector.

XML for detector description at GLAST

International Nuclear Information System (INIS)

Bogart, J.; Favretto, D.; Giannitrapani, R.

2001-01-01

The problem of representing a detector in a form which is accessible to a variety of applications, allows retrieval of information in ways which are natural to those applications, and is maintainable has been vexing physicists for some time. Although invented to address an entirely different problem domain, the document markup meta-language XML is well-suited to detector description. The author describes its use for a GLAST detector

XML for Detector Description at GLAST

International Nuclear Information System (INIS)

Bogart, Joanne

2002-01-01

The problem of representing a detector in a form which is accessible to a variety of applications, allows retrieval of information in ways which are natural to those applications, and is maintainable has been vexing physicists for some time. Although invented to address an entirely different problem domain, the document markup meta-language XML is well-suited to detector description. This paper describes its use for a GLAST detector

Superfund Query

Data.gov (United States)

U.S. Environmental Protection Agency — The Superfund Query allows users to retrieve data from the Comprehensive Environmental Response, Compensation, and Liability Information System (CERCLIS) database.

Optimizing queries in distributed systems

Directory of Open Access Journals (Sweden)

Ion LUNGU

2006-01-01

Full Text Available This research presents the main elements of query optimizations in distributed systems. First, data architecture according with system level architecture in a distributed environment is presented. Then the architecture of a distributed database management system (DDBMS is described on conceptual level followed by the presentation of the distributed query execution steps on these information systems. The research ends with presentation of some aspects of distributed database query optimization and strategies used for that.

Advanced Query Formulation in Deductive Databases.

Science.gov (United States)

Niemi, Timo; Jarvelin, Kalervo

1992-01-01

Discusses deductive databases and database management systems (DBMS) and introduces a framework for advanced query formulation for end users. Recursive processing is described, a sample extensional database is presented, query types are explained, and criteria for advanced query formulation from the end user's viewpoint are examined. (31…

XML/TEI Stand-off Markup. One step beyond.

NARCIS (Netherlands)

Spadini, E.; Turska, Magdalena

2018-01-01

Stand-off markup is widely considered as a possible solution for overcoming the limitation of inline XML markup, primarily dealing with multiple overlapping hierarchies. Considering previous contributions on the subject and implementations of stand-off markup, we propose a new TEI-based model for

LINQ The Future of Data Access in C# 30

CERN Document Server

Hummel, Joe

2006-01-01

Language Integrated Query (LINQ) is Microsoft's new technology for powerful, general purpose data access. This technology provides a fully-integrated query language, available in both C# 3.0 and VB 9.0, for high-level data access against objects, relational databases, and XML documents. In this Short Cut you'll learn about LINQ and the proposed C# 3.0 extensions that support it. You'll also see how you can use LINQ and C# to accomplish a variety of tasks, from querying objects to accessing relational data and XML. Best of all, you'll be able to test the examples and run your own code using t

Dynamic Planar Range Maxima Queries

DEFF Research Database (Denmark)

Brodal, Gerth Stølting; Tsakalidis, Konstantinos

2011-01-01

We consider the dynamic two-dimensional maxima query problem. Let P be a set of n points in the plane. A point is maximal if it is not dominated by any other point in P. We describe two data structures that support the reporting of the t maximal points that dominate a given query point, and allow...... for insertions and deletions of points in P. In the pointer machine model we present a linear space data structure with O(logn + t) worst case query time and O(logn) worst case update time. This is the first dynamic data structure for the planar maxima dominance query problem that achieves these bounds...... are integers in the range U = {0, …,2 w  − 1 }. We present a linear space data structure that supports 3-sided range maxima queries in O(logn/loglogn+t) worst case time and updates in O(logn/loglogn) worst case time. These are the first sublogarithmic worst case bounds for all operations in the RAM model....

Comparing Emerging XML Based Formats from a Multi-discipline Perspective

Science.gov (United States)

Sawyer, D. M.; Reich, L. I.; Nikhinson, S.

2002-12-01

This paper analyzes the similarity and differences among several examples of an emerging generation of Scientific Data Formats that are based on XML technologies. Some of the factors evaluated include the goals of these efforts, the data models, and XML technologies used, and the maturity of currently available software. This paper then investigates the practicality of developing a single set of structural data objects and basic scientific concepts, such as units, that could be used across discipline boundaries and extended by disciplines and missions to create Scientific Data Formats for their communities. This analysis is partly based on an effort sponsored by the ESDIS office at GSFC to compare the Earth Science Markup Language (ESML) and the eXtensible Data Format( XDF), two members of this new generation of XML based Data Description Languages that have been developed by NASA funded efforts in recent years. This paper adds FITSML and potentially CDFML to the list of XML based Scientific Data Formats discussed. This paper draws heavily a Formats Evolution Process Committee (http://ssdoo.gsfc.nasa.gov/nost/fep/) draft white paper primarily developed by Lou Reich, Mike Folk and Don Sawyer to assist the Space Science community in understanding Scientific Data Formats. One of primary conclusions of that paper is that a scientific data format object model should be examined along two basic axes. The first is the complexity of the computer/mathematical data types supported and the second is the level of scientific domain specialization incorporated. This paper also discusses several of the issues that affect the decision on whether to implement a discipline or project specific Scientific Data Format as a formal extension of a general purpose Scientific Data Format or to implement the APIs independently.

Towards P2P XML Database Technology

NARCIS (Netherlands)

Y. Zhang (Ying)

2007-01-01

textabstractTo ease the development of data-intensive P2P applications, we envision a P2P XML Database Management System (P2P XDBMS) that acts as a database middle-ware, providing a uniform database abstraction on top of a dynamic set of distributed data sources. In this PhD work, we research which

Standardization of XML Database Exchanges and the James Webb Space Telescope Experience

Science.gov (United States)

Gal-Edd, Jonathan; Detter, Ryan; Jones, Ron; Fatig, Curtis C.

2007-01-01

Personnel from the National Aeronautics and Space Administration (NASA) James Webb Space Telescope (JWST) Project have been working with various standard communities such the Object Management Group (OMG) and the Consultative Committee for Space Data Systems (CCSDS) to assist in the definition of a common extensible Markup Language (XML) for database exchange format. The CCSDS and OMG standards are intended for the exchange of core command and telemetry information, not for all database information needed to exercise a NASA space mission. The mission-specific database, containing all the information needed for a space mission, is translated from/to the standard using a translator. The standard is meant to provide a system that encompasses 90% of the information needed for command and telemetry processing. This paper will discuss standardization of the XML database exchange format, tools used, and the JWST experience, as well as future work with XML standard groups both commercial and government.

Nearest Neighbor Queries in Road Networks

DEFF Research Database (Denmark)

Jensen, Christian Søndergaard; Kolar, Jan; Pedersen, Torben Bach

2003-01-01

in road networks. Such queries may be of use in many services. Specifically, we present an easily implementable data model that serves well as a foundation for such queries. We also present the design of a prototype system that implements the queries based on the data model. The algorithm used...

Fingerprinting Keywords in Search Queries over Tor

Directory of Open Access Journals (Sweden)

Oh Se Eun

2017-10-01

Full Text Available Search engine queries contain a great deal of private and potentially compromising information about users. One technique to prevent search engines from identifying the source of a query, and Internet service providers (ISPs from identifying the contents of queries is to query the search engine over an anonymous network such as Tor.

Adding Query Privacy to Robust DHTs

DEFF Research Database (Denmark)

Backes, Michael; Goldberg, Ian; Kate, Aniket

2011-01-01

intermediate peers that (help to) route the queries towards their destinations. In this paper, we satisfy this requirement by presenting an approach for providing privacy for the keys in DHT queries. We use the concept of oblivious transfer (OT) in communication over DHTs to preserve query privacy without...... of obtaining query privacy over robust DHTs. Finally, we compare the performance of our privacy-preserving protocols with their more privacy-invasive counterparts. We observe that there is no increase in the message complexity and only a small overhead in the computational complexity....

QUERY SUPPORT FOR GMZ

Directory of Open Access Journals (Sweden)

A. Khandelwal

2017-07-01

Full Text Available Generic text-based compression models are simple and fast but there are two issues that needs to be addressed. They cannot leverage the structure that exists in data to achieve better compression and there is an unnecessary decompression step before the user can actually use the data. To address these issues, we came up with GMZ, a lossless compression model aimed at achieving high compression ratios. The decision to design GMZ (Khandelwal and Rajan, 2017 exclusively for GML's Simple Features Profile (SFP seems fair because of the high use of SFP in WFS and that it facilitates high optimisation of the compression model. This is an extension of our work on GMZ. In a typical server-client model such as Web Feature Service, the server is the primary creator and provider of GML, and therefore, requires compression and query capabilities. On the other hand, the client is the primary consumer of GML, and therefore, requires decompression and visualisation capabilities. In the first part of our work, we demonstrated compression using a python script that can be plugged in a server architecture, and decompression and visualisation in a web browser using a Firefox addon. The focus of this work is to develop the already existing tools to provide query capability to server. Our model provides the ability to decompress individual features in isolation, which is an essential requirement for realising query in compressed state. We con - struct an R-Tree index for spatial data and a custom index for non-spatial data and store these in a separate index file to prevent alter - ing the compression model. This facilitates independent use of compressed GMZ file where index can be constructed when required. The focus of this work is the bounding-box or range query commonly used in webGIS with provision for other spatial and non-spatial queries. The decrement in compression ratios due to the new index file is in the range of 1–3 percent which is trivial considering

Ranking Queries on Uncertain Data

CERN Document Server

Hua, Ming

2011-01-01

Uncertain data is inherent in many important applications, such as environmental surveillance, market analysis, and quantitative economics research. Due to the importance of those applications and rapidly increasing amounts of uncertain data collected and accumulated, analyzing large collections of uncertain data has become an important task. Ranking queries (also known as top-k queries) are often natural and useful in analyzing uncertain data. Ranking Queries on Uncertain Data discusses the motivations/applications, challenging problems, the fundamental principles, and the evaluation algorith

Recommendation Sets and Choice Queries

DEFF Research Database (Denmark)

Viappiani, Paolo Renato; Boutilier, Craig

2011-01-01

Utility elicitation is an important component of many applications, such as decision support systems and recommender systems. Such systems query users about their preferences and offer recommendations based on the system's belief about the user's utility function. We analyze the connection between...... the problem of generating optimal recommendation sets and the problem of generating optimal choice queries, considering both Bayesian and regret-based elicitation. Our results show that, somewhat surprisingly, under very general circumstances, the optimal recommendation set coincides with the optimal query....

Predecessor queries in dynamic integer sets

DEFF Research Database (Denmark)

Brodal, Gerth Stølting

1997-01-01

We consider the problem of maintaining a set of n integers in the range 0.2w–1 under the operations of insertion, deletion, predecessor queries, minimum queries and maximum queries on a unit cost RAM with word size w bits. Let f (n) be an arbitrary nondecreasing smooth function satisfying n...

Flexible Query Answering Systems 2006

DEFF Research Database (Denmark)

-computer interaction. The overall theme of the FQAS conferences is innovative query systems aimed at providing easy, flexible, and intuitive access to information. Such systems are intended to facilitate retrieval from information repositories such as databases, libraries, and the World-Wide Web. These repositories......This volume constitutes the proceedings of the Seventh International Conference on Flexible Query Answering Systems, FQAS 2006, held in Milan, Italy, on June 7--10, 2006. FQAS is the premier conference for researchers and practitioners concerned with the vital task of providing easy, flexible...... are typically equipped with standard query systems which are often inadequate, and the focus of FQAS is the development of query systems that are more expressive, informative, cooperative, and productive. These proceedings contain contributions from invited speakers and 53 original papers out of about 100...

WaterML: an XML Language for Communicating Water Observations Data

Science.gov (United States)

Maidment, D. R.; Zaslavsky, I.; Valentine, D.

2007-12-01

One of the great impediments to the synthesis of water information is the plethora of formats used to publish such data. Each water agency uses its own approach. XML (eXtended Markup Languages) are generalizations of Hypertext Markup Language to communicate specific kinds of information via the internet. WaterML is an XML language for water observations data - streamflow, water quality, groundwater levels, climate, precipitation and aquatic biology data, recorded at fixed, point locations as a function of time. The Hydrologic Information System project of the Consortium of Universities for the Advancement of Hydrologic Science, Inc (CUAHSI) has defined WaterML and prepared a set of web service functions called WaterOneFLow that use WaterML to provide information about observation sites, the variables measured there and the values of those measurments. WaterML has been submitted to the Open GIS Consortium for harmonization with its standards for XML languages. Academic investigators at a number of testbed locations in the WATERS network are providing data in WaterML format using WaterOneFlow web services. The USGS and other federal agencies are also working with CUAHSI to similarly provide access to their data in WaterML through WaterOneFlow services.

Spatio-temporal databases complex motion pattern queries

CERN Document Server

Vieira, Marcos R

2013-01-01

This brief presents several new query processing techniques, called complex motion pattern queries, specifically designed for very large spatio-temporal databases of moving objects. The brief begins with the definition of flexible pattern queries, which are powerful because of the integration of variables and motion patterns. This is followed by a summary of the expressive power of patterns and flexibility of pattern queries. The brief then present the Spatio-Temporal Pattern System (STPS) and density-based pattern queries. STPS databases contain millions of records with information about mobi

XML Schema of PaGE-OM: page-om.xsd [

Lifescience Database Archive (English)

Full Text Available one or more variation assays (e.g. assay multiplexing Assay_set). Note: These are optional laboratory specif...fication is used for data exchange formats (e.g. xml-schema). Therefore, it has optional direct associations

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

Directory of Open Access Journals (Sweden)

Toni U Wagner

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

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

Science.gov (United States)

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

2011-01-01

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

Multi-Dimensional Top-k Dominating Queries

DEFF Research Database (Denmark)

Yiu, Man Lung; Mamoulis, Nikos

2009-01-01

The top-k dominating query returns k data objects which dominate the highest number of objects in a dataset. This query is an important tool for decision support since it provides data analysts an intuitive way for finding significant objects. In addition, it combines the advantages of top......-k and skyline queries without sharing their disadvantages: (i) the output size can be controlled, (ii) no ranking functions need to be specified by users, and (iii) the result is independent of the scales at different dimensions. Despite their importance, top-k dominating queries have not received adequate...

Query optimization over crowdsourced data

KAUST Repository

Park, Hyunjung; Widom, Jennifer

2013-01-01

Deco is a comprehensive system for answering declarative queries posed over stored relational data together with data obtained on-demand from the crowd. In this paper we describe Deco's cost-based query optimizer, building on Deco's data model

Query Optimizations over Decentralized RDF Graphs

KAUST Repository

Abdelaziz, Ibrahim

2017-05-18

Applications in life sciences, decentralized social networks, Internet of Things, and statistical linked dataspaces integrate data from multiple decentralized RDF graphs via SPARQL queries. Several approaches have been proposed to optimize query processing over a small number of heterogeneous data sources by utilizing schema information. In the case of schema similarity and interlinks among sources, these approaches cause unnecessary data retrieval and communication, leading to poor scalability and response time. This paper addresses these limitations and presents Lusail, a system for scalable and efficient SPARQL query processing over decentralized graphs. Lusail achieves scalability and low query response time through various optimizations at compile and run times. At compile time, we use a novel locality-aware query decomposition technique that maximizes the number of query triple patterns sent together to a source based on the actual location of the instances satisfying these triple patterns. At run time, we use selectivity-awareness and parallel query execution to reduce network latency and to increase parallelism by delaying the execution of subqueries expected to return large results. We evaluate Lusail using real and synthetic benchmarks, with data sizes up to billions of triples on an in-house cluster and a public cloud. We show that Lusail outperforms state-of-the-art systems by orders of magnitude in terms of scalability and response time.

jQuery UI 1.10 the user interface library for jQuery

CERN Document Server

Libby, Alex

2013-01-01

This book consists of an easy-to-follow, example-based approach that leads you step-by-step through the implementation and customization of each library component.This book is for frontend designers and developers who need to learn how to use jQuery UI quickly. To get the most out of this book, you should have a good working knowledge of HTML, CSS, and JavaScript, and should ideally be comfortable using jQuery.

Optimal Planar Orthogonal Skyline Counting Queries

DEFF Research Database (Denmark)

Brodal, Gerth Stølting; Larsen, Kasper Green

2014-01-01

counting queries, i.e. given a query rectangle R to report the size of the skyline of P\\cap R. We present a data structure for storing n points with integer coordinates having query time O(lg n/lglg n) and space usage O(n). The model of computation is a unit cost RAM with logarithmic word size. We prove...

XML for nuclear instrument control and monitoring: an approach towards standardisation

International Nuclear Information System (INIS)

Bharade, S.K.; Ananthakrishnan, T.S.; Kataria, S.K.; Singh, S.K.

2004-01-01

Communication among heterogeneous system with applications running under different operating systems and applications developed under different platforms has undergone rapid changes due to the adoption of XML standards. These are being developed for different industries like Chemical, Medical, Commercial etc. The High Energy Physics community has already a standard for exchange of data among different applications , under heterogeneous distributed systems like the CMS Data Acquisition System. There are a large number of Nuclear Instruments supplied by different manufactures which are increasingly getting connected. This approach is getting wider acceptance in instruments at reactor sites, accelerator sites and complex nuclear experiments -especially at centres like CERN. In order for these instruments to be able to describe the data which is available from them in a platform independent manner XML approach has been developed. This paper is the first attempt at Electronics Division for proposing an XML standard for control, monitoring, Data Acquisition and Analysis generated by Nuclear Instruments at Accelerator sites, Nuclear Reactor plant and Laboratory. The gamut of Nuclear Instruments include Multichannel Analysers, Health Physics Instruments, Accelerator Control Systems, Reactor Regulating systems, Flux mapping Systems etc. (author)

Printing--Graphic Arts--Graphic Communications

Science.gov (United States)

Hauenstein, A. Dean

1975-01-01

Recently, "graphic arts" has shifted from printing skills to a conceptual approach of production processes. "Graphic communications" must embrace the total system of communication through graphic media, to serve broad career education purposes; students taught concepts and principles can be flexible and adaptive. The author…

PFTijah: text search in an XML database system

NARCIS (Netherlands)

Hiemstra, Djoerd; Rode, H.; van Os, R.; Flokstra, Jan

2006-01-01

This paper introduces the PFTijah system, a text search system that is integrated with an XML/XQuery database management system. We present examples of its use, we explain some of the system internals, and discuss plans for future work. PFTijah is part of the open source release of MonetDB/XQuery.

A conceptual basis to encode and detect organic functional groups in XML.

Science.gov (United States)

Sankar, Punnaivanam; Krief, Alain; Vijayasarathi, Durairaj

2013-06-01

A conceptual basis to define and detect organic functional groups is developed. The basic model of a functional group is termed as a primary functional group and is characterized by a group center composed of one or more group center atoms bonded to terminal atoms and skeletal carbon atoms. The generic group center patterns are identified from the structures of known functional groups. Accordingly, a chemical ontology 'Font' is developed to organize the existing functional groups as well as the new ones to be defined by the chemists. The basic model is extended to accommodate various combinations of primary functional groups as functional group assemblies. A concept of skeletal group is proposed to define the characteristic groups composed of only carbon atoms to be regarded as equivalent to functional groups. The combination of primary functional groups with skeletal groups is categorized as skeletal group assembly. In order to make the model suitable for reaction modeling purpose, a Graphical User Interface (GUI) is developed to define the functional groups and to encode in XML format appropriate to detect them in chemical structures. The system is capable of detecting multiple instances of primary functional groups as well as the overlapping poly-functional groups as the respective assemblies. Copyright © 2013 Elsevier Inc. All rights reserved.

A Novel Approach for Configuring The Stimulator of A BCI Framework Using XML

Directory of Open Access Journals (Sweden)

Indar Sugiarto

2009-08-01

Full Text Available In a working BCI framework, all aspects must be considered as an integral part that contributes to the successful operation of a BCI system. This also includes the development of robust but flexible stimulator, especially the one that closely related to the feedback of a BCI system. This paper describes a novel approach in providing flexible visual stimulator using XML which has been applied for a BCI (brain-computer interface framework. Using XML file format for configuring the visual stimulator of a BCI system, we can develop BCI applications which can accommodate many experiment strategies in BCI research. The BCI framework and its configuration platform is developed using C++ programming language which incorporate Qt’s most powerful XML parser named QXmlStream. The implementation and experiment shows that the XML configuration file can be well executed within the proposed BCI framework. Beside its capability in presenting flexible flickering frequencies and text formatting for SSVEP-based BCI, the configuration platform also provides 3 shapes, 16 colors, and 5 distinct feedback bars. It is not necessary to increase the number of shapes nor colors since those parameters are less important for the BCI stimulator. The proposed method can then be extended to enhance the usability of currently existed BCI framework such as BF++ Toys and BCI 2000.

PAQ: Persistent Adaptive Query Middleware for Dynamic Environments

Science.gov (United States)

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

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

Pareto-depth for multiple-query image retrieval.

Science.gov (United States)

Hsiao, Ko-Jen; Calder, Jeff; Hero, Alfred O

2015-02-01

Most content-based image retrieval systems consider either one single query, or multiple queries that include the same object or represent the same semantic information. In this paper, we consider the content-based image retrieval problem for multiple query images corresponding to different image semantics. We propose a novel multiple-query information retrieval algorithm that combines the Pareto front method with efficient manifold ranking. We show that our proposed algorithm outperforms state of the art multiple-query retrieval algorithms on real-world image databases. We attribute this performance improvement to concavity properties of the Pareto fronts, and prove a theoretical result that characterizes the asymptotic concavity of the fronts.

QUERY RESPONSE TIME COMPARISON NOSQLDB MONGODB WITH SQLDB ORACLE

Directory of Open Access Journals (Sweden)

Humasak T. A. Simanjuntak

2015-01-01

Full Text Available Penyimpanan data saat ini terdapat dua jenis yakni relational database dan non-relational database. Kedua jenis DBMS (Database Managemnet System tersebut berbeda dalam berbagai aspek seperti per-formansi eksekusi query, scalability, reliability maupun struktur penyimpanan data. Kajian ini memiliki tujuan untuk mengetahui perbandingan performansi DBMS antara Oracle sebagai jenis relational data-base dan MongoDB sebagai jenis non-relational database dalam mengolah data terstruktur. Eksperimen dilakukan untuk mengetahui perbandingan performansi kedua DBMS tersebut untuk operasi insert, select, update dan delete dengan menggunakan query sederhana maupun kompleks pada database Northwind. Untuk mencapai tujuan eksperimen, 18 query yang terdiri dari 2 insert query, 10 select query, 2 update query dan 2 delete query dieksekusi. Query dieksekusi melalui sebuah aplikasi .Net yang dibangun sebagai perantara antara user dengan basis data. Eksperimen dilakukan pada tabel dengan atau tanpa relasi pada Oracle dan embedded atau bukan embedded dokumen pada MongoDB. Response time untuk setiap eksekusi query dibandingkan dengan menggunakan metode statistik. Eksperimen menunjukkan response time query untuk proses select, insert, dan update pada MongoDB lebih cepatdaripada Oracle. MongoDB lebih cepat 64.8 % untuk select query;MongoDB lebihcepat 72.8 % untuk insert query dan MongoDB lebih cepat 33.9 % untuk update query. Pada delete query, Oracle lebih cepat 96.8 % daripada MongoDB untuk table yang berelasi, tetapi MongoDB lebih cepat 83.8 % daripada Oracle untuk table yang tidak memiliki relasi.Untuk query kompleks dengan Map Reduce pada MongoDB lebih lambat 97.6% daripada kompleks query dengan aggregate function pada Oracle.

Learning jQuery

CERN Document Server

Chaffer, Jonathan

2013-01-01

Step through each of the core concepts of the jQuery library, building an overall picture of its capabilities. Once you have thoroughly covered the basics, the book returns to each concept to cover more advanced examples and techniques.This book is for web designers who want to create interactive elements for their designs, and for developers who want to create the best user interface for their web applications. Basic JavaScript programming and knowledge of HTML and CSS is required. No knowledge of jQuery is assumed, nor is experience with any other JavaScript libraries.

Knowledge Query Language (KQL)

Science.gov (United States)

2016-02-12

described as a sparse, distributed multidimensional sorted map. Unlike a relational database , BigTable has no multicolumn primary keys or constraints. The...in query languages such as SQL. Figure 3. Address expression-based querying. Each circled step in Figure 3 is described below. Datastore/ Database ...implementation we describe in later sections stores the instance of registry ontology in JSON files. 7 Throughout the rest of this report, we use the

Knowledge-based systems and interactive graphics for reactor control using the Automated Reasoning Tool(ART) system

International Nuclear Information System (INIS)

Ragheb, M.; Clayton, B.; Davies, P.

1987-01-01

The use of Knowledge-Based systems and advanced graphic concepts are described using the Automated Reasoning Tool (ART) for a model nuclear plant system. Through the sue of asynchronous graphic input/output, the user is allowed to communicate through a graphical display to a Production-Rule Analysis System modelling the plant while its rules are actively being fired. The user changes the status of system components by pointing at them on the system configuration display with a mouse cursor and clicking one of the buttons on the mouse. The Production-Rule Analysis System accepts the new input and immediately displays its diagnosis of the system state and any associated recommendations as to the appropriate course of action. This approach offers a distinct advantage over typing the components statuses in response to queries by a conventional Production-Rule Analysis system. Moreover, two effective ways of communication between man and machine are combined

Enhancing Recall in Semantic Querying

DEFF Research Database (Denmark)

Rouces, Jacobo

2013-01-01

lexically and structurally different, which we will introduce in the next section. As RDF graphs from different sources are expected to be linked, the modeling heterogeneities will make the federated graph become sparser and inconsistent. This is detrimental to the recall of SPARQL queries, as the query...

Semi-automated XML markup of biosystematic legacy literature with the GoldenGATE editor.

Science.gov (United States)

Sautter, Guido; Böhm, Klemens; Agosti, Donat

2007-01-01

Today, digitization of legacy literature is a big issue. This also applies to the domain of biosystematics, where this process has just started. Digitized biosystematics literature requires a very precise and fine grained markup in order to be useful for detailed search, data linkage and mining. However, manual markup on sentence level and below is cumbersome and time consuming. In this paper, we present and evaluate the GoldenGATE editor, which is designed for the special needs of marking up OCR output with XML. It is built in order to support the user in this process as far as possible: Its functionality ranges from easy, intuitive tagging through markup conversion to dynamic binding of configurable plug-ins provided by third parties. Our evaluation shows that marking up an OCR document using GoldenGATE is three to four times faster than with an off-the-shelf XML editor like XML-Spy. Using domain-specific NLP-based plug-ins, these numbers are even higher.

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank.

Science.gov (United States)

Sehnal, David; Pravda, Lukáš; Svobodová Vařeková, Radka; Ionescu, Crina-Maria; Koča, Jaroslav

2015-07-01

Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a unique query language with Python-like syntax to define the patterns that will be extracted from datasets provided by the user, or from the entire Protein Data Bank (PDB). Moreover, the database-wide search can be restricted using a variety of criteria, such as PDB ID, resolution, and organism of origin, to provide only relevant data. The extraction generally takes a few seconds for several hundreds of entries, up to approximately one hour for the whole PDB. The detected patterns are made available for download to enable further processing, as well as presented in a clear tabular and graphical form directly in the browser. The unique design of the language and the provided service could pave the way towards novel PDB-wide analyses, which were either difficult or unfeasible in the past. The application is available free of charge at http://ncbr.muni.cz/PatternQuery. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Location-Dependent Query Processing Under Soft Real-Time Constraints

Directory of Open Access Journals (Sweden)

Zoubir Mammeri

2009-01-01

Full Text Available In recent years, mobile devices and applications achieved an increasing development. In database field, this development required methods to consider new query types like location-dependent queries (i.e. the query results depend on the query issuer location. Although several researches addressed problems related to location-dependent query processing, a few works considered timing requirements that may be associated with queries (i.e., the query results must be delivered to mobile clients on time. The main objective of this paper is to propose a solution for location-dependent query processing under soft real-time constraints. Hence, we propose methods to take into account client location-dependency and to maximize the percentage of queries respecting their deadlines. We validate our proposal by implementing a prototype based on Oracle DBMS. Performance evaluation results show that the proposed solution optimizes the percentage of queries meeting their deadlines and the communication cost.

SCRY: Enabling quantitative reasoning in SPARQL queries

NARCIS (Netherlands)

Meroño-Peñuela, A.; Stringer, Bas; Loizou, Antonis; Abeln, Sanne; Heringa, Jaap

2015-01-01

The inability to include quantitative reasoning in SPARQL queries slows down the application of Semantic Web technology in the life sciences. SCRY, our SPARQL compatible service layer, improves this by executing services at query time and making their outputs query-accessible, generating RDF data on

Answering SPARQL queries modulo RDF Schema with paths

OpenAIRE

Alkhateeb, Faisal; Euzenat, Jérôme

2013-01-01

alkhateeb2013a; SPARQL is the standard query language for RDF graphs. In its strict instantiation, it only offers querying according to the RDF semantics and would thus ignore the semantics of data expressed with respect to (RDF) schemas or (OWL) ontologies. Several extensions to SPARQL have been proposed to query RDF data modulo RDFS, i.e., interpreting the query with RDFS semantics and/or considering external ontologies. We introduce a general framework which allows for expressing query ans...

Automatic Query Generation and Query Relevance Measurement for Unsupervised Language Model Adaptation of Speech Recognition

Directory of Open Access Journals (Sweden)

Suzuki Motoyuki

2009-01-01

Full Text Available Abstract We are developing a method of Web-based unsupervised language model adaptation for recognition of spoken documents. The proposed method chooses keywords from the preliminary recognition result and retrieves Web documents using the chosen keywords. A problem is that the selected keywords tend to contain misrecognized words. The proposed method introduces two new ideas for avoiding the effects of keywords derived from misrecognized words. The first idea is to compose multiple queries from selected keyword candidates so that the misrecognized words and correct words do not fall into one query. The second idea is that the number of Web documents downloaded for each query is determined according to the "query relevance." Combining these two ideas, we can alleviate bad effect of misrecognized keywords by decreasing the number of downloaded Web documents from queries that contain misrecognized keywords. Finally, we examine a method of determining the number of iterative adaptations based on the recognition likelihood. Experiments have shown that the proposed stopping criterion can determine almost the optimum number of iterations. In the final experiment, the word accuracy without adaptation (55.29% was improved to 60.38%, which was 1.13 point better than the result of the conventional unsupervised adaptation method (59.25%.

Automatic Query Generation and Query Relevance Measurement for Unsupervised Language Model Adaptation of Speech Recognition

Directory of Open Access Journals (Sweden)

Akinori Ito

2009-01-01

Full Text Available We are developing a method of Web-based unsupervised language model adaptation for recognition of spoken documents. The proposed method chooses keywords from the preliminary recognition result and retrieves Web documents using the chosen keywords. A problem is that the selected keywords tend to contain misrecognized words. The proposed method introduces two new ideas for avoiding the effects of keywords derived from misrecognized words. The first idea is to compose multiple queries from selected keyword candidates so that the misrecognized words and correct words do not fall into one query. The second idea is that the number of Web documents downloaded for each query is determined according to the “query relevance.” Combining these two ideas, we can alleviate bad effect of misrecognized keywords by decreasing the number of downloaded Web documents from queries that contain misrecognized keywords. Finally, we examine a method of determining the number of iterative adaptations based on the recognition likelihood. Experiments have shown that the proposed stopping criterion can determine almost the optimum number of iterations. In the final experiment, the word accuracy without adaptation (55.29% was improved to 60.38%, which was 1.13 point better than the result of the conventional unsupervised adaptation method (59.25%.

GeoCrystal: graphic-interactive access to geodata archives

Science.gov (United States)

Goebel, Stefan; Haist, Joerg; Jasnoch, Uwe

2002-03-01

Recently there is spent a lot of effort to establish information systems and global infrastructures enabling both data suppliers and users to describe (-> eCommerce, metadata) as well as to find appropriate data. Examples for this are metadata information systems, online-shops or portals for geodata. The main disadvantages of existing approaches are insufficient methods and mechanisms leading users to (e.g. spatial) data archives. This affects aspects concerning usability and personalization in general as well as visual feedback techniques in the different steps of the information retrieval process. Several approaches aim at the improvement of graphical user interfaces by using intuitive metaphors, but only some of them offer 3D interfaces in the form of information landscapes or geographic result scenes in the context of information systems for geodata. This paper presents GeoCrystal, which basic idea is to adopt Venn diagrams to compose complex queries and to visualize search results in a 3D information and navigation space for geodata. These concepts are enhanced with spatial metaphors and 3D information landscapes (library for geodata) wherein users can specify searches for appropriate geodata and are enabled to graphic-interactively communicate with search results (book metaphor).

Understanding Content-and-Structure

NARCIS (Netherlands)

Kamps, J.; Marx, M.J.; de Rijke, M.; Sigurbjörnsson, B.; Trotman, A.; Lalmas, M.; Fuhr, N.

2005-01-01

Document-centric XML is a mixture of text and structure. +With the increased availability of document-centric XML content comes a need for query facilities in which both structural constraints and constraints on the content of the documents can be expressed. This has generated considerable interest

Implementation of Quantum Private Queries Using Nuclear Magnetic Resonance

International Nuclear Information System (INIS)

Wang Chuan; Hao Liang; Zhao Lian-Jie

2011-01-01

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

SPARQL Query Re-writing Using Partonomy Based Transformation Rules

Science.gov (United States)

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

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

Mobile Information Access with Spoken Query Answering

DEFF Research Database (Denmark)

Brøndsted, Tom; Larsen, Henrik Legind; Larsen, Lars Bo

2006-01-01

window focused over the part which most likely contains an answer to the query. The two systems are integrated into a full spoken query answering system. The prototype can answer queries and questions within the chosen football (soccer) test domain, but the system has the flexibility for being ported...